Metabarcoding reveals potentially mixotrophic flagellates and picophytoplankton as key groups of phytoplankton in the Elbe estuary.

In estuaries, phytoplankton are faced with strong environmental forcing (e.g. high turbidity, salinity gradients). Taxa that appear under such conditions may play a critical role in maintaining food webs and biological carbon pumping, but knowledge about estuarine biota remains limited. This is also the case in the Elbe estuary where the lower 70 km of the water body are largely unexplored. In the present study, we investigated the phytoplankton composition in the Elbe estuary via metabarcoding. Our aim was to identify key taxa in the unmonitored reaches of this ecosystem and compare our results from the monitored area with available microscopy data. Phytoplankton communities followed distinct seasonal and spatial patterns. Community composition was similar across methods. Contributions of key classes and genera were correlated to each other (p < 0.05) when obtained from reads and biovolume (R = 0.59 and 0.33, respectively). Centric diatoms (e.g. Stephanodiscus) were the dominant group - comprising on average 55 % of the reads and 66-69 % of the biovolume. However, results from metabarcoding imply that microscopy underestimates the prevalence of picophytoplankton and flagellates with a potential for mixotrophy (e.g. cryptophytes). This might be due to their small size and sensitivity to fixation agents. We argue that mixotrophic flagellates are ecologically relevant in the mid to lower estuary, where, e.g., high turbidity render living conditions rather unfavorable, and skills such as phagotrophy provide fundamental advantages. Nevertheless, further findings - e.g. important taxa missing from the metabarcoding dataset - emphasize potential limitations of this method and quantitative biases can result from varying numbers of gene copies in different taxa. Further research should address these methodological issues but also shed light on the causal relationship of taxa with the environmental conditions, also with respect to active mixotrophic behavior.