Plasmids are DNA molecules that can replicate independently of chromosomal DNA in a cell. This ability allows them to “collect” and move genes, such as through lateral gene transfer, and is a factor that allows prokaryotic genomes to evolve over time.
To understand the depth and breadth of this plasmid gene pool in prokaryotes, researchers including a team of DOE Joint Genome Institute researchers isolated, sequenced and compared plasmids from two activated wastewater sludge communities. In their report published February 14, 2013 in The ISME Journal, they noted the work done allowed them to study the “mobilome” or totality of mobile elements in a genome.
Activated sludge wastewater treatment processes are used throughout the world to purify trillions of gallons of sewage annually. These wastewater treatments arguably form the world’s largest microbially mediated biotechnology process. A metagenomic study of activated sludge microbial communities was previously done as part of a 2007 DOE JGI Community Sequencing Program project.
To study the mobilome, the team had to specifically separate and purify closed circular supercoiled DNAs (CCSD) originating from the plasmids. “In contrast to current ultrahigh throughput metagenomic sequencing on total DNA,” the team wrote, “mobilome metagenomics requires tedious separation and purification of CCSD, and is therefore still more constrained by technical and not sequencing limitations.” They found that the plasmids isolated from the activated sludge wastewater microbial communities turned out to contain primarily uncharacterized coding sequences, lending credence to the idea that plasmids are crucial to genome innovation and evolution.