Fungal communities across a surface water permanence gradient in a non-perennial prairie stream network

Over half of the world's streams are non-perennial, drying at some point in space and time, but most research on stream-inhabiting fungi comes from perennial (continuously flowing) streams. To improve our understanding of fungal communities in non-perennial streams, we used ITS rDNA metabarcoding to survey fungal communities in three natural substrates (rock surfaces, decaying leaves, and sediments) across a surface water permanence gradient (determined via in-stream sensors) in a non-perennial prairie stream system in Kansas, USA. Fungal community composition varied along a continuum from wooded downstream reaches to increasingly open canopies (with grassy riparian vegetation) further upstream. Independently of position along this continuum, fungal community composition varied with annual surface water permanence. Communities on rock surfaces were the most sensitive to water impermanence, where rock-inhabiting freshwater lichens (<i>Verrucariaceae</i>) were bioindicators of wetter (<i>Verrucaria humida</i>) or drier (<i>V. tallbackaensis</i>) conditions. Position along the stream continuum explained more variation in fungal community composition than surface water permanence, possibly because of increasing network connectivity downstream or distinct fungal assemblages associated with grassy versus woody plants. Known drying-tolerant decomposers were among the dominant taxa (e.g. <i>Alternaria</i> spp. and <i>Tetracladium marchalianum</i>). However, DNA-based studies of stream fungal communities remain challenging due to underrepresentation of aquatic hyphomycetes in reference databases and contributions of terrestrial fungi (some of which may be active in non-perennial streams) to measured diversity. As streamflow intermittency increases globally, this study provides unprecedented intra-watershed coverage of fungal communities and insights into how hydrology and riparian plants influence fungi across different benthic substrates.