Abstract
Summary To better understand the functional responses in prokaryotes to dissolved organic matter ( DOM ), we compared the transcriptional pattern of natural prokaryotic communities grown in continuous cultures on seawater amended with phytoplankton‐derived DOM . Metatranscriptomic reads were classified taxonomically (by genomic binning) and functionally (using K yoto Encyclopedia of G enes and G enomes), and the relative gene expression of individual taxa (genome bins) was compared with the total community response. In the first experiment comparing seawater and seawater amended with diatom‐derived DOM , metatranscriptomes revealed pronounced differences in pathways involved in carbohydrate and lipid metabolism. In the second experiment comparing seawater amended with cyanobacteria‐ and diatom‐derived DOM , metatranscriptomes had similar functional profiles, likely reflecting more similar DOM regimes in this experimental setup. Among the five most abundant taxa investigated in more detail, two featured pronounced differences in transcript abundance between treatments suggesting that they were specialized in the use of only one of the two DOM regimes. However, these two taxa were less involved in carbohydrate metabolism than others and had few genes that were significantly regulated in response to the DOM source. Our results indicate that both substrate composition and the competitive interplay of community members were decisive for the functional response of a microbial system.