Environmental DNA provides information on sediment sources: A study in catchments affected by Fukushima radioactive fallout

Determination of sediment sources following a major wildfire and evaluation of the use of color properties and polycyclic aromatic hydrocarbons (PAHs) as tracers

Purpose

This research aimed to determine if a severe wildfire caused changes in the source of sediment being delivered to downstream aquatic systems and evaluate the use of polycyclic aromatic hydrocarbons (PAHs) and color properties as tracers.

Methods

Sediment samples were collected from 2018 to 2021 in three tributaries impacted by the 2018 Shovel Lake wildfire and from two sites on the mainstem of the Nechako River, British Columbia. Source samples were collected from burned and unburned soils as well as from channel banks and road-deposited sediment. Samples were analyzed for color properties and for the 16 US Environmental Protection Agency priority PAHs. After statistical tests to determine the conservatism and ability to discriminate between sources by the tracers, the MixSIAR unmixing model was used, and its outputs were tested using virtual mixtures.

Result

In the tributaries, burned topsoil was an important contributor to sediment (up to 50%). The mainstem Nechako River was not influenced as significantly by the fires as the greatest contributor was banks (up to 89%). The color properties provided more realistic results than those based on PAHs.

Conclusion

In smaller watersheds, the wildfire had a noticeable impact on sediment sources, though the impacts of the fire seemed to be diluted in the distal mainstem Nechako River. Color tracers behaved conservatively and discriminated between contrasting sources. Due to their low cost and reliability, they should be considered more widely. While PAHs did not work in this study, there are reasons to believe they could be a useful tracer, but more needs to be understood about their behavior and degradation over time.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11368-023-03565-0.

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.

Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs

It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.

Improving the design and implementation of sediment fingerprinting studies: summary and outcomes of the TRACING 2021 Scientific School

PURPOSE

Identifying best practices for sediment fingerprinting or tracing is important to allow the quantification of sediment contributions from catchment sources. Although sediment fingerprinting has been applied with reasonable success, the deployment of this method remains associated with many issues and limitations.

METHODS

Seminars and debates were organised during a 4-day Thematic School in October 2021 to come up with concrete suggestions to improve the design and implementation of tracing methods.

RESULTS

First, we suggest a better use of geomorphological information to improve study design. Researchers are invited to scrutinise all the knowledge available on the catchment of interest, and to obtain multiple lines of evidence regarding sediment source contributions. Second, we think that scientific knowledge could be improved with local knowledge and we propose a scale of participation describing different levels of involvement of locals in research. Third, we recommend the use of state-of-the-art sediment tracing protocols to conduct sampling, deal with particle size, and examine data before modelling and accounting for the hydro-meteorological context under investigation. Fourth, we promote best practices in modelling, including the importance of running multiple models, selecting appropriate tracers, and reporting on model errors and uncertainty. Fifth, we suggest best practices to share tracing data and samples, which will increase the visibility of the fingerprinting technique in geoscience. Sixth, we suggest that a better formulation of hypotheses could improve our knowledge about erosion and sediment transport processes in a more unified way.

CONCLUSION

With the suggested improvements, sediment fingerprinting, which is interdisciplinary in nature, could play a major role to meet the current and future challenges associated with global change.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11368-022-03203-1.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes

eDNA refers to DNA extracted from an environmental sample with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDNA records. To investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil samples were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, samples were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the samples as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. Overall, these results illustrate the potential of eDNA analyses for identifying the recent (< 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. The capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales.

Consensus ranking as a method to identify non-conservative and dissenting tracers in fingerprinting studies

Soil erosion and fine particle transport are two of the major challenges in food security and water quality for the growing global population. Information of the areas prone to erosion is needed to prevent the release of pollutants and the loss of nutrients. Sediment fingerprinting is becoming a widely used tool to tackle this problem, allowing to identify the sources of sediments in a catchment. Methods in fingerprinting techniques are still under discussion with tracer selection at the centre of the debate. We propose a novel method, termed as consensus ranking (CR), that combines the predictions of single-tracer models to identify non-conservative tracers. In this context, a numerical procedure to quantify the predictions of individual tracers is first delivered. The scoring function to rank the tracers is based on several random debates between tracers in which the tracer that prevents consensus is discarded. Based on these results, a conservativeness index (CI) is presented along with a clustering method to identify groups of similar tracers. To illustrate the CI and CR procedures, an artificial mixture created with real soil to independently test the method is analysed. The results demonstrate the capability of our method to identify non-conservative tracers beyond the capability of currently used selection methods. Further, a real sediment sample from a Mediterranean mountain catchment is evaluated to emphasise its utility in complex natural environments. To test the utility of our method, it was decided to include the conservative and consensus-enforcing tracers extracted by this new approach with two different unmixing models. Furthermore, CR and CI procedures are displayed together with the most widespread statistical tests and the within-a-polygon approach used for tracer selection in fingerprinting studies. The new proposed method will enable the research community to homogenise results for replicability as well as allowing comparisons among study areas.

Sediment source fingerprinting: benchmarking recent outputs, remaining challenges and emerging themes

PURPOSE

This review of sediment source fingerprinting assesses the current state-of-the-art, remaining challenges and emerging themes. It combines inputs from international scientists either with track records in the approach or with expertise relevant to progressing the science.

METHODS

Web of Science and Google Scholar were used to review published papers spanning the period 2013-2019, inclusive, to confirm publication trends in quantities of papers by study area country and the types of tracers used. The most recent (2018-2019, inclusive) papers were also benchmarked using a methodological decision-tree published in 2017.

SCOPE

Areas requiring further research and international consensus on methodological detail are reviewed, and these comprise spatial variability in tracers and corresponding sampling implications for end-members, temporal variability in tracers and sampling implications for end-members and target sediment, tracer conservation and knowledge-based pre-selection, the physico-chemical basis for source discrimination and dissemination of fingerprinting results to stakeholders. Emerging themes are also discussed: novel tracers, concentration-dependence for biomarkers, combining sediment fingerprinting and age-dating, applications to sediment-bound pollutants, incorporation of supportive spatial information to augment discrimination and modelling, aeolian sediment source fingerprinting, integration with process-based models and development of open-access software tools for data processing.

CONCLUSIONS

The popularity of sediment source fingerprinting continues on an upward trend globally, but with this growth comes issues surrounding lack of standardisation and procedural diversity. Nonetheless, the last 2 years have also evidenced growing uptake of critical requirements for robust applications and this review is intended to signpost investigators, both old and new, towards these benchmarks and remaining research challenges for, and emerging options for different applications of, the fingerprinting approach.

New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).