Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water

Size‐dependent community patterns differ between microbial eukaryotes and bacteria in a permafrost lake–river–sea continuum

“…Such dominance of homogeneous selection was previously noted in the Yarlung Zangbo River (Tibet) for microbial eukaryotes (Yang et al 2023) and in the Aulne River estuary (France) for both free-living and particle-based bacterial fractions (Urvoy et al 2022). Homogeneous selection was most pronounced in our large bacterial fraction, in line with previous findings in the aquatic continuum of the Tsurumi River (Japan), where this pattern was attributed to the homogeneity of metabolites in particles across sampling sites (Yokoyama and Kikuchi 2023). Homogeneous selection is observed when community turnover is lower than expected by chance, suggesting that these communities inhabit a common selective environment (Stegen et al 2015).…”

“…Particle-associated cells may be buffered from external changes, given the constancy of their microhabitats inside organic aggregates relative to freeliving cells that are directly exposed to chemical fluctuations in the aqueous environment (Grossart 2010). Consistent with this effect, free-living bacterial communities showed a rapid phylogenetic shift in the freshwater-saltwater transition of a Japanese urban river, while particle-associated bacteria did not (Yokoyama and Kikuchi 2023). Filter size fractionation of these two broad categories of bacteria is therefore useful to distinguish these patterns.…”

“…While some species may increase in abundance throughout the length of a river, others may decline with distance from the headwaters ("seed" vs. "tourist" taxa; Ruiz-Gonz alez et al 2017). Selection is especially apparent in the freshwater-saltwater transition zone, with pronounced shifts in environmental properties and microbial community composition taking place as river waters discharge into and mix with the sea (Crump et al 2004;Jacquemot et al 2021;Yokoyama and Kikuchi 2023). Community composition may also differ depending on the presence of a headwater lake (Crump et al 2007).…”