Baranski, D. | bioRxiv Science

bioRxiv2025

Two decades of compositional restructuring of soil biodiversity in Germany despite stable a- and b-diversity indices

Soil ecosystems host some of the most taxonomically and functionally diverse biological communities on Earth, yet long-term trends in their biodiversity remain poorly understood. Here, we analysed soil biodiversity dynamics over 20 years with samples archived in the German Environmental Specimen Bank. We assessed temporal and spatial patterns in -diversity and {beta}-diversity with shotgun metagenomics across bacteria, fungi, and metazoa. We found no statistically significant temporal trends in -diversity for any group. Total {beta}-diversity also appeared temporally stable. However, decomposing {beta}-diversity into its balanced variation and abundance gradients revealed taxon-specific compositional restructuring. Bacterial and fungal communities showed signs of compositional homogenisation, while metazoan communities remained more stable. Spatial structuring was pronounced across all groups. Land use emerged as a key spatial predictor of community composition for bacteria and fungi, and geographic locality for metazoans. Our findings show that apparent stability in standard biodiversity indices may mask significant underlying community change. This highlights the need for integrative, taxonomically inclusive approaches to biodiversity monitoring. The combination of environmental specimen banking with metagenomic sequencing offers a powerful framework for uncovering hidden biodiversity trends in soil ecosystems and identifying the drivers of ecological reorganisation under global change.

ecology↗

bioRxiv2024

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BackgroundSequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data. ResultsIn this study, we present the chromosome-level genome assembly and annotation of the marine sacoglossan species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the Long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are 100-fold and 4-fold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa. We detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds. ConclusionsWe can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

genomics↗