Seasonal and Landscape Influences on Plant Diversity in Freshwater Ecosystems: Insights From eDNA Metabarcoding

ABSTRACT

Freshwater ecosystems provide critical services to human societies; however, the plant communities that sustain these ecosystems face increasing threats from human activities, highlighting the need for effective monitoring strategies. While environmental DNA (eDNA) metabarcoding has emerged as a powerful, non‐invasive tool for biodiversity monitoring, its application to plant community monitoring remains underutilized. This study evaluated the use of eDNA metabarcoding based on the orbcL2 marker to simultaneously quantify aquatic, terrestrial, and wetland plant community composition and diversity within and among 22 inland lakes in Michigan, USA. eDNA metabarcoding surveys identified 221 plant species, including 28 aquatic, 62 wetland, and 131 terrestrial species. Notably, the richness of terrestrial species exceeded those reported in previous studies, comprising 44%–81% of all taxa detected per lake, with wind‐pollinated trees constituting a substantial component of the dataset. Terrestrial species were more prevalent in lakes within landscapes characterized by greater forest cover and lower human development. Sampling timing affected species richness. Lakes sampled early in the season had greater species richness from both terrestrial and wetland communities. Wind‐pollinated species dominated early‐season detections, indicating their disproportionate influence on diversity measures. The diversity of aquatic plants showed minimal sensitivity to sampling date, and no significant seasonal variation in alpha diversity, contrasting with previous studies. However, the relatively short duration of our sampling may explain the absence of trends typically observed later in the season when plant decay increases. Beta diversity of aquatic plant communities was affected by land use, particularly agricultural activity in surrounding landscapes. Results highlight how seasonal and landscape characteristics can affect diversity estimates of freshwater plant communities, underscoring the need to account for temporal and spatial dynamics in eDNA‐based biodiversity monitoring. The study also emphasizes the limitations of relying on a single marker for accurate detection of aquatic invasive plant species.