Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by ...target‐species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost‐effective tools for conservation, eDNA‐based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data‐structures and simultaneously assess rates of false positive and negative results. Further, we introduce process‐based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target‐species assessments. These tools will be most effective when capitalizing on multi‐source data sets collating eDNA with classical survey and citizen‐science approaches, paving the way for more robust decision‐making processes in conservation planning.
Environmental DNA (eDNA) barcoding has a high potential to increase the cost-efficiency of species detection and monitoring in aquatic habitats. However, despite vast developments in the field, many ...published assays often lack detailed validation and there is little to no commonly (agreed upon) standardization of protocols. In this study, we evaluated the reliability of eDNA detection and quantification using published primers and assays targeting the Freshwater Pearl Mussel as a model organism. We first assessed limits of detection for two different target genes (COI and 16S) following the MIQE guidelines, and then tested the reliability of quantification in a double-blind mesocosm experiment. Our results reveal that different methodological indicators, namely accuracy, repeatability and detection probability affected the reliability of eDNA measurement at the different levels tested. The selection of the optimal analytical method was mainly determined by detection probability. Both the COI and 16S assays were highly specific for the targeted organism and showed similar accuracy and repeatability, whilst the limit of detection was clearly lower for the COI based approach. In contrast, the reliability of eDNA quantification hinged on repeatability, reflected by the scattering (r
= 0.87) around the relationship between eDNA and mussel density in mesocosms. A bootstrapping approach, which allowed for the assignment of measures associated with repeatability of samples, revealed that variability between natural replicates (i.e. accuracy) strongly influenced the number of replicates required for a reliable species detection and quantification in the field.
Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may ...strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.
Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.
Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase β-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.
Zooplankton blooms are a frequent phenomenon in tropical systems. However, drivers of bloom formation and the contribution of emerging resting eggs are largely unexplored. We investigated the ...dynamics and the triggers of rotifer blooms in African soda-lakes and assessed their impact on other trophic levels. A metaanalysis of rotifer peak densities including abundances of up to 6 × 10⁵ individuals L-1 demonstrated that rotifer bloom formation was uncoupled from the food environment and the seasonality of climatic conditions. A time series with weekly sampling intervals from Lake Nakuru (Kenya) revealed that intrinsic growth factors (food quality and the physicochemical environment) significantly affected rotifer population fluctuations, but were of minor importance for bloom formation. Instead, rotifer bloom formation was linked to sediment resuspension, a prerequisite for hatching of resting-eggs. Population growth rates exceed pelagic birth rates and simulations of rotifer dynamics confirmed the quantitative importance of rotifer emergence from the sediment egg-bank and signifying a decoupling of bloom formation from pelagic reproduction. Rotifer blooms led to a top-down control of small-sized algae and facilitated a switch to more grazingresistant, filamentous cyanobacteria. This shift in phytoplankton composition cascaded up the food chain and triggered the return of filter-feeding flamingos. Calculations of consequent changes in the lake’s energy budget and export of aquatic primary production to terrestrial ecosystems demonstrated the large potential impact of nonseasonal disturbances on the functioning of shallow tropical lakes.
Conventional agriculture is frequently associated with large-scale environmental degradation and landscape homogenization. In contrast, ecological intensification incorporates natural habitat ...conservation and landscape complexity to improve important ecosystem services such as pollination and crop yields. In an observational study of 105 fields in the Argentinean Pampas Region, we explored whether sunflower yields were related to landscape composition (percentage of natural habitat) and configuration (field size and edge density), and covariates of agricultural management practices such as nitrogen fertilizer addition, seed density, sowing date and crop cultivar. Our mixed-effects models revealed that field size and edge densities between crop and natural habitat are important predictors of yield. For example, a doubling of edge density from 40 m/ha to 80 m/ha predicted an 11.3% (269 kg/ha) yield increase, while a doubling in the field size from 40 ha to 80 ha predicted a 6.1% (149 kg/ha) yield decrease. We suggest that pollination is an important driver of both effects as higher edge densities and smaller field sizes reduce wild pollinator flight distances to crop flowers and thus increases the chances for effective crop pollination. This study provides key information for sustainable management of sunflower agroecosystems.
Molecular‐based monitoring relying on environmental DNA (eDNA) detection became routinely used around the world in the last few years, especially in aquatic environments. The large potential and ...increasing applications of this technique calls for technical improvements to optimize the reliability of these surveys. An important technical aspect in the eDNA workflow is the appropriate preservation of samples taken in the field, as it can significantly affect eDNA recovery and ultimately false negative rates. In this study, we explored the efficiency of five different preservation strategies by using a controlled mesocosm experiment in which we included three fish communities of different composition. Specifically, we compared eDNA recovery in DNA extractions (a) performed immediately following collection, or after eight months storage from (b) frozen filters, (c) unfiltered water samples stored at −20°C, and filters preserved at room temperature with (d) Longmire and (e) Sarkosyl buffer. Effects of different preservation strategies were quantified using ddPCR measurements of three fish species (Neogobius melanostomus, Rutilus rutilus, and Lota lota) and total fish DNA content using group‐specific primers for Teleostei. Samples extracted immediately following collection without any further preservation yielded significantly less DNA compared to the other approaches. Overall, Longmire's buffer facilitated the best eDNA recovery across all fish species although approaches such as filter freezing or the use of Sarkosyl buffer yielded similar recovery results. Relative measurement variability, an important indicator for reliable eDNA quantification, was lowest when using Longmire's and Sarkosyl buffers and generally decreased when increasing eDNA quantity. Overall, our results clearly highlight the significant impact of sample preservation and how this can substantially affect the performance and reliability of eDNA‐based approaches.
We explored the efficiency of five different preservation strategies to optimize the reliability of eDNA surveys. Using a controlled mesocosms experiment and ddPCR measurements, we found that Longmire's buffer facilitated the best eDNA recovery. Samples extracted immediately following collection without any further preservation yielded significantly less DNA compared than all other approaches. Our results clearly highlight the significant impact of sample conservation.
Humans have fundamentally altered the cycling of multiple elements on a global scale. These changes impact the structure and function of terrestrial and aquatic ecosystems, with many implications for ...human health. Most prior studies linking biogeochemical changes to human health have evaluated the effects of single elements in isolation. However, the relative availability of multiple elements often determines the biological impact of shifts in the concentration of a single element. The balance of multiple elements is the focus of ecological stoichiometry, which highlights the importance of elemental ratios in biological function across all systems and scales of organization. Consequently, ecological stoichiometry is a promising framework to inform research on the links between global changes to elemental cycles and human health. We synthesize evidence that elemental ratios link global change with human health through biological processes occurring at two scales: in the environment (natural ecosystems and food systems) and within the human body. Elemental ratios in the environment impact the key ecosystem processes of productivity and biodiversity, both of which contribute to the production of food, toxins, allergens, and parasites. Elemental ratios in diet impact processes within the human body, including the function and interactions of the immune system, parasites, and the non-pathogenic microbiome. Collectively, these stoichiometric effects contribute to a wide range of non-infectious and infectious diseases. By describing stoichiometric mechanisms linking global change, ecological processes, and human health, we hope to inspire future empirical and theoretical research on this theme.
Display omitted
•Introduction of the marine environment as a crucial component of the One Health concept.•Highlighting how corals act as canaries in the coal mine with regard to impacts from climate ...change.•Recognition of the difficulties around coral disease identification, yet still advocating for assessment in surveys aimed at monitoring reef health.•Introduction of a new ‘ecosystem homogenisation index’ exploring habitat homogenisation across environmental gradients.•Exploration of future tools like citizen science, eDNA and biomarkers in the assessment of reef health.
‘One World – One Health’ is a developing concept which aims to explicitly incorporate linkages between the environment and human society into wildlife and human health care. Past work in the field has concentrated on aspects of disease, particularly emerging zoonoses, and focused on terrestrial systems. Here, we argue that marine environments are crucial components of the ‘One World – One Health’ framework, and that coral reefs are the epitome of its underlying philosophy. That is, they provide vast contributions to a wide range of ecosystem services with strong and direct links to human well-being. Further, the sensitivity of corals to climate change, and the current emergence of a wide range of diseases, make coral reefs ideal study systems to assess links, impacts, and feedback mechanisms that can affect human and ecosystem health. There are well established protocols for monitoring corals, as well as global networks of coral researchers, but there remain substantial challenges to understanding these complex systems, their health and links to provisioning of ecosystem services. We explore these challenges and conclude with a look at how developing technology offers potential ways of addressing them. We argue that a greater integration of coral reef research into the ‘One World – One Health’ framework will enrich our understanding of the many links within, and between, ecosystems and human society. This will ultimately support the development of measures for improving the health of both humans and the environment.
In recent years, eDNA-based assessments have evolved as valuable tools for research and conservation. Most eDNA-based applications rely on comparisons across time or space. However, temporal, and ...spatial dynamics of eDNA concentrations are shaped by various drivers that can affect the reliability of such comparative approaches. Here, we assessed (i) seasonal variability, (ii) degradation rates and (iii) micro-habitat heterogeneity of eDNA concentrations as key factors likely to inflict uncertainty in across site and time comparisons. In a controlled mesocosm experiment, using the white-clawed crayfish as a model organism, we found detection probabilities of technical replicates to vary substantially and range from as little as 20 to upwards of 80% between seasons. Further, degradation rates of crayfish eDNA were low and target eDNA was still detectable 14–21 days after the removal of crayfish. Finally, we recorded substantial small-scale in-situ heterogeneity and large variability among sampling sites in a single pond of merely 1000m2 in size. Consequently, all three tested drivers of spatial and temporal variation have the potential to severely impact the reliability of eDNA-based site comparisons and need to be accounted for in sampling design and data analysis of field-based applications.
Display omitted
•eDNA detection and concentrations can vary substantially across the seasons.•White-clawed crayfish eDNA is detectable upwards of 14 days in the environment.•Substantial small scale in-situ heterogeneity in eDNA distribution was observed.•Highlights the importance of addressing temporal and spatial dynamics of eDNA.
PDF
