Gerard Arjen de Groot

Sedimentary ancient DNA (sedaDNA) can expand archaeological research by recovering broad biological signals from small amounts of sediment. Here, we apply shotgun sedaDNA metagenomics and target capture (also known as hybridization capture) to disused Roman wells from the vicus of Harelbeke, Belgium, dated to ca. 160-300 CE, and integrate the results with existing bioarchaeological datasets. Moving beyond individual introduced taxa as proxies for Roman influence, we reconstruct community-level profiles spanning consumption-related, synanthropic, and environmental organisms. SedaDNA reproduced most established bioarchaeological signals, including cultivated plants and domestic animals, while also recovering additional environmental taxa that established methods underrepresented. Mitochondrial target capture strengthened selected faunal detections and enabled phylogenetic placement of a pig (Sus scrofa) within the European mitochondrial lineage. The predominance of previously established consumption-related taxa is consistent with subsistence continuity and selective adoption of Roman-introduced resources, although taxon counts alone cannot establish their relative importance. Analytical-effort modeling further indicates that batch-based sedaDNA workflows can provide broad biological profiles at lower cost and time investment than established archaeological methods. Overall, sedaDNA complements conventional bioarchaeology by broadening taxonomic recovery, supporting scalable sampling, and providing a broad-spectrum approach to reconstructing settlement ecology, subsistence, and human-environment interaction.

Monitoring biodiversity patterns and their changes in Arctic coastal ecosystems is critical under ongoing climate change. However, common current approaches require high effort and expertise and this in turn limits the spatial and temporal scale of these monitoring efforts. Here, we investigated both the fish and the marine invertebrate communities across Svalbard using a multi-marker environmental DNA metabarcoding approach. We collected and analysed marine water, sediment and zooplankton filtered from marine water from sites influenced by the warm West Spitsbergen Current and the cold East Spitsbergen Current. Following metabarcoding amplification using mitochondrial COI, 12S, 16S and nuclear 18S markers and high-throughput sequencing, we retrieved an extensive overview of Svalbard marine biodiversity. Water, sediment and especially zooplankton samples collected across Svalbard revealed spatial differences in community composition, with significantly distinct assemblages in the northwest and southeast of Svalbard. We identified potential bioindicator species for use in rapid assessment of impacts of marine temperature increase and confirmed observed patterns of ongoing shifts in community structure as a response to changes in dominant water masses. Overall, our findings show that species composition depending on fine-scale climate variation of Arctic waters can be effectively studied and monitored using environmental DNA. These insights can help us understand current and evolving climate-driven changes.

Arthropod diversity is rapidly declining in semi‐natural grasslands. Among the driving factors are nitrogen deposition and climate change, which typically increase vegetation productivity and extend the growing season. These changes can negatively affect plant diversity and simplify vegetation structure and thereby indirectly reduce arthropod diversity. Adjusting the mowing frequency, height and/or timing may counteract these effects and address shifts in seasonal activity of arthropods. This study evaluated the effects of these adjustments on arthropod diversity under current environmental conditions. We performed a 3‐year (2021–2023) field experiment in 10 Dutch roadside grasslands across a productivity gradient. The standard late August mowing (control) was compared to early November mowing and to June mowing at high (15 cm) or low (6 cm) height followed by either late August or early November mowing. In 2023, we assessed the effects of these mowing treatments on ground‐dwelling arthropods (sampled using pitfall traps), emerging arthropods (soil‐ and vegetation‐dwelling arthropods sampled using emergence traps) and flower availability (used as a proxy for food availability for pollinators). Our results show that delaying the final cut to early November was advantageous for late‐season emerging arthropods and flower availability regardless of site productivity. Emerging arthropod biomass in early autumn was approximately equal to that in spring and summer, underscoring the importance of delaying the final cut. In low‐productive sites, increasing the mowing frequency from one to two cuts per year did not benefit any species group. Conversely, in high‐productive sites, increasing the mowing frequency generally increased the diversity of ground‐dwelling arthropods, particularly in summer, and increased flower availability in spring. These benefits were most pronounced with a low cut in June. Yet, the June cut caused a relatively long (>1 month) reduction in flower availability and a lower summer biomass of emerging arthropods, regardless of cutting height. This suggests that regimes with two cuts per year could be more beneficial if applied in a phased or rotational manner. Synthesis and applications . Adjusted mowing dates and, in productive grasslands, an increased mowing frequency may benefit grassland arthropod communities under current environmental conditions.

Apple is one of the most important pollinator‐dependent fruit crops worldwide. To secure high‐quality yields, it is crucial to know which, and to what extent, pollinating insects contribute to its pollination success as measured by fruit set, fruit weight and seed set. We perform a meta‐analysis of field studies conducted across multiple orchards on insect‐mediated pollination in apple cultivation, using raw data from 29 studies, totalling 532 orchard replicates. We assessed the extent of pollen limitation on different pollination outcomes and assessed the contribution of honeybees, wild bees and bee species richness to apple pollination. Across all studies, we detected strong evidence of pollen limitation for fruit set and seed set, but not for fruit weight. Honeybees were the most abundant flower visitors (average relative visitation of 71.9%) compared to wild bees; but when correcting for their pollination efficiency, the relative pollination contribution of honeybees was lower compared to their relative visitation (vice versa for solitary bees). We conclude that honeybee visitation rate did not influence fruit or seed set; yet increasing honeybee visitation had a small, negative effect on fruit weight. Fruit set was not influenced by wild bee visitation rate, whereas wild bee visitation had a small, but clear positive effect on fruit weight and seed set. Bee species richness had a small, positive effect on seed set; whereas it did not affect fruit set and fruit weight. Syntheses and applications. Our study highlights that pollen limitation is common in this global crop. While managed honeybees are dominant pollinators, a diverse community of wild bees contributes significantly to apple pollination and high‐quality yield. The positive effect of wild bees and species richness on fruit weight and seed set demonstrates that wild bee pollination results in better‐quality fruit production (increased weight & seed set). Therefore, our synthesis highlights the importance of conserving pollinator diversity to maintain pollination services. The absence of a clear effect of honeybee visitation rate on fruit and seed set, coupled with its negative impact on fruit weight, suggests a need for further optimisation of honeybee management to improve the cost‐efficiency of pollination management.

Background and aims: Deadwood plays a vital role in forest ecosystems, influencing soil biodiversity through nutrient enrichment and niche partitioning. While the effects of specific attributes of deadwood logs on soil biodiversity are well studied, it remains unclear whether and how the volume of deadwood affects soil biodiversity at the scale of forest stands. Additionally, the effects on soil biodiversity may differ between gradually accumulated deadwood and large volumes resulting from sudden stand-level disturbance events. In this study, we aim to assess such effects on alpha and beta diversity of soil microbes and microfauna. Methods: Soil samples were gathered from forest plots following a gradient of deadwood volumes in European temperate forests in Germany and The Netherlands. Using extracellular DNA metabarcoding, we analysed the soil diversity of bacteria, fungi and microarthropods. For the Bavarian Forest National Park, we also compared the diversity patterns of these biotas between areas affected by bark beetle outbreaks and unaffected areas of Norway spruce forest. Results: Increased deadwood stock had a marginal effect on soil microbial and microarthropod community composition, with no impact on overall diversity. Bark beetle-affected areas had distinct soil communities, with a lower fungal and microarthropod diversity. Conclusion: Our study provides the first insights into soil diversity patterns associated with increased deadwood volume at the forest stand. While shifts in soil biodiversity composition were minimal, the retention of deadwood in European temperate forests can promote heterogeneity in soil communities. Furthermore, changes in soil biodiversity following bark beetle outbreaks may have long-term consequences on forest regeneration.

Fungi represent a significant portion of Earth's biological diversity and are essential for ecosystem functions like organic matter decomposition and nutrient cycling. While fungi associated with plant roots have been extensively studied, our understanding of fungi in the forest canopies remains limited. To investigate the landscape-scale variation in the canopy mycobiome of temperate beech and spruce forest stands in the Bavarian Forest National Park (Germany), we examined the influence of geophysical conditions and host traits. We found that elevation significantly influenced fungal diversity and composition, with distinct effects observed in both beech and spruce stands. Moreover, canopy water content, a key indicator of tree vitality, was also strongly associated with changes in the canopy fungi community, suggesting a potential link between forest water stress and the forest canopy mycobiome. Our differential abundance analysis further identified a total of 41 fungal families as potential bioindicators: 17 families in beech stands and 9 in spruce stands were significantly associated with elevation, while 9 families in beech stands and 6 in spruce stands were linked to variations in leaf water content. These findings enhance our understanding of the spatial patterns of forest canopy microbial biodiversity and species distributions.