Biology subjects

Haase, P.

Publications and source records attributed to Haase, P..

4 recordsLinked to original sources

bioRxiv2026

eDNA metabarcoding provides scalable and continuous biodiversity monitoring across the tree of life

Environmental DNA (eDNA) metabarcoding has the potential to substantially expand our knowledge of global biodiversity beyond that provided by conventional approaches. However, the degree to which eDNA data provides real ecological insight, rather than primarily reflecting environmental factors that affect eDNA shedding and degradation, remains unclear. Additional uncertainties arise in terms of cost-effectiveness and whether the price is worth any extra biodiversity information that is gleaned. Here, we established a high-resolution, bi-weekly eDNA time-series in Germany across aquatic and riparian habitats to quantify seasonal biodiversity dynamics, to relate eDNA to different potential environmental drivers, and to parametrize cost estimates. Over one year, eDNA metabarcoding detected more than 1,000 species across multiple trophic levels and primarily revealed real, taxon-specific seasonal patterns, in addition to some relationships to water temperature, discharge, and conductivity. Compared to historical records dating back to 1891, year-round eDNA monitoring increased reported species numbers by 2.4-fold for invertebrates, 2.2-fold for mammals, 1.7-fold for diatoms, 1.2-fold for fish and lamprey, and 1.03-fold for birds. Cumulative biodiversity estimates increased strongly with sampling frequency, demonstrating the value of eDNA for high-frequency time-series monitoring. Moreover, eDNA monitoring was highly cost-effective, providing more than twice the biodiversity information of many conventional surveys for one-sixth the cost, enabling scalable, high-resolution freshwater biodiversity assessments.

ecology↗

bioRxiv2023

German-wide Malaise trap metabarcoding estimates over 33,000 insect species

Mitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale and long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that requires prohibitively high investments of time, funding, and taxonomic expertise. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 {euro} per sample, including supplies, labor and maintenance. With on average 1.4M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single OTU. We estimated another 21,403 plausible species, which likely either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany ([~]35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow ([~]80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.

ecology↗

bioRxiv2021

Climate, latitude, and land cover predict flying insect biomass across a German malaise trap network

O_LIAmong the many concerns for biodiversity in the Anthropocene, recent reports of flying insect loss are particularly alarming, given their importance as pollinators and as a food source for many predators. Few insect monitoring programs cover large spatial scales required to provide more generalizable estimates of insect responses to global change drivers. C_LIO_LIWe ask how climate and surrounding habitat affect flying insect biomass and day of peak biomass using data from the first year of a new standardized distributed monitoring network at 84 locations across Germany comprising spatial gradient of land-cover types from protected to urban areas. C_LIO_LIFlying insect biomass increased linearly with monthly temperature across Germany. However, the effect of temperature on flying insect biomass flipped to negative in the hot months of June and July when local temperatures most exceeded long-term averages. C_LIO_LILand-cover explained little variation in insect biomass, but biomass was lowest in forested sites. Grasslands, pastures and orchards harbored the highest insect biomass. The date of peak biomass was primarily driven by surrounding land-cover type, with grasslands especially having earlier insect biomass phenologies. C_LIO_LIStandardized, large-scale monitoring is pivotal to uncover underlying processes of insect decline and to develop climate-adapted strategies to promote insect diversity. In a temperate climate region, we find that the benefits of temperature on flying insect biomass diminish in a German summer at locations where temperatures most exceeded long-term averages. These results highlighting the importance of local adaptation in climate change-driven impacts on insect communities. C_LI

ecology↗

bioRxiv2020

Improved freshwater macroinvertebrate detection from eDNA through minimized non-target amplification

DNA metabarcoding of freshwater communities typically relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase (COI) gene with degenerate primers. The advantage of COI is its taxonomic resolution and the availability of an extensive reference database. However, when universal primers are used on environmental DNA (eDNA) isolated from stream water, macroinvertebrate read and OTU numbers are typically "watered down", i.e. diluted, compared to whole specimen bulk samples due to greater co-amplification of abundant non-target taxa such as algae and bacteria. Because stream macroinvertebrate taxa are of prime importance for regulatory biomonitoring, more effective ways to capture their diversity via eDNA isolated from water are important. In this study, we aimed to improve macroinvertebrate assessment from eDNA by minimizing non-target amplification. Therefore, we generated data using universal primers BF2/BR2 throughout 15 months from a German Long-Term Ecological Research (LTER) site, the River Kinzig, to identify most abundant non-target taxa. Based on these data, we designed a new reverse primer (EPTDr2n) with 3-specificity towards macrozoobenthic taxa and validated its specificity in silico together with universal forward primer fwhF2 using available data from GenBank and BOLD. We then performed in vitro tests using 20 eDNA samples taken in the Kinzig catchment. We found that the percentage of target reads was much higher for the new primer combination compared to two universal macrozoobenthic primer pairs, BF2/BR2 and fwhF2/fwhR2n (>99 % vs. 21.4 % and 41.25 %, respectively). Likewise, number of detected macroinvertebrate taxa was substantially higher (351 vs. 46 and 170, respectively) and exceeded the number of 257 taxa identified by expert taxonomists at nearby sites across two decades of sampling. While few taxa such as Turbellaria were not detected, we show that the optimized primer avoids the dilution problem and thus significantly improves macroinvertebrate detection for bioassessment and -monitoring.

ecology↗