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Metagenomic Sequencing Unearths Strange New Bacteria From Bioremediation Site

NEW YORK (GenomeWeb) – Metagenomic sequencing has unearthed dozens of new bacterial phyla — forming an apparent radiation of miniscule microbes with streamlined genomes, irregular ribosomes, and an apparent inability to produce their own amino acids or nucleotides.

"The unusual ribosomes, the small genomes — between 600 and 1,100 genes — the inability to synthesize amino acids and nucleotides, and a consistent metabolic story really connects these bacteria together in a pretty surprising way," Christopher Brown, a graduate student in the University of California at Berkeley plant and microbial biology, said in a statement.

Brown is first author on a paper published online today in Nature that described the microbes and methods used to detect them. He is a graduate student working with senior author Jillian Banfield, an earth sciences researcher affiliated with UC Berkeley and the Lawrence Berkeley National Laboratory.

Brown, Banfield, and colleagues did shotgun metagenomic sequencing on samples collected at a groundwater bioremediation site in Rifle, Colorado in 2011. With these sequences, they detected DNA from 35 previously unknown bacterial phyla, which fell into a new branch of the microbial tree characterized by organisms with compact genomes and bizarre biology.

Together, this so-called candidate phyla radiation (CPR) appears to account for an estimated 15 percent of all bacteria found on Earth, according to the team's calculations, suggesting bacterial lifestyles may be far broader than previously appreciated.

For the study, collaborators at LBNL used Illumina HiSeq instruments to sequence DNA and RNA from a dozen groundwater samples, focusing on microbes that could slip through fine, 0.2-micron filters used to purify the water.

From the hundreds of billions of bases of metagenome and metatranscriptome sequences produced, the team narrowed in on groups of bacterial sequence that corresponded with 789 draft genomes for bacteria with CPR-like features.

The researchers also went on to assemble eight complete bacterial genomes from the available sequence data, representing one known and four new bacterial phyla.

As a group, the newly detected phyla typically contained around half of the predicted protein-coding genes described in bacteria in the past. And they had other strange features, too.

For instance, researchers found that introns often intersected parts of the 16S ribosomal RNA gene sequence in these bugs, which would make them tricky to see with the 16S rRNA gene sequencing approach that's often used to tally up the species composition in a microbial community.

Indeed, the team suspects that anywhere from half to all of the organisms in each of the new phyla would be missed by 16S rRNA gene sequencing.

The newfound microbes also contained several other peculiar ribosome features, with many lacking proteins that are widespread across all other known bacteria, Banfield noted.

Moreover, bacteria from the new phyla were frequently missing machinery used to produce amino acids or nucleotide bases, suggesting they may rely on other organisms for such functions.

The team has tacked monikers onto more than 20 of the new bacteria phyla, including one dubbed Berkelbacteria after the home institution of researchers leading the study.

Based on the estimated size of the bacterial family tree and the prevalence of the CPR bacteria found in the current study, the researchers suspect there may be 250 or more CPR phyla.