Environmental DNA最新文献

Despite the widespread use of metabarcoding approaches in wood-inhabiting fungal studies, there is currently no standardized procedure for sampling deadwood. How to sample and how much to replicate within logs varies among studies, making comparisons difficult. Here, we provide quantitative results about how bark- and wood-inhabiting fungi vary along logs in early decay stages, compared to how they vary between logs. For this, we used two datasets: one representing variation in the sample's location along the logs (tree part; bottom, middle or top) and across tree species (pine or spruce), and another representing small-scale variation (tens of centimeters) in sampling location and variation in sample type (wood or bark). Additionally, we conducted a visual survey of epiphytic lichens to assess the efficiency of bark metabarcoding for surveying epiphytic lichens. Our results show that the diversity of fungi varies greatly between tree species and among the tree parts. Yet, within the tree parts, fungal community composition is relatively homogeneous, with an increasing number of samples only moderately increasing the number of species detected. Strikingly, our results reveal bark samples to be especially species-rich, holding threefold the diversity of the wood beneath it, which represents a subset of the diversity found in bark. This finding suggests that the common practice of excluding bark-inhabiting fungal diversity in studies of saproxylic species in early decay-stage logs overlooks a substantial part of the saproxylic diversity. We found a poor overlap between lichen species identified morphologically and those detected via bark metabarcoding; however, both methods captured consistent patterns in how lichen diversity varied across the logs. We conclude that to gain a representative view of the fungal community composition in early decay-stage deadwood, bark should be included in fungal surveys and that replication within logs should focus on covering the different tree parts.

The field of environmental DNA (eDNA) analysis has revolutionized our ability to detect and monitor biodiversity in aquatic and terrestrial ecosystems. However, traditional eDNA sampling methods often present limitations in terms of temporal and spatial coverage, resulting in a loss of resolution associated with infrequent events or those prohibitive to onsite fieldwork. In recent years, the emergence of autonomous eDNA sampling technology has provided researchers with a powerful tool for collecting high-resolution genetic data, overcoming many of the challenges associated with manual sample acquisition. This review focuses exclusively on eDNA technologies designed for the collection and preservation of water samples, to provide a comprehensive overview of the current landscape of aquatic autonomous eDNA sampling technology and instrumentation. A new era of instrument development and capabilities is emerging; the result of knowledge gained through experience with long-tested marine biological observation instrumentation. Lastly, we highlight current research to develop an in situ eDNA analytical capability, as well as explore the challenges and future prospects associated with this rapidly evolving field.

Takahashi, M., Frøslev, T.G., Paupério, J., Thalinger, B., Klymus, K., Helbing, C.C., Villacorta-Rath, C., Silliman, K., Thompson, L.R., Jungbluth, S.P., Yong, S.Y., Formel, S., Jenkins, G., Laporte, M., Deagle, B., Rajbhandari, S., Jeppesen, T.S., Bissett, A., Jerde, C., Hahn, E.E., Schriml, L.M., Hunter, C., Newman, P., Woollard, P., Harper, L.R., Dunn, N., West, K., Haderlé, R., Wilkinson, S., Acharya-Patel, N., Lopez, M.L.D., Cochrane, G. and Berry, O. (2025). A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable). Environmental DNA, 7: e70100. https://doi.org/10.1002/edn3.70100

In paragraph 4 of the “Section 5.2”, the text “extending these requirements to additional journals including Molecular Ecology and Evolution.” was incorrect. This should have read “extending these requirements to additional journals including Molecular Ecology and Ecology and Evolution.”

This has now been fixed in the published article.

We apologize for this error.

Coastal environments serve as essential nursing, feeding, and spawning grounds for commercially and ecologically important fish species, some of which use nearshore habitats as transitional steps in their ontogenetic migration. Understanding fish communities' spatial and temporal dynamics in coastal habitats is fundamental for sustainable ecosystems and fisheries management. Despite the importance of long-term monitoring to obtain information on fish movements and distribution, fine-scale temporal datasets on fish communities remain scarce due to the intense field work required. In the present study, we explored the use of eDNA 12S metabarcoding of seawater samples to monitor fine-scale temporal and spatial patterns in fish communities. In total, 168 samples were collected across 20 sampling campaigns conducted monthly between August 2021 and August 2023 within the 12 nautical miles of the Belgian part of the North Sea. eDNA patterns revealed no marked temporal or spatial patterns at the community levels due to the ubiquitous presence of the dominant Southern North Sea fish species linked to their non-migratory behavior and use of the coastal Belgian waters as nursing and spawning grounds. However, species-specific temporal patterns reflected their reproductive activity and seasonal migrations. Additionally, fish species spatial distribution was consistent with previous beam trawl and eDNA-based surveys conducted within the Belgian part of the North Sea and was mainly driven by the environmental gradient created by freshwater discharge from the Scheldt estuary. Our findings demonstrate that eDNA metabarcoding is a valuable biomonitoring tool and provides insight into fish distribution, migration, and reproductive activity.

Tropical estuaries are hyper-diverse ecosystems, hosting essential habitats for freshwater, euryhaline, and marine life. Understanding how biological communities are distributed in these systems has long been a challenge because of their inherent dynamic nature and the diversity of interacting natural pressures and anthropogenic stressors they are subjected to. In addition, most studies focus on a single taxonomic group, hindering a comprehensive understanding of the interactive effects of natural and human-driven environmental variations on the different components of tropical estuarian biodiversity. In this study, we used environmental DNA (eDNA) metabarcoding to examine the structure of multi-taxonomic communities, from diatoms to fish, and their relationships with environmental drivers in three differentially impacted locations facing the Great Barrier Reef in Central Queensland (Australia). We first demonstrated that eDNA signals from sediment and water matrices provide complementary information and that both should be monitored for a more holistic understanding of community trajectories in anthropogenically impacted aquatic environments. We also observed that, independently of the taxonomic group considered, communities were primarily structured by the ecological conditions of the estuary. A within-estuary differentiation along an upstream–downstream gradient was detected but only for small-bodied organisms, which further adds credence to eDNA approaches as an ecologically relevant tool for monitoring fine-scale biodiversity patterns even in profoundly dynamic environments. Finally, the different communities exhibited contrasting response patterns, in terms of diversity, composition, and uniqueness, to the anthropogenic gradient. Hence, our findings emphasize the need for multi-taxonomic assessments, for which eDNA is well suited, to better understand the impacts of multiple stressors on biodiversity and thereby assist decision makers in the protection and management of tropical estuaries.

Flower-derived eDNA holds great promise as a rapid and non-invasive tool for monitoring pollinators and their plant associations. However, pollinators often only briefly interact with a plant and leave little eDNA, making them particularly challenging to detect. In addition, taxonomic biases in eDNA deposition and PCR amplification prevent quantitative analysis of pollinator diversity. These limitations have so far precluded the widespread use of eDNA in pollinator monitoring. Comparing flower-derived eDNA with conventional monitoring in flower strips, we here explore the utility of eDNA to detect community diversity, species abundances, and ecological specificity of plant-associated arthropods. We show that read abundances are a bad predictor of true abundances at the community level. Instead, the occupancy of individual species in replicated flower eDNA samples provides reliable quantitative estimates of pollinator biodiversity and detects their ecological specificity very well. Also, we find that pollinator eDNA can be collected non-invasively, by washing off from flowers in the field. Our work highlights eDNA analysis as a powerful tool for the rapid future monitoring of plant-arthropod interactions and plant-pollinator networks.

Current population genetics studies of sea turtles primarily rely on invasive tissue sampling or blood draws, which involve the capture and handling of the animals that require specific permits and resources. Moreover, this approach is limited by the sporadic visibility of turtles. In this study, we assessed the applicability of eDNA-based sampling to obtain mitochondrial haplotype data for leatherback turtle (Dermochelys coriacea) populations at three beaches in Sumatra, Indonesia (Northeast Indian Ocean). We collected seawater samples at two time points: immediately after a female left the beach (night samples) and 12 h later (morning samples) to reflect the common practice of conducting beach monitoring surveys at dawn. Our findings revealed that the eDNA samples captured identical haplotypes to those obtained from tissue samples. The haplotypes persisted in the eDNA from seawater samples up to 12 h after the females left the beach. We identified five haplotypes that correspond to those previously recorded in the Pacific, Atlantic, and Indian Oceans, showing the broad phylogeographic links between the Sumatra population and other global populations. Our results provide further evidence that noninvasive eDNA techniques could supplement traditional tissue sampling for studying sea turtle population genetics. This applies particularly to understudied populations or remote rookeries where traditional methods are difficult to implement and opens the possibility of using eDNA for population structure studies that could complement traditional monitoring programs.

Environmental DNA (eDNA) provides a powerful means of monitoring biodiversity, offering high taxonomic resolution and broad spatial coverage beyond traditional methods. To characterize ecological communities, it is critical to understand shifts in species composition through time to potentially differentiate resident from transient species in the studied habitats. This study used eDNA metabarcoding to examine temporal and spatial patterns of α- and β-diversity across three distinct habitat types (sandy, rocky, and mangrove) at four coastal sites in Singapore over 1 year. We targeted invertebrates using the cytochrome oxidase subunit I (COI) gene and vertebrates using the 16S rRNA gene. We recorded lower diversity at nature reserves, which harbor more rare species than unprotected habitats. β-diversity differed significantly by site and time for both markers, though β-dispersion generally remained consistent over time within sites for both invertebrate and vertebrate communities. The difference in marine metazoan communities was driven by high spatial and temporal turnover without strong directional trends across Singapore's coastal sites. These patterns reflect distinct, cohesive communities with limited seasonality, characteristic of equatorial climates. However, certain taxa showed monsoon-associated distributions, except in mangrove habitats. Importantly, we suggest more mid- to long-term surveys to elucidate the community of resident species. Our findings highlight the value of using eDNA methods to identify dynamic biodiversity patterns and support its use in long-term ecological monitoring and conservation planning.

Coffee is a globally important commodity that supports millions of livelihoods, from smallholder farmers to international traders. However, the sustainability of the coffee value chain is increasingly threatened by environmental changes. In this context, the phytomicrobiome, shaped by both environmental factors and plant genotypes, plays a vital role in plant health, productivity, and the quality of coffee beans. In this study, we explored the diversity and ecological functions of the endosphere microbiome in the leaves and fruits of Coffea arabica L. cultivated under an agroforestry system on Mount Gorongosa, within Gorongosa National Park, Mozambique. Using next-generation sequencing, we characterized microbial communities along gradients of elevation and shade to assess how environmental variables shape microbiome composition and function. Our findings revealed a rich diversity of microbial communities, with elevation emerging as the primary driver of community structure. Taxonomic analyses showed that both elevation and shade significantly influenced the composition of bacterial and fungal communities. Microbial families such as Debaryomycetaceae, Enterobacteriaceae, Eremotheciaceae, Nocardiaceae, and Pseudonocardiaceae exhibited distinct adaptations to environmental conditions. Notably, we detected the presence of pathogenic genera (e.g., Colletotrichum, Erwinia, Fusarium, and Phaeosphaeria) without visible disease symptoms, indicating possible plant tolerance to biotic stressors. Predicted functional pathways, including heme biosynthesis and phospholipid metabolism, alongside ecological guilds such as saprotrophs and fungal parasites, suggested microbial adaptations essential to maintaining plant health and coffee quality. Key microbial biomarkers, including Debaryomyces, Eremothecium, and Rhodococcus, emerged as indicators of functional adaptations across environmental gradients, highlighting their potential for informing optimized, environmentally responsive coffee management strategies. Altogether, the results highlight the integral role of coffee-associated endophytes, in concert with plant genotypes, in shaping innovative, biodiversity-driven strategies for sustainable coffee production.

Environmental DNA (eDNA) metabarcoding is a powerful tool for uncovering hidden biodiversity and identifying underestimated taxa in aquatic ecosystems. In this study, we applied eDNA metabarcoding to assess fish species in isolated environments of the Tibagi River basin, specifically sinkholes. Water samples were collected from three sinkholes (Sites 1, 2, and 4), one site at Dourada Lake within the Vila Velha State Park (VVSP), and two sites along the main channel of the Tibagi River. A fragment of the mitochondrial 12S rDNA gene was amplified and sequenced, yielding a final dataset of 975,197 reads after filtering. We identified 31 Molecular Operational Taxonomic Units (MOTUs) belonging to Actinopterygii, distributed across four taxonomic orders: Characiformes, Cichliformes, Gymnotiformes, and Siluriformes. No MOTUs were detected in sinkhole 1, indicating local extinction. A single MOTU (Psalidodon fasciatus) was identified in sinkhole 2. In sinkhole 4, two distinct MOTUs were found, corresponding to the family Heptapteridae and the genus Cambeva, but the potential presence of P. fasciatus was not confirmed. As expected, the highest species richness was observed in the Tibagi River. Despite the lack of a local reference database, our findings offer valuable insights into the detection of diverse taxa in isolated aquatic environments using eDNA metabarcoding. This study underscores the potential of eDNA to inform conservation strategies in ecologically unique and underexplored habitats and highlights the need for developing region-specific genetic reference databases to enhance taxonomic resolution and monitoring efforts in the future.