Centimetre scale variability of copiotrophic freshwater bacteria

This study contains raw data from 16S rRNA gene sequencing of enriched samples collected from Lake Zurich in autumn 2021. The sample was enriched on the single carbon sources D-cellobiose, L-serine or N-acetyl-D-glucosamine as part of a larger screening of single-carbon source consumption on BIOLOG EcoPlates. The amplified 16S rRNA genes of the enriched community were sequenced with Illumina MiSeq V3 (samples illumina s1-s180) by LGC genomics and Nanopore MinION (samples nanopore s1-s24). The Nanopore derived reads also contain enrichments on putrescine which were included during basecalling but disregarded in the data analysis and corresponding publication due to a lack of successful enrichments available for Illumina sequencing. The freshwater microbiome harbors numerous copiotrophic bacterial taxa that rapidly respond to elevated substrate concentrations. We hypothesized that the previously observed high centimeter-scale beta diversity of this rare biosphere would translate into equally pronounced metabolic variability, and that a significant fraction of the regional microbial 'metabolic potential' in lake water would originate from infrequent point sources such as fragile organic aggregates. Three experiments were performed during different stages of a harmful cyanobacterial bloom in pre-alpine Lake Zurich: Spatially explicit 9 mL 'syringe samples' were collected from 5 m depth at centimeter distances along with equally sized replicate 'mixed samples' drawn from 5 L of homogenized lake water. All samples were then incubated separately in BIOLOG EcoPlate substrate arrays. Fewer compounds promoted bacterial growth in the syringe than in the mixed samples, in particular during the pre- and late bloom periods. Community analysis of enrichments on three frequently utilized substrates revealed pronounced dispersal limitation and, consequently, functional redundancy. Moreover, bacterial consortia had higher richness in mixed than in syringe samples and differed in composition. The composition of the enriched assemblages changed over a cyanobacterial bloom: During the mid-bloom period they were dominated by members of the Enterobacter cloacae complex irrespective of treatment or substrate. We conclude that small-scale 'functional dispersal limitation' among free-living copiotrophs in lake water reduces local biotransformation potential, and that lacustrine blooms of harmful cyanobacteria can be environmental reservoirs for metabolically highly versatile potential pathogens.