Environmental DNA最新文献

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.

Estuarine ecosystems experience a range of anthropogenic pressures. Consequently, robust monitoring tools are essential for their management and protection. Utilizing environmental DNA in routine monitoring programs enables the inclusion of benthic microorganisms, which are not only good indicators of environmental condition, but also play critical roles in ecosystem functioning. We collected eDNA sediment samples in six estuaries from the Basque coast (Spain) with different levels of disturbance: first, to better understand the dynamics of microbial communities and their ecological associations; and second, to unveil how contamination affects them. For the first time in estuarine sediments, time series data were used to examine consensus networks to identify potential indicators of biotic integrity and to compare their topology (network structure). In general, sediment communities were relatively temporally stable, with the moderately and heavily disturbed sites showing more variation. The consensus networks also differed significantly in their topologies, with more impacted estuaries having fewer nodes, edges, and connectance, among others, and higher modularity compared to those less impacted. Moreover, the potential keystone taxa and predicted functional profiles differed between consensus networks. This illustrates how modeled association networks can reveal new insights regarding the state of estuarine ecosystems and their potential functional processes.

Environmental DNA (eDNA) metabarcoding offers a powerful tool for rapid species monitoring in diverse river basins. However, the success of eDNA-based species detection is influenced by various biotic and abiotic factors (i.e., eDNA ecology). To overcome challenges posed by funding limitations and remote locations in the Neotropics, deploying affordable, portable sampling kits and low-effort sampling protocols could significantly expand the use of eDNA for monitoring anthropogenic impacts on fish biodiversity. This approach would enable timely and cost-effective assessments of biodiversity changes in these often-overlooked regions. Here, we investigated whether rapid eDNA sampling using a portable on-site kit with syringe filters and a moderate water volume (average of 360 mL/site) could provide a reliable assessment of fish communities and shed light on fish eDNA ecology upstream and downstream of a large hydroelectric reservoir. Water samples were collected from five sites along a 400-km stretch of free-flowing river in the lotic remnant of the Upper Paraná River and one site downstream of Emborcação hydroelectric dam. Using eDNA metabarcoding and the 12S MiFish molecular marker, we detected 68 fish taxa across the six sampling locations. After careful data curation, 28 taxa were confidently assigned to species level, 36 to genus level, and four taxa to family level. eDNA-assessed fish richness displayed a negative correlation with river elevation (R = −0.82, p = 0.001), corroborating the hypothesis that in freshwater river systems, species richness generally increases along the upstream–downstream gradient. The site below the dam exhibited the highest species richness due to its community composition and not to upstream uptake and accumulation of eDNA. In conclusion, our eDNA metabarcoding approach using a portable kit and low water volume per sample site effectively provided a rapid, robust snapshot of fish biodiversity, particularly valuable for rapid decision-making regarding the conservation importance of specific regions.

Sedimentary DNA (sedDNA), a form of environmental DNA (eDNA) shed by aquatic organisms and preserved in sediment, is crucial for reconstructing historical community compositions in aquatic ecosystems. In Cowpar Lake (Dene name: Doghostú), Alberta, a significant landslide event in the early 1940s CE impacted the lake's geochemistry and fish populations, as documented by Indigenous Knowledge from the Chipewyan Prairie First Nation and corroborated by targeted fish sedDNA analyses. The present study used 18S rRNA and cytochrome oxidase I (COI) genes for DNA metabarcoding of a sediment core from Cowpar Lake to assess the effect of the documented landslide and to reconstruct the historical community composition of eukaryotic functional trophic groups, including photoautotrophs, mixotrophs, parasites, and consumers. Between 1948 and 1956 CE, a notable shift in community composition occurred, with a decline in the alpha diversity of eukaryotic amplicon sequence variants. The increased primary productivity and terrestrial organic input post-1950 is correlated with an increased diversity of phototrophs and mixotrophs, suggesting potential algal blooms. While parasite diversity remained stable, consumer diversity declined, likely due to increased microbial respiration of organic matter, reducing oxygen levels and making the lake less hospitable for consumers like whitefish, which eventually disappeared in the lake. The reconstructed eukaryotic community profiles from sedDNA were consistent with Indigenous Knowledge of natural changes around the lake. The present study highlights the potential of braiding sedDNA data with Indigenous Knowledge to reconstruct long-term changes in aquatic communities, offering high-resolution baseline data for environmental monitoring and a deeper understanding of how freshwater systems respond to natural and human-induced impacts.

Environmental DNA (eDNA) is broadly assumed to be highly fragmented (< 600 bp) in seawater. However, several marine eDNA studies that have successfully amplified longer fragments (from 600 up to 16,000 bp) are challenging this notion. We hypothesized that a small, yet amplifiable, proportion of eDNA templates contain fragment lengths exceeding 600 bp. To test this, we designed primers to target a series of mitochondrial fragment lengths between 119 and 15,727 bp for the tiger shark (Galeocerdo cuvier) and performed qPCR on seawater eDNA samples collected from the offshore, tropical Kimberley and Roebuck Marine Parks in Western Australia. We observed a steep decrease in eDNA copy number with increasing fragment size between 119 and 1518 bp, beyond which amplification was not successful. Importantly, we demonstrate that fragment sizes larger than conventionally targeted (e.g., 636, 840, and 1518 bp) can still be successfully amplified from seawater eDNA samples. Estimated mean nucleotide damage in seawater eDNA samples was found to be 3.9 breaks per 1000 bp; this equates to a mean undamaged fragment size of 256 bp and is less than damage observed in modern fecal DNA and ancient DNA. Characterizing the extent of eDNA fragmentation in various environmental samples will improve understanding of the genetic material available and enable practitioners to target standard length barcodes and longer hypervariable gene regions. Through the recovery of more informative data, eDNA applications will extend to finer-scale taxonomic resolution, including complex species and sub-species discrimination, as well as population analyses.

Healthy ecosystems are critical for maintaining ecosystem services and water security; yet many freshwater ecosystems have been subject to environmental degradation. Impacts are often greatest in water-scarce and developing regions, including across much of Sub-Saharan Africa, where many people lack access to basic drinking water. However, environmental monitoring programmes to track ecosystem health are generally lacking across this region due to limited resources and funding. Recent advances in environmental DNA (eDNA) methods offer an increasingly cost-effective and information-rich solution. Here, we explore the potential of eDNA as a tool for ecological monitoring of freshwater ecosystems in Uganda, East Africa. We sampled eDNA to quantify the bacterial diversity of rivers, streams, and swamps across a gradient of human disturbance in and around Kibale National Park, using off-the-shelf sampling methods that require minimal pre-existing infrastructure. We found distinct bacterial communities between intact and degraded habitats, but the bacterial community in rivers converged when flowing through intact forest. We identified several taxa with differential abundances that might serve as potential bioindicators of degraded ecosystems, and showed that a machine learning tool trained on eDNA can accurately differentiate between intact and degraded habitats. Our proof-of-concept study demonstrates the potential of eDNA as a practical and cost-effective biomonitoring tool for freshwater ecosystems in resource-limited regions, including Sub-Saharan Africa. We also highlight the potential benefits of protected forest in modulating bacterial composition in freshwater ecosystems.