Biology subjects

Deiner, K.

Publications and source records attributed to Deiner, K..

8 recordsLinked to original sources

bioRxiv2026

Stream and lake network position structures freshwater microbial communities across multiple catchments

Streams and lakes form hydrologically connected freshwater networks. Different environmental conditions and dispersal dynamics along the stream to lake continuum potentially affect bacterial community composition, although the strength of such effects may vary among individual catchments. Here, we analysed 224 water samples from 58 streams draining into eight lakes across Switzerland, covering the full continuum from headwaters to lake outlets. Bacterial community composition analyzed via 16S metabarcoding differed between streams and lakes, with a sharp turnover at stream and lake confluence, and this pattern was repeatable across all catchments. Lake communities had lower alpha diversity and lower overall beta dispersion than stream communities, despite hydrological connectivity with a diverse stream microbiome. Community composition in both lakes and streams differed between catchments, but this pattern was more pronounced in lakes. Lake communities were dominated by a small set of widespread and abundant core taxa, primarily established pelagic freshwater genera, that captured the catchment-level differences through shifts in relative abundance. In contrast, stream communities contained a comparatively less abundant core microbiome dominated by soil- and groundwater-associated genera, together with a larger and more diverse peripheral microbiome. Together, these findings show that bacterial community composition changes repeatably across the different positions of hydrological networks.

microbiology↗

bioRxiv2025

Sorting States of Environmental DNA Reveals State-Specific Biodiversity Signals and Transport Patterns in Eight Alpine Watersheds

Environmental DNA (eDNA) exists in three states: membrane-bound, adsorbed, and dissolved. These states differ in persistence and degradation, strongly influencing the interpretation of eDNA data. Despite this, they have rarely been separated and analyzed independently from environmental samples. We developed a state-sorting workflow to isolate and analyze them, applying it to samples from 221 sites from 58 streams across eight lake watersheds with COI and ITS metabarcoding to reveal differences in biodiversity content and transport dynamics. Our results show that all three states contain both shared and unique taxonomic diversity for COI, and that plant DNA was only detected in the membrane-bound state. For COI, membrane-bound eDNA contained 87.8% of observed ASVs, far exceeding the adsorbed (37.2%) and dissolved (20.5%) states. Only membrane-bound eDNA showed evidence of downstream transport, but its extent varied among watersheds due to local hydrology. While upstream eDNA was transported to stream-lake confluences, lake surface samples showed marked turnover in community composition. Clarifying the fate of membrane-bound eDNA within lakes will enhance catchment-level detection from lake samples and understanding of lake hydrodynamics. Of the environmental parameters assessed, water temperature was most strongly aligned with changes in community composition between sites. Most previous studies have likely captured the majority of the eDNA diversity within their samples by inadvertently targeting the membrane-bound state. This study demonstrates the utility of eDNA state-sorting, but the methods require further refinement. Analyzing states independently improves the interpretation of eDNA data and elucidates the processes governing eDNA fate and transport.

molecular biology↗

bioRxiv2025

Real-time Malaria Detection in the Amazon Rainforest via Drone-Collected eDNA and Portable qPCR

Emerging zoonotic parasites such as Plasmodium spp. in remote ecosystems demand rapid, field-deployable surveillance. We developed a drone-based environmental DNA (eDNA) sampling approach integrated with a portable quantitative PCR (qPCR) assay for in situ detection of Plasmodium DNA. Field trials confirmed malaria parasite DNA in canopy swabs, coinciding spatially with acoustic detection of howler monkeys (Alouatta sp.), suspected reservoir hosts. No Anopheles mosquitoes were captured in simultaneously deployed insect traps. The end-to-end workflow, from drone deployment to diagnostic readout, averaged 1.5 hours per assay, required only basic mobile-laboratory infrastructure, and bypassed cold-chain logistics. This rapid, non-invasive method delivers actionable surveillance data in real-time, enabling near-real-time trigger points for vector-control interventions and clinical response in remote settings. By merging environmental genomics with portable diagnostics, we establish a scalable One Health framework adaptable to diverse vector-borne parasites and ecosystems, with potential for early detection and spillover risk mitigation in under-monitored, high-risk environments.

molecular biology↗

bioRxiv2023

Can we sort states of environmental DNA (eDNA) from a single sample?

Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 {+/-} 19.24 %), followed by the adsorbed state (5.08 {+/-} 2.28 %), and the dissolved state had the lowest total recovery (2.21 {+/-} 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.

molecular biology↗

bioRxiv2022

A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess aquatic macroinvertebrate biodiversity

Monitoring freshwater biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution models (SDM). Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared a triad of approaches in order to understand assessment of aquatic macroinvertebrate biodiversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species distribution model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species distribution model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the two approaches, particularly at local scale. Overall, the more specific set of primers, namely fwhF2/EPTDr2n, was most efficient for the detection of target species and for characterizing the diversity of EPT. Moreover, we found that the species richness measured by eDNA was poorly correlated to the richness measured by kicknet sampling and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the statistical model. Overall, however, neither eDNA nor the traditional approach had strong links to the predictive models, indicating inherent limitations in upscaling species richness estimates. Future challenges include improving the accuracy and sensitivity of each approach individually yet also acknowledge their respective limitations, in order to best meet stakeholder demands addressing the biodiversity crisis we are facing.

ecology↗

bioRxiv2020

A rapid urban biodiversity blitz using aquatic environmental DNA

Background As global biodiversity declines, there’s an increasing need to create an educated and engaged society. Having people from all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we test whether sampling eDNA and metabarcoding can be used for rapid urban biodiversity surveys for educational purposes.Materials & Methods We sampled 2×1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine and brackish habitats. DNA was extracted, amplified in triplicate for the COI gene and sequenced. The obtained data were analysed on the novel mBRAVE platform, an online open access software and computing resource.Results The water samples were collected in two days by two people and the lab analysis was completed in five days by one person. Overall, we detected the presence of 501 taxa identified as belonging to 435 species, representing 90 orders and 18 phyla. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota.Discussion Our results match expected patterns of biodiversity in the landscape and show that with minimal sampling effort, hundreds of species can be detected. Thus, using eDNA analysis of water is promising for rapid biodiversity surveys, and it is likely that more detailed results could be obtained by optimising field and lab methods for particular groups of interest. We recommend that rapid eDNA surveys, with openly available services and softwares, can be used to raise awareness in the importance of biodiversity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. "in silico analysis"), and arranged on a 5-level validation scale from "incomplete" to "operational" with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.

molecular biology↗

bioRxiv2020

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between {beta}-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high -diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

ecology↗