Microbial Dark Matter and the Diversity of Uncultured Microbes

Over the last five years, advances in DNA sequencing technologies have completely changed our perspective of life on Earth.

Microbial dark matter

Next generation sequencing techniques allow microbiologists to look at entire populations of microbes living in diverse environments, from your belly button to the muddy sediment of the seafloor (metagenomics). Microbiologists can now even sequence a genome from just one microbial cell.

Before these techniques took off, DNA sequencing required large samples. For single celled organisms this meant culturing in the lab and allowing them to grow and multiply many times. Organisms that didn’t grow in standard lab media, or multiply quickly enough, were therefore “invisible” to scientists.

A new review paper in Current Opinion in Microbiology recaps the major impact next generation sequencing has had on mapping the so-called dark biosphere [1]. In the review, Lindsey Solden (The Ohio State University, USA) and DCO collaborators Karen Lloyd (DCO Executive Committee, University of Tennessee Knoxville, USA) and Kelly Wrighton (The Ohio State University, USA) discuss the far-reaching consequences of investigating microbial diversity.

Next generation sequencing techniques allow microbiologists to study microbial populations in their native state, as they exist in the environment. Bacteria and Archaea living in subsurface environments, for example, tend to replicate slowly, making them challenging to study in the lab. Metagenomic analyses of whole populations, combined with single cell genomics, provide a snapshot of the ecosystem as a whole, without speeding up all the microbial cells for the sake of analyzing them in lab.

The impacts of such genomic studies are far-reaching. For example, studies have called into question the three-domain model of life, with new Archaeal genomes suggesting Eukarya may have originated within the Archaeal radiation. Other studies point to the metabolic diversity of Archaea and Bacteria, finding new phyla with unique genomic compositions. Work has shown that organisms with tiny genomes might be common, lacking certain basic metabolic machinery. Nevertheless, they are able to survive in particular ecosystems, relying on interdependent relationships with other microorganisms. Such interdependence, it turns out, might be very common.

Solden et al. conclude with a discussion of what this vast collection of sequence data tells us, and what it misses. Gene annotation is generally based on homology with other organisms, but over evolutionary time sequences diverge. Therefore, some organisms may do more (or less) than meets the eye. Further experiments will require laboratory cultivation of the dark biosphere, using new techniques developed to accommodate slow growing or interdependent organisms.

Image credit: Lindsey Solden

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