16S and 18S rRNA gene sequencing data for: Differential utilization of submerged leaf litter by microbial biofilms and macroinvertebrates in a large dryland river

Microbial biofilms may enhance the nutritional quality of terrestrial (allochthonous) resources for aquatic macroinvertebrates. We used 16S and 18S rRNA gene sequencing and essential amino acid carbon stable isotope analysis to characterize microbial biofilms and quantify proportional contributions of essential amino acids derived from algae, terrestrial plants, and microbes (Archaea, Bacteria, fungi) to macroinvertebrates across a series of mesocosm and in situ leaf pack experiments in the middle Rio Grande of central New Mexico, USA. Our mesocosm experiment showed that the microbial composition and diversity of submerged leaf packs varied across leaf types and time, while our field experiment showed that river sediment was the main source of microbes colonizing submerged leaf packs. Although heterotrophic microbes likely facilitated the initial breakdown of submerged leaves and the proportion of microbially derived essential amino acids in leaf packs generally increased over time, microbes were significant sources of essential amino acids to macroinvertebrates only in Sporobolus contracts (Spike Dropseed) leaf packs in the mesocosm experiment. DNA was extracted using a modified CTAB method with phenol:chloroform:IAA purification. PCR was was used to amplify the V4 region of the 16S rRNA gene using Illumina 515f and 806r primers to identify Bacteria and Archaea and the V9 region of the 18S rRNA gene using Illumina Euk1391f and EukBr primers to identify Eukaryota. Dual-indexed, paired-end amplicons were sequenced on an Illumina MiSeq at the University of New Mexico.