Terrestrial-aquatic ecosystem links on the Tibetan Plateau inferred from sedaDNA shotgun sequencing

Climate change and associated species interactions are responsible for many vital mechanisms governing the dynamics of ecological communities. However, the long-term contribution of environmental conditions and species connections to community assembly remain mostly unknown. Here, we present changes of terrestrial and freshwater communities based on metagenomic shotgun data retrieved from lacustrine sediments of an alpine freshwater lake on the south-eastern Tibetan Plateau (Hengduan Mountains) covering the past 15,100 thousand years (ka). Terrestrial assemblages between 15.1-14 ka are explained by the harsh environment and facilitative interactions due to diverse cushion plants, while the abundant ice-age algae (Nannochloropsis and N. limnnetica) indicate dominance of glacial meltwaters. A sharp decrease in alpine herbs (e.g Asteraceae, Carex and Poaceae) corresponded to competitive interactions with the colonization of woody plants (Salicaceae, Salix, Rhododendron and R. delavayi) since 14 ka, leading to a decline of large herbivores (Bovidae and Bos mutus) that predominated. Meanwhile, the disappearance of ice-age algae and the expansion of submerged plants (e.g., Potamogeton, P. perfoliatus, Myriophyllum, and M. spicatum) are consistent with an increase in temperature and a plentiful supply of nutrients due to weathering and soil erosion. The loss of submerged plants during the late Holocene (~3.6 ka) is probably related to environmental deterioration; however, it could also be related to the Cyanobacteria boom. Our study highlights that shotgun sequencing of lake sediments is an important tool for exploring ecological processes of communities in the past.