From microbes to mammals: agriculture homogenizes pond biodiversity across different land-use types

The diversity and composition of biological communities in ecosystems is typically linked to land use. Consequently, intensive agriculture has a strong influence on these patterns, including reduction homogenization species diversity. Kettle holes (KH; also known as potholes) are small water bodies (<1 ha) typical formerly glaciated the northern hemisphere, reaching densities up several dozen per km 2 . They often function drainage centers, linking various landscape elements their surroundings hotspots aquatic biodiversity terrestrial landscapes. In 1950s, use surrounding KH Europe (e.g., Germany, Poland, Netherlands) North America (USA Canada) shifted towards agriculture, likely affecting local regional KH. Reports ponds agricultural landscapes scarce, mostly focus single taxa. We used deep eDNA amplicon sequencing eukaryotic, bacterial, archaeal SSU rRNA genes assess effects overall 67 either arable fields, grasslands, or forests, all embedded subjected for decades. These were later contrasted with Berlin city ponds. Metatranscriptomic analyses conducted parallel investigate taxonomic functionality active communities. data, >300 million reads, analyzed phyloFlash Kraken2 using SILVA_SSU_Ref database. Subsequently, sequences grouped based taxonomy. different annotation pipelines resulted similar patterns. A subset data was DADA2, generating sequence variants. Clustering variants according taxonomy identical suggesting that broad taxonomical groupings provide sufficient resolution general overviews. Annotation eukaryotic community challenging, none currently available databases contains high-quality cover entire phylogenetic breadth. To overcome this limitation, we SILVA_SSU_Parc database, which short excluded from SILVA_SSU_Ref, thus extending base analysis. curated, PR2 database did not better results than An incompatibility between SILVA classical nomenclature ‘language barrier,’ could be partly resolved by EMBL provided databases. Nevertheless, propose short-read SSU-based annotations should validated other means. Despite such methodological limitations, our study demonstrates return reliable picture complex ecosystems. Such information identify patterns across three domains life can serve pinpoint groups investigated more detailed approach. Our concluded long-term exposure diverse groups, removing most differences among land-use types. This outcome contrasts associated sediments KH, where temporal coverage extends back at least onset agriculture. However, metatranscriptomic analyses, reflecting distribution activities rather relative abundance, revealed structure types, matching times field fertilization. Thus, even been homogenized, inputs result short-term activity changes organisms. needs considered when developing new management schemes needed counteract current loss.