The average genome size of a microbial community represents an informative and overlooked metric for assessing the relationship between microbial communities and their environment. Streamlining theory suggests that bacteria reduce the size of their genomes to reduce reproductive costs in response to nutrient limitation. Streamlined genomes, in addition to their small genome size, have distinct genomic characteristics, such as fewer rRNA copies, fewer regulatory mechanisms, and reduced GC content. These characteristics have been well characterized in vitro from environmental isolates and have been demonstrated in single amplified genomes. However, few studies have observed and compared the average genome size of whole microbial communities, and no study has yet made this comparison across a number of diverse environments. In order to understand the environmental distribution of genome reduction in microbial communities, we analyzed 120 environmental metagenomes collected from terrestrial, marine, and thermophilic communities. Environmental metagenomes were downloaded from the Joint Genome Institute (JGI) genome portal and their annotations from the Integrated Microbial Genomes & Microbiomes (IMG/M) database. We expected to find trends previously shown in environmental isolates, namely: (1) Smaller genomes in thermophilic and ocean communities; (2) Fewer 16s copies, regulatory genes, and lower GC content in communities with smaller genomes.
Results/Conclusions
Marine and thermophilic microbial communities generally had a smaller average genome size than communities in soil, consistent with results from isolate studies. Although traits associated with streamlining largely followed known trends from isolates, these relationships differed depending on environment. Notably, the distribution of regulatory genes in relation to average genome size varied considerably between systems. Generally, the total abundance of regulatory genes per genome decreased with genome size, however this relationship varied for different regulatory genes in each system. These relationships suggest that genome reduction exhibits environmentally dependent gene selection. In summary, this work confirms several known trends in genome reduction using metagenomic data and contributes several new concepts concerning environmentally driven patterns of reduction.