Biodiversity is threatened by a wide range of anthropogenic activities. Monitoring offers critical insights into how and why biodiversity is changing, helping to identify effective measures for maintaining biodiversity and its ecosystem services. However, conventional biodiversity monitoring methods are labor-intensive, and standardized long-term monitoring series are scarce. DNA-based approaches like metabarcoding environmental DNA (eDNA) promise rapid, cost-efficient, and highly resolved community data. At the same time, scientists are looking for alternative data sources that can compensate for the lack of long-term monitoring data to study past biodiversity changes. This work explores the potential of the German Environmental Specimen Bank (ESB), a pollution monitoring archive, which appears particularly promising for retrospective biodiversity monitoring. Biota samples from different ecosystems across the country are collected and archived at an exceptional level of standardization. Sampling species act as natural eDNA samplers, accumulating genetic traces from surrounding organisms. The cryogenic storage at the ESB preserves any eDNA in the samples in its original state. In this thesis, Chapter I serves as an introductory chapter, outlining the general chances and challenges of metabarcoding for assessing biodiversity. Chapter II focuses on primer design and testing the utility of ESB sampling species like mussels and macroalgae for characterizing the surrounding community. Both chapters form the basis for Chapters III to V, which report the use of ESB time series to uncover sample-associated communities and the changes they undergo. Chapter III illustrates the value of these time series by revealing the invasion trajectory of an alien barnacle into German coastal waters and linking the process to climate change. Chapter IV forms the core of this thesis by presenting an expanded measurement of biodiversity change in ESB time series across different taxonomic groups and ecosystem types. Here, a gradual compositional change (turnover) is reported from bacterial, fungal, microeukaryotic, and metazoan communities tending to either spatial homogenization or differentiation. Observed trends are tested for significance using a dynamic model of community ecology based on the equilibrium theory of island biogeography. The model reveals significantly accelerated turnover rates across all taxonomic groups and ecosystems investigated, suggesting a common, anthropogenically induced driver of biodiversity change. Since these analyses most likely include DNA derived from dead as well as from living organisms, Chapter V aims to separate both groups by metabarcoding both DNA and less stable ribosomal RNA from mussel samples. Contrary to the hypothesis, RNA is detectable from both living endobionts and dietary taxa. However, it outcompetes DNA in detecting microeukaryotic biodiversity. In summary, this thesis demonstrates the outstanding potential of archived ESB samples for retrospective biodiversity monitoring, a resource that offers many further untapped opportunities for future biodiversity research at multiple scales.

Perennial crops eliminate soil disturbance and reduce the amount of synthetic chemicals that are applied to the soil, improving soil biodiversity and food web structure. Additionally, perennial cropping is characterised by all year-round surface coverage which benefits soil biota in terms of habitat and food sources. Perennial intermediate wheatgrass (Thinopyrum intermedium, IWG) was domesticated and commercialised by The Land Institute in Kansas as Kernza® and serves as an example for these nature-based solutions. It develops an extensive root system that has a higher nutrient retention, possibly reducing nutrient runoff. It thereby follows a more resource-conservative strategy with improved belowground-oriented resource allocation in its root system. This may reduce the need for excessive fertiliser as the crop has a higher nitrogen efficiency, among other things. IWG promoted the earthworm community and its diversity, more specifically, the occurrence of epigeic species (litter inhabitants), since those species benefit from the increased soil coverage and elimination of disturbances in the soil. As IWG creates a dense and extensive root system, as shown by the increased occurrence of root-feeding nematodes, endogeic species (horizontal burrowers) are supported through the provision of a reliable food source. IWG was characterised as a mostly undisturbed system with a highly structured food web through nematode analysis, as expressed through the promotion of structure indicators, for example, that are sensitive to disturbances in the soil and are therefore supported under no-till management. The root microbiome is continuously being shaped by the host as the crop regrows from the roots each vegetation period. This creates a symbiotic relationship and a beneficial feedback loop for the crop. Resultantly, the root-endophytic microbiome under IWG had a higher network complexity, connectivity and stability compared to annual wheat. The regrowth from the roots for IWG requires increased nutrient and energy storage, which was indicated by increased starch values. Correspondingly, the longer residence time of the roots in the soil resulted in higher lignin values. Furthermore, the decomposition pathway was dominated by fungivorous nematodes which may correspond to stimulated nutrient cycling and a heterogeneous resource environment, as seen for low input systems. Overall, perennial wheat cultivation improved soil biodiversity already after an establishment of 3-6 years. As those benefits were present for all three countries, the varying soil and climate conditions do not seem to interfere with the positive effect of perennial wheat on the soil ecosystem, demonstrating a wide transferability and adaptability of the crop onto other study sites as well. Enhanced complexity and connectivity of the food web in comparison to annual wheat may indicate a resistance against abiotic stress, suggesting IWG cultivation as a viable option for a sustainable and resilient agriculture. The improvement in nutrient cycling and the resource-efficient cultivation strategy for IWG could enable cultivation on marginal land where annual crop cultivation is not possible as the soils are susceptible to erosion and nutrient runoff. This opens up new possibilities for agricultural cultivation on previously unused land, thus contributing to food security in the future.