In recent years, biodiversity loss has become one of the most serious environmental issues worldwide, especially in aquatic ecosystems. To avoid diversity loss, it is necessary to monitor biological ...communities, and environmental DNA (eDNA) metabarcoding has been developed as a rapid, noninvasive, and cost-effective method for aquatic biodiversity monitoring. Although this method has been applied to various environments and taxa, a detailed assessment of the efficient sampling methods for monitoring is still required. In this study, we explored eDNA metabarcoding sampling methods for fish at a single site to maximize the number of detected species using realistic effort in a natural, small river. We considered the following three parameters: sample type (water or sediment), sample position at a site (right and left shore and center of the river), and water volume (10–4000 mL). The results suggested that the number of detected species from sedimentary eDNA was equivalent to that from aqueous eDNA, although the species composition was different. The number of detected species could be saturated by collecting a 1000 mL water sample, regardless of sampling position within a survey site. However, sedimentary eDNA showed a spatially heterogeneous species composition between sampling positions within a survey site despite the short distance (5 m) between positions, without apparent differences in physical properties such as velocity and sediment particle distribution. By completing eDNA biodiversity monitoring of fish with 1000 mL water samples across the whole river, we detected more fish species than in previous traditional surveys conducted at the same sites. Thus, the aqueous eDNA metabarcoding method is as efficient as traditional surveys, while sedimentary eDNA metabarcoding could complement the results of aqueous eDNA metabarcoding.
Environmental DNA (eDNA) is becoming an established tool across the biological and medical sciences. Despite the evident successes and wide adoption of eDNA approaches, some fundamental questions ...remain. For instance, there is almost a dogma in the field around the superiority of mitochondrial DNA for use in eDNA studies, however robust comparison with nuclear eDNA is widely lacking. The dominance of mitochondrial-based eDNA for animal and plant studies appears to be largely settled, despite a widespread lack of rigorous nuclear eDNA testing. Outside of the source organism the protections conferred on eDNA by the cell, mitochondrial and nuclear membranes are poorly understood, including the contribution of each to eDNA persistence and degradation. Utilizing shotgun sequencing to unbiasedly assess the level of nuclear and mitochondrial eDNA across samples, we reveal stark differences in nuclear versus mitochondrial eDNA persistence and abundance. By focusing too heavily on mitochondrial DNA alone the field is underutilizing eDNA's full potential.
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•With multiple mitochondria (mt) per cell, sequenced tissue has a high ratio of mt to nuclear DNA (genome length adjusted)•Mitochondrial (mt) to nuclear (nu) ratio of eDNA begins declining immediately after release from the source organism•The mt to nu ratio continues declining the longer DNA is in the environment, making eDNA fraction an important consideration•Nu sequences were detected in some eDNA samples when mt sequences were not, with implications for false negatives/positives•Shotgun sequencing approaches or nuclear marker incorporation may increase eDNA eukaryotic species detection sensitivity
•Marine protection showed varied conservation effects on different bioindicators.•Taxonomic diversity was the highest in the marine reserve.•Fish community was the most evenly distributed in marine ...parks.•Species turnover was the main component of fish beta diversity.•Protection level was the primary factor influencing phylogenetic beta diversity.•Various protection levels are necessary for fishery conservation.
Marine protected areas are set up across the globe to safeguard biodiversity and support coastal ecosystem functioning. In Hong Kong, partially protected marine parks and a no-take marine reserve have been managed under legislation for years, yet a comprehensive evaluation of their conservation impact is still pending despite the region’s reputation for high marine diversity. Most studies assess conservation effectiveness solely in terms of taxonomic diversity, without delving into the contributions of functional and phylogenetic diversity. In this study, we used environmental DNA combined with multifaceted diversity indicators to assess the impact of the level of protection on the fish community in Hong Kong waters. Our results indicated that the marine protected areas significantly contributed to fish community conservation. The no-take marine reserve exhibited the highest taxonomic and phylogenetic diversity, while partially protected marine parks showed the most balanced community composition. No significant increase in fish functional diversity was found in the protected areas. Water quality, hydrological condition, and protection level were the primary factors affecting community variation for taxonomic, functional, and phylogenetic diversity, respectively. Fish species composition significantly varied with different protection levels, and species turnover was the main component of the dissimilarity. Future management of marine protected areas should assess multifaceted biological indicators and establish a rational conservation scheme.
Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to ...revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.
Fish environmental DNA (eDNA) studies have made substantial progress during the past decade, and significant advances in monitoring fishes have been gained by taking advantage of this technology. ...Although a number of reviews concerning eDNA are available and some recent fish eDNA reviews focused on fisheries or standard method have been published, a systematic review of methodology of fish eDNA and its applications in ecology and environment has not yet been published. To our knowledge, this is the first review of fish eDNA for solving ecological and environmental issues. First, the most comprehensive literature analysis of fish eDNA was presented and analyzed. Then, we systematically discuss the relevant experiments and analyses of fish eDNA, and infers that standard workflow is on the way to consensus. We additionally provide reference sequence databases and the primers used to amplify the reference sequences or detecting fish eDNA. The abiotic and biotic conditions affecting fish eDNA persistence are also summarized in a schematic diagram. Subsequently, we focus on the major achievements of fish eDNA in ecology and environment. We additionally highlight the exciting new tools, including in situ autonomous monitoring devices, CRISPR nucleic acid detection technology, and meta-omics technology for fish eDNA detection in future. Ultimately, methodology of fish eDNA will provide a wholly new paradigm for conservation actions of fishes, ecological and environmental management at a global scale.
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•Fish eDNA can be used well for solving ecological and environmental issues.•Statistic models for fish eDNA are presented.•Suggestions for quantifying the abundance/biomass are provided.•The ecology of eDNA is helpful for biomonitoring effectively.•The concept of in situ monitoring of fish eDNA is proposed.
The atmospheric microbiome is one of the least studied microbiomes of our planet. One of the most abundant, diverse and impactful parts of this microbiome is arguably fungal spores. They can be very ...potent outdoor aeroallergens and pathogens, causing an enormous socio-economic burden on health services and annual damages to crops costing billions of Euros. We find through hypothesis testing that an expected warmer and drier climate has a dramatic impact on the atmospheric microbiome, conceivably through alteration of the hydrological cycle impacting agricultural systems, with significant differences in leaf wetness between years (p-value <0.05). The data were measured via high-throughput sequencing analysis using the DNA barcode marker, ITS2. This was complemented by remote sensing analysis of land cover and dry matter productivity based on the Sentinel satellites, on-site detection of atmospheric and vegetation variables, GIS analysis, harvesting analysis and footprint modelling on trajectory clusters using the atmospheric transport model HYSPLIT. We find the seasonal spore composition varies between rural and urban zones reflecting both human activities (e.g. harvest), type and status of the vegetation and the prevailing climate rather than mesoscale atmospheric transport. We find that crop harvesting governs the composition of the atmospheric microbiome through a clear distinction between harvest and post-harvest beta-diversity by PERMANOVA on Bray-Curtis dissimilarity (p-value <0.05). Land cover impacted significantly by two-way ANOVA (p-value <0.05), while there was minimal impact from air mass transport over the 3 years. The hypothesis suggests that the fungal spore composition will change dramatically due to climate change, an until now unforeseen effect affecting both food security, human health and the atmospheric hydrological cycle. Consequently the management of crop diseases and impact on human health through aeroallergen exposure need to consider the timing of crop treatments and land management, including post harvest, to minimize exposure of aeroallergens and pathogens.
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•DNA metabarcoding of atmospheric spore data coving 3 years from 2 sites•Rural and urban sites display very different results and relate to harvesting pattern.•The warm and dry year of 2018 significantly affected the atmospheric microbiome.•Remote sensing and atmospheric footprint modelling with HYSPLIT•Leaf wetness, and lack thereof, is the key parameter for the atmospheric microbiome.
Background
Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid ...progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ).
Aims
Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies.
Materials & Methods/ Results
We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method.
Discussion/Conclusions
Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.
We propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. We demonstrate the use of both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for these assays. Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.
To effectively monitor, manage and protect aquatic species and understand their interactions, knowledge of their spatiotemporal distribution is needed. In this study, we used a fine‐scale ...spatiotemporal water sampling design, followed by environmental DNA (eDNA) 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal dispersion of eDNA by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5–10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected 1 week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven of the nine cage species, the presence of a single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine‐scale sampling design in combination with eDNA metabarcoding can cover total biodiversity very precisely and allows the construction of consistent spatiotemporal patterns of relative abundance and local distribution of free‐living fish and amphibian species in a lentic ecosystem.
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