New technology for microbial single cell genomics

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Over the past decade, single cell genomics (SCG) transitioned from science fiction to a robust technology that has been instrumental in research fields ranging from microbiology to cancer studies and neurobiology. Arguably, SCG’s impact and progress have been greatest in environmental microbiology. The approach has helped decipher biological features of many deep, previously unknown microbial branches of the tree of life that constitute a significant fraction of our planets biological diversity. In addition, due to its ability to retrieve genetic information from all DNA molecules in a cell, SCG has allowed for the study of physical microbial interactions – such as infections, symbioses and predation – directly in their natural environment. Finally, by circumventing the need for the arbitrary taxonomic binning required by metagenomic assemblies, SCG has improved our understanding of microbial microevolutionary processes and helped calibrate the performance and interpretation of community omics tools.

At the same time that SCG has revolutionized environmental microbiology, it has also been rapidly evolving. Our publication describes several recent enhancements we have made to the SCG technology and demonstrates the utility of these enhancements in studies of marine and soil microbiomes. Firstly, we describe WGA-X, a new method for DNA amplification from individual cells and viral particles. We show that this method increases the fraction of a genome that gets recovered from cells of bacteria and protists, as well as from individual viral particles. The improvement is particularly large for genomes with G+C above 50%, which often dominate microbiomes of soil, subsurface and other environments. Better genome recovery with WGA-X will undoubtedly produce more complete and less biased genomic information. 

Another technical improvement reported in this publication is the integration of genomic sequencing with the analyses of size, pigment content, and other physical properties of the individual cell. Direct coupling of a cell’s size and genome when analyzing uncultured microorganisms is important. Size is a major factor in cellular capacity to accumulate chemical constituents, perform metabolic functions and interact with other cells in the environment. In the future, this technique could be extended into diverse natural and induced fluorescence signals in order to link cellular genomic content and its chemical composition, antigen presence and specific metabolic activities.

Our publication also demonstrates the value of high-throughput, low-coverage shotgun sequencing (LoCoS) of individual microbial cells as a replacement of PCR-based pre-screens of the SSU rRNA gene. This new strategy eliminates biases caused by PCR primer mismatches, inserts in PCR templates, and variable numbers of target gene copies per cell. In addition to improvements in taxonomic assignment, LoCoS also offers insights into metabolic features, viral infections and other genome-encoded features of hundreds of individual, uncultured cells in a single experiment.

Our Nature Communications paper can be found here:

Ramunas Stepanauskas

Senior Research Scientist, Director of Bigelow Laboratory Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences

Genomics and ecology of marine microorganisms; evolution of Bacteria and Archaea