The Power of One: Revealing Microbial Dark Matter Using Single-Cell Sequencing

abstract digital backgroundMicroorganisms; they are the most abundant form of life. They are all around us, silent, unseen and undetected. The number of ‘species’ of archaea and bacteria climbs every year and is predicted to rise well past one million (1). Despite their abundance, we know very little about all but a small fraction of these diverse cellular life forms because we are unable to cultivate most in a laboratory setting. In fact, 88% of all our microbial isolates belong to just four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacterioidetes; 2). The remaining branches of the microbial phylogenetic tree range from underrepresented to virtually unknown and are collectively referred to as “microbial dark matter”.

If you want to target those shadowy, ill-defined branches where exotic and underrepresented organisms belong, you go to environments that might harbor them. Towards this end, Christian Rinke and a large coalition of co-authors collected samples from a wide and varied choice of habitats including the South Atlantic tropical gyre, the Homestake Mine in South Dakota, the Great Boiling Spring in Nevada, the sediment at the bottom of the Etoliko Lagoon in Greece and even a bioreactor. Continue reading “The Power of One: Revealing Microbial Dark Matter Using Single-Cell Sequencing”

How a Musical Petri Dish Could Waste Your Whole Morning

You know those things you occasionally come across that look kind of cool and you think might be good for a minute or two of diversion? You know how it’s all fine and dandy until you somehow get sucked in and, before you know it, half the day is gone? Yeah. Meet Seaquence.

Seaquence is an online web app created by Ryan Alexander, Gabriel Dunne, and Daniel Massey, with support from Gray Area Foundation for the Arts. It is described as “an experiment in musical composition,” where “adopting a biological metaphor, you can create and combine musical lifeforms resulting in an organic, dynamic composition.” It’s basically an online petri dish where you add little squiggly creatures that make music. You control what combination of sounds each creature makes by adding antennae or changing the wiggle pattern of their bodies. When you’re done, you have a little virtual ambient orchestra; an ecosystem of minuscule musicians that you have guided, shaped and molded to your exact specifications. Oh, the power! Muaaa-haa-haa! Continue reading “How a Musical Petri Dish Could Waste Your Whole Morning”

Taking on Pathogenic Biofilms: An Apple a Day?

When finally ready to commit, as a college undergraduate, to a specific area of biological science,  I chose microbiology because of a fascination with infectious disease and its causation and cure. And let’s be clear, my interest was primarily in bacteriology—the big microbes. (The  virologists I knew back then teased that I wasn’t smart enough to study viruses, the small microbes; we’ll save that debate for another day.)

Bacterial biofilms were just beginning to come on the microbiological radar back in the 1980s, and were not yet part of the microbiology curriculum. However, we now know that biofilms are important, both as pathogenic organisms and in good health. This research on a means of interrupting pathogenic biofilms, while not harming commensal biofilms, both caught my attention and provided some fascinating information on the state of biofilms and biofilm research.

Biofilms are groups or large colonies of bacterial cells that adhere to and form coatings on living and nonliving surfaces. Such surfaces can include human and animal tissues, the floor and walls of a shower or even a medical device, such as a heart valve or indwelling catheter. Continue reading “Taking on Pathogenic Biofilms: An Apple a Day?”