Cotton strips as a model substrate for analysis of leaf‐litter‐colonizing microbial assemblages in streams

Abstract Leaf‐litter decomposition is a key indicator of the functional integrity of stream ecosystems and cotton strips have been employed as a standard substrate for quantification of litter‐decomposition rates in streams across the globe. Cotton strips also offer a standardized method for assessing structural integrity of stream microbial assemblages involved in leaf‐litter decomposition. A key assumption of this approach is that microbiomes that colonize cotton are similar to those that colonize decomposing leaves, but this assumption has not been explicitly tested. We incubated cotton strips and leaves from four tree species that differ in litter quality (shagbark hickory [ Carya ovata ], white oak [ Quercus alba ], red oak [ Quercus rubra ], and red maple [ Acer rubrum ]) in the Chicago River (Illinois, USA) for 14 and 28 d. We analyzed the taxonomic composition of microbiomes that colonized the substrates using amplicon sequencing and quantified functional genes linked to cellulose decomposition. Cotton was colonized by bacterial and fungal assemblages that did not differ in species richness and diversity from leaves, and cotton microbiomes included bacterial and fungal orders that also colonized leaves and are associated with leaf detritus in streams. The similarity between cotton and leaf microbiomes increased during incubation in the stream, but there remained substrate‐specific differences in fungal and bacterial assemblages between cotton and leaves and between each of the leaf species. Cotton was also colonized by a greater abundance of cellulose‐degrading bacteria and fungi than leaves. These results support use of cotton strips to assess stream structural integrity (e.g., biodiversity, composition) but suggest that this assessment will be biased toward cellulose‐degrading microbes.