Biological Dark Matter
John P. Millis, Ph.D. for redOrbit.com – Your Universe Online
A hot topic in astronomy is the search for dark matter – mass that seems to dominate the Universe, yet eludes our detection. Similarly, the field of biology encounters its own “dark matter” problem. Microbial dark matter, as it’s called, draws its parallels from its cosmological cousin in that it is all around us, dominating this Earthly domain. Yet, it is incredibly difficult to characterize.
“Microbes are the most abundant and diverse forms of life on Earth,” said Tanja Woyke, Department of Energy Joint Genome Institute (DOE JGI) Microbial Program Head and one of the study’s authors. “They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts. However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory. So we have only recently become aware of their roles in various ecosystems through cultivation-independent methods, such as metagenomics and single-cell genomics. What we are now discovering are unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the domains of life.”
To better understand the microbes, and therefore fill in crucial gaps in the tree of life – which traces the origins and evolution of life on Earth – the team harvested uncultivated microbial cells from nine diverse habitats: Sakinaw Lake in British Columbia, the Etoliko Lagoon of western Greece, a sludge reactor in Mexico, the Gulf of Maine, off the north coast of Oahu (Hawaii), the Tropical Gyre in the south Atlantic, the East Pacific Rise, the Homestake Mine in South Dakota, and the Great Boiling Spring in Nevada.
The team then laser sorted the samples and isolated 9,000 individual cells. From this collection of cells, 201 distinct genomes were identified, falling on 28 previously uncharted branches of the tree of life. “Microbial genome representation in the databases is quite skewed,” said Chris Rinke, DOE JGI postdoctoral fellow and first author of the study. “More than three-quarters of all sequenced genomes fall into three taxonomic groups or phyla but there are over 60 phyla we know of.”
Isolating the 16S ribosomal RNA genes – responsible for critical “housekeeping” processes and therefore common across all microbes – researchers have a tool to conducting surveys of these microbes, instead of attempting the arduous task of growing cultures in the lab. Though, the rest of the sequence has proven a slow process.
“Based on 16S surveys we know they’re out there, but we don’t know much about them; that’s why we call them microbial dark matter,” Woyke added. “Using modern single-cell techniques allowed us to access the genetic make-up for some of them, even without growing them in the lab.”
Summarizing their research, the team identified three specific areas where their work broke new ground. First, they found new metabolic features in the microbes, some of which had only previously been found in bacteria.
Additionally, the team was able to reassign more than 340 million DNA fragments to their proper lineage. This brings a new crispness to the forming image of how these microbes function in their individual ecosystems.
And finally, the research revealed new relationships between, and within, the microbial phyla. Ultimately, this led the team to propose two new superphyla – associations between phyla. “Our single-cell genomes gave us a glimpse into the evolutionary relationships between uncultivated organisms – insights that extend beyond the single locus resolution of the 16S rRNA tree and are essential for studying bacterial and archaeal diversity and evolution,” Woyke said. “It’s a bit like looking at a family tree to figure out who your sisters and brothers are. Here we did this for groups of organisms for which we solely have fragments of genetic information. We interpreted millions of these bits of genetic information like distant stars in the night sky, trying to align them into recognizable constellations. At first, we didn’t know what they should look like, but we could estimate their relationship to each other, not spatially, but over evolutionary time.”
“For almost 20 years now we have been astonished by how little there is known about massive regions of the tree of life. This project is the first systematic effort to address this enormous knowledge gap. One of the most significant contributions is that based on these data, we provided names for many of these lineages which, like most star systems, were just numbered previously. For me, taxonomic assignment is important as it welcomes in strangers and makes them part of the family. Yet this is just a start. We are talking about probably millions of microbial species that remain to be described,” says Phil Hugenholtz, Director of the Australian Centre for Ecogenomics at The University of Queensland, and one of the study’s authors.
While this work makes great strides in the search for biological dark matter, it really only scratches the surface. “There is still a staggering amount of diversity to explore,” Woyke said. “To try to capture 50 percent of just the currently known phylogenetic diversity, we would have to sequence 20,000 more genomes, and these would have to be selected based on being members of underrepresented branches on the tree. And, to be sure, these are only what are known to exist.”
Results of their work are published in the journal Nature.