Researchers glimpse microbial ‘dark matter’

From Nature:

BacteriaSingle-cell sequencing enables scientists to decipher the genome of just one cell by amplifying its DNA by 1-billion-fold, opening the way to studying ‘microbial dark matter’. These are organisms that have been discovered through methods such as metagenomics studies — which examine batches of micro-organisms living in a common environment — but are difficult or impossible to grow in the lab. Woyke and her group attempted to explore this dark matter by selecting a highly diverse range of microbes and sequencing a portion of their genomes (which could range from less than 10% to more than 90% depending on the cell). The sequences clarified the microbes’ relationships to one another and to other species. The work reveals that some conventional boundaries between the kingdoms of life are not as rigid as has been thought. For instance, the researchers suggest that one bacterial lineage synthesizes purine bases — building blocks of DNA and RNA — using enzymes previously thought to exist only in archaea. Meanwhile, three of the archaeal cells sequenced in the study harbour sigma factors, which initiate RNA transcription and have previously been found only in bacteria. The researchers also found a bacterium that has ‘recoded’ the three-letter series of bases UGA — known as the opal stop codon. In almost every other organism, this nucleotide sequence signals the cell to stop translating RNA into protein. But in this organism, it tells the cell to make the amino acid glycine. The team propose to place it into a new bacterial phylum, called Gracilibacteria. A similar recoding has been found in another bacterium, suggesting that the code of life may be more flexible than scientists have assumed. “If you consider all the novelty we found in these 201 genomes, it’s astounding, because we’re only looking at a small part of the tremendous diversity out there,” Woyke says.

The researchers say that their work can help put more leaves on the bare branches of the tree of life.

More here.