Data from: From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape

Local biodiversity patterns are expected to strongly reflect variation in
topography, land use, dispersal boundaries, nutrient supplies, contaminant
spread, management practices and other anthropogenic influences. In
contrast, studies focusing on specific taxa revealed a biodiversity
homogenization effect in areas subjected to long-term intensive industrial
agriculture. We investigated whether land use affects biodiversity levels
and community composition (α & β diversity) in 67 kettle holes
(KH) representing small aquatic islands embedded in the patchwork matrix
of a largely agricultural landscape comprising grassland, forest, and
arable fields. These KH, similar to millions of standing water bodies of
glacial origin, spread across northern Europe, Asia, and North America,
are physico-chemically diverse, differ in the degree of coupling with
their surroundings. We assessed biodiversity patterns of eukaryotes,
Bacteria and Archaea in relation to environmental features of the KH,
using deep-amplicon-sequencing of environmental DNA (eDNA). First, we
asked whether deep sequencing of eDNA provides a representative picture of
KH biodiversity across the Bacteria, Archaea, and Eukaryotes. Second, we
investigated if and to what extent KH biodiversity is influenced by the
surrounding land-use. Our data shows that deep eDNA amplicon sequencing is
useful for in-depth assessments of cross-domain biodiversity comprising
both micro- and macro-organisms, but, has limitations with respect to
single-taxa conservation studies. Using this broad method, we show that
sediment eDNA, integrating several years to decades, depicts the history
of agricultural land-use intensification. The latter, coupled with
landscape wide nutrient enrichment (including by atmospheric deposition),
groundwater connectivity between KH and organismal (active and passive)
dispersal in the tight network of ponds, resulted in a biodiversity
homogenization in the KH water, levelling off today’s detectable
differences in KH biodiversity between land-use types.