Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological ...interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single‐species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost‐effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
Advances in biotechnology to treat and cure human disease have markedly improved human health and the development of modern societies. However, substantial challenges remain to overcome innate ...biological factors that thwart the activity and efficacy of pharmaceutical therapeutics. Until recently, the importance of extracellular DNA (eDNA) in biofilms was overlooked. New data reveal its extensive role in biofilm formation, adhesion, and structural integrity. Different approaches to target eDNA as anti‐biofilm therapies have been proposed, but eDNA and the corresponding biofilm barriers are still difficult to disrupt. Therefore, more creative approaches to eradicate biofilms are needed. The production of eDNA often originates with the genetic material of bacterial cells through cell lysis. However, genomic DNA and eDNA are not necessarily structurally or compositionally identical. Variations are noteworthy because they dictate important interactions within the biofilm. Interactions between eDNA and biofilm components may as well be exploited as alternative anti‐biofilm strategies. In this review, we discuss recent developments in eDNA research, emphasizing potential ways to disrupt biofilms. This review also highlights proteins, exopolysaccharides, and other molecules interacting with eDNA that can serve as anti‐biofilm therapeutic targets. Overall, the array of diverse interactions with eDNA is important in biofilm structure, architecture, and stability.
Biofilms can be disrupted and dispersed by targeting eDNA.
Environmental DNA (eDNA) is a technique increasingly used for monitoring organisms in the natural environment including riverine macroinvertebrates. However, the effectiveness of eDNA for monitoring ...riverine macroinvertebrates compared with the more traditional method of sampling the organisms directly and identifying them via morphological analysis, has not been well established. Furthermore, the ability of the various gene markers and PCR primer sets to detect the full range of riverine invertebrate taxa has not been quantified. Here we conducted a meta-analysis of the available literature, to assess the effectiveness of eDNA sampling for detecting riverine macroinvertebrates compared with sampling for the organisms directly and applying morphological analysis. We found, on average, eDNA sampling, irrespective of the gene marker used, detected fewer riverine invertebrates than morphological sampling. The most effective PCR primer set for identifying taxa was mlCOIintF/jgHCO2198, (mlCOIintF– forward primer, jgHCO2198, − reverse primer). Regardless of the gene marker or primer sets used, however, many taxa were not detected by eDNA metabarcoding that were detected by sampling directly for these invertebrates, including over 100 members of Arthropoda. eDNA sampling failed to detect any species belonging to Nematoda, Platyhelminthes, Cnidaria or Nematomorpha and these markers applied for eDNA sampling in terrestrial systems also do not detect members of Nematoda. In addition to these issues, uncertainties relating to false positives from upstream DNA sources, the stability of DNA from different species, differences in the propensity for DNA release into the environment for different organisms, and lack of available sequence information for numerous taxa illustrates the use of eDNA is not yet applicable as a robust stand-alone method for the monitoring of riverine invertebrates. As a primary consideration, further methodological developments are needed to ensure eDNA captures some of the key freshwater taxa, notably taxa belonging to the phyla Arthropoda, Nematoda, Platyhelminthes, Cnidaria and Nematomorpha.
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•eDNA metabarcoding detects fewer riverine invertebrates than morphological methods.•CO1 gene marker and mlCOIintF/jgHCO2198 primer set is the most effective.•Nematoda, Platyhelminthes, Cnidaria and Nematomorpha taxa were not detected by eDNA.•eDNA method alone is not sufficiently robust for monitoring riverine invertebrates.
Environmental (e)DNA metabarcoding holds great promise for biomonitoring and ecotoxicological applications. However, few studies have compared the performance of eDNA versus eRNA metabarcoding in ...assessing organismal response to marine pollution, in experimental conditions. Here, we performed a chromium (Cr)-spiked mesocosm experimental test on benthic foraminiferal community to investigate the effects on species diversity by analysing both eDNA and eRNA metabarcoding data across different Cr concentrations in the sediment. Foraminiferal diversity in the eRNA data showed a significant negative correlation with the Cr concentration in the sediment, while a positive response was observed in the eDNA data. The foraminiferal OTUs exhibited a higher turnover rate in eRNA than in the eDNA-derived community. Furthermore, in the eRNA samples, OTUs abundance was significantly affected by the Cr gradient in the sediment (Pseudo-R2 = 0.28, p = 0.05), while no significant trend was observed in the eDNA samples. The correlation between Cr concentration and foraminiferal diversity in eRNA datasets was stronger when the less abundant OTUs (<100 reads) were removed and the analyses were conducted exclusively on OTUs shared between eRNA and eDNA datasets. This indicates the importance of metabarcoding data filtering to capture ecological impacts, in addition to using the putatively active organisms in the eRNA dataset. The comparative analyses on foraminiferal diversity revealed that eRNA-based metabarcoding can better assess the response to heavy metal exposure in presence of subtle concentrations of the pollutant. Furthermore, our results suggest that to unlock the full potential for ecosystem assessment, eDNA and eRNA should be studied in parallel to control for potential sequence artifacts in routine ecosystem surveys.
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•eDNA and eRNA biomonitoring potential was assessed in mesocosm experiment.•Chromium concentration negatively influenced organismal diversity in eRNA samples.•eDNA-derived diversity was not affected by chromium levels in the sediment.•eDNA-informed filtering improved assessment of response signals in eRNA samples.
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.
Phytophthora capsici is a highly destructive pathogen of crops. Although chemical pesticides are the most widely used strategy to counter phytopathogens, they have been inefficient to combat P. ...capsici and have produced significant environmental and health problems. Therefore, sustainable alternatives to control soilborne pathogens, such as the inhibitory effect of self‐extracellular DNA (eDNA), have been proposed. This inhibition phenomenon has been attributed to the action of self‐eDNA as a damage‐associated molecular pattern (DAMP). Here, we describe the effect of self‐eDNA on P. capsici zoospore germination rate, antioxidant enzymes activity and MAPK gene expression. Also, the effect of P. capsici eDNA on the protection of chilli pepper (Capsicum annuum) plants against P. capsici was investigated. The results highlight that P. capsici can sense 2–500 µg/ml self‐eDNA and induce stress‐related responses like SAK1 gene expression, and superoxide dismutase and catalase activities. Moreover, in vitro zoospore germination rate was suppressed with self‐eDNA concentrations ranging from 50 to 500 µg/ml. Interestingly, drench applications of P. capsici eDNA at 60 and 100 µg/ml on chilli pepper plants did not show any protective effect against the phytopathogen, whereas 2 µg/ml of P. capsici eDNA drench application showed a lower percentage of plants with symptoms and lower disease severity. Moreover, phenols and total flavonoids were increased in chilli pepper plants, therefore inducing plant immunity. This study showed that self‐eDNA acts as a DAMP in P. capsici and provides insight into the use of eDNA for the protection of crops of agronomic interest.
This study showed that self‐eDNA acts as a DAMP in P. capsici inducing stress‐related responses, giving an insight into the use of self‐eDNA in field‐like conditions against the phytopathogen.
In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the ...biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.
•Conservation of freshwater fishes is dependent on accurate and precise data.•Environmental DNA analysis has the potential to improve species conservation.•eDNA can improve sampling effectiveness and ...efficiency compared to capture sampling.•This review describes eDNA analysis as it relates to fisheries conservation.
Conservation of fishes is dependent on accurate and precise data about the distributions and population status of at-risk species. Moreover, effective management of fisheries requires that data be collected in ecologically and politically actionable timeframes. Environmental DNA (eDNA) analysis, the extraction and identification of DNA from environmental samples, is a relatively new bioassessment method with the potential to improve species detection probabilities and efficiency compared to traditional capture or observation-based sampling approaches. Here, we provide a primer on eDNA analysis as it pertains to fisheries ecology and conservation. We provide a summary of the history and current status of eDNA analysis with particular attention paid to the study of fishes. We highlight the major advances that have transformed eDNA analysis into an application-ready tool that can assist fisheries professionals in achieving research and conservation goals. Furthermore, we provide an overview of the limitations of eDNA as they pertain to fisheries science.
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