Freshwater Microbes: From Temporal Dynamics to Biodegradation, They Have Their Lake and Eat It Too
Despite the global significance of freshwater systems, the use of ‘omics approaches to understand their microbial communities trails behind other environments such as oceanic, soil, and human, where most of the efforts have been concentrated so far (e.g., less than 2% of the metagenome projects in the NCBI Sequence Read Archive are related to freshwater). I will show some results from recent, extensive surveys of microbial genes and gene transcripts in Lake Lanier, an important source of drinking water and recreation in North Georgia.
First, I will discuss 16S rRNA amplicon vs. metagenomic assessments of community composition over time while also showing the advantages, limitations and current challenges in using these approaches.
Secondly, I will present some comparisons with metatranscriptomic data from the lake, focusing in particular on the knowledge gained from using a variety of biological and technical replicates.
Finally, I will provide an example of applied metagenomics to explore adaptation in Lake Lanier microbial communities in the context of biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D), a synthetic herbicide, and 3-nitrotyrosine (3-Nty), a naturally occurring nitro-aromatic compound. Together, these three stories provide technical guidelines for general environmental omics while advancing the understanding of gene content, flow, expression, and adaptation in freshwater systems.