There is growing recognition that winter is an important season for growth of photoautotrophs in ice-covered freshwater environments. Exemplifying this are expansive under-ice blooms of filamentous diatoms in Lake Erie. Here we describe a metatranscriptome constructed from a phytoplankton community dominated by filamentous diatoms. As expected, a high percentage (>73%) of the sequences with BLAST hits to nucleotides or proteins in National Center for Biotechnology Information databases were associated with photosynthetic algae of which the majority were diatoms, mainly Aulacoseira spp. and Stephanodiscus spp. which was confirmed by analysis of 18S rRNA gene transcripts and microscopy. Consistent with the winter growth environment, psychrophilic and low light adaptations were observed. Prominent among adaptations to cold were transcripts for genes involved in biosynthesis of unsaturated fatty acids, which were consistent with expected increased membrane fluidity at low temperatures. Reflecting the combined effect of low winter insolation and high light attenuation were an abundant complement of reads for light-harvesting antennae, mainly genes encoding fucoxanthin chlorophyll a/c proteins. The presence of virulence factors originating from oomycetes offers support for new hypotheses into the eventual decline of Lake Erie's winter diatom bloom. Whereas fungi were identified both through the metatranscriptome and by microscopy, dsRNA viruses of fungi were detected that may indirectly counter against fungal infection. This study demonstrates the utility of an environmental omics approach to yield insights underlying phototrophic life as well as the interactions of the entire microbial community in an extreme environment. (C) 2016 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved.