Structural dynamics of community gene expression In a freshwater cyanobacterial bloom over a day-night cycle

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 124-131).Studies of community gene expression, or metatranscriptomics, provide a powerful approach for quantifying changes in both the taxonomic composition (structure) and activity (function) of complex microbial systems in response to dynamic environmental conditions. We have used next-generation Illumina sequencing to characterize the metatranscriptome of a tropical eutrophic drinking water reservoir dominated by the toxigenic cyanobacterium Microcystis aeruginosa over a day-night cycle. Cyanobacterial blooms are a major problem in eutrophic lakes and reservoirs, negatively impacting the ecology of the water body through oxygen depletion upon bloom decay and in some cases through production of toxins. Waterborne Cyanobacterial toxins pose a public health risk through drinking and recreational exposure. The frequency of harmful Cyanobacterial blooms (CyanoHABs) is predicted to increase due to warming regional climates and increases in non-point source pollution due to urban expansion. CyanoHABs represent complex consortia of Cyanobacteria that live in association with diverse assemblages of heterotrophic and anoxygenic- photosynthetic bacteria, archaea, microbial Eukaryotes (algae, protozoa, and fungi) as well as viruses and zooplanktonic grazers. Water sampling was carried out at six time points over a 24 hour period to capture variability associated with changes in the balance between phototrophic and heterotrophic activity. Total RNA was extracted and subjected to ribosomal depletion followed by cDNA synthesis, sequencing, and quality control, generating 493,468 to 678,064 95-101 bp reads per sample. Hierarchical clustering of transcription profiles supported sorting of samples into two clusters corresponding to "day" and "night" collection times. Annotation of reads through the MGRAST pipeline (Metagenomics- Rapid Annotation using Subsystem Technology) revealed that the community taxonomic composition was relatively constant throughout the day-night cycle and was dominated by transcripts with highest identity to members of the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes (in decreasing order) where Microcystis transcripts represented 15.3 to 25.6% of the total Bacterial transcriptomes (Eave=10~ ). Community transcripts were enriched with genes from the Cyanobacterial photosynthetic KEGG pathway during the day (p=0.004). In contrast, Proteobacterial transcripts were enriched at night (20.4% of the total Bacterial transcriptome compared to 14.3% in the day, p=0.039). Metatranscriptomic quantification of microbial community gene expression in a Cyanobacterial bloom dominated by M. aeruginosa contributes to a fundamental understanding of nutrient and energy cycling over a day-night cycle. A better understanding of the structure, function, and interaction between members of the complex communities that support the proliferation of toxigenic Cyanobacteria will improve our ability to prevent and control CyanoHABs.by Jia Wang.S.M