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Metagenomics Uncovers Unexpected Sea Floor Microbial Diversity

NEW YORK (GenomeWeb News) – There are more microbes on the sea floor than in the waters above, new research suggests.
In a paper published online today in Nature, a group of researchers from across the country used quantitative PCR, metagenomics, and phylogenetic analysis to quantify the microbial diversity in unsedimented mid-ocean ridges in the Pacific Ocean and near Hawaii. Based on these samples, the researchers concluded that there are thousands to tens-of-thousands of times more bacteria residing on the sea floor than in the vast sea above.
The region — a seam of glassy basalt rock in the mid-ocean that’s some 37,000 miles long — represents “potentially the largest surface area for microbes to colonize on Earth,” senior author Katrina Edwards, a geomicrobiologist at the University of Southern California, said in a statement.
“These scientists used modern molecular methods to quantify the diversity of microbes in remote deep-sea environments,” said David Garrison, director of the National Science Foundation’s biological oceanography program, who was not involved in the study. “As a result, we know that there are many more such microbes than anyone had guessed.”
Previous research indicated that there was microbial life on the sea floor. But until now, no one had quantified these microbial communities. To quantify these microbes, Edwards and her colleagues sampled basalt sea floor lava that was up to 20 thousand years old, using qPCR to determine the bacterial and archeal population densities in different samples.
This data, combined with the team’s catalyzed reporter deposition-fluorescent in situ hybridization experiments suggested that bacteria outnumbered archea on the sea floor. Meanwhile, 16S ribosomal RNA profiles helped the team tease out the specific taxonomic groups present in the sea floor bacterial communities.
The researchers found more than 20 taxonomic groups from sea floor basalt. The Proteobacteria phylum was particularly well represented, although the team also detected sequences from Plantomycetes, Actinobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, and other phyla.
Their results suggested that the East Pacific Rise contained more “bacterial richness” than other marine habitats. For instance, they estimated that the bacterial diversity was similar to that found in soil microbial communities. The team found similar bacterial richness in samples collected from the sea floor lava offshore from Hawaii’s big island.
Initially though, it was unclear how the bugs manage to eke out enough energy to survive in that environment, where there is very little organic carbon. The team speculated that the basalt on which the microbes grow may provide them with energy through so-called alteration reactions, in which the basalt is exposed to oxidation and hydration. Indeed, laboratory measurements of basalt chemical reactions seemed to be consistent with that notion.
And, the team says, the findings may inform future studies of everything from the carbon cycle under the sea to evolution. For instance, many have proposed that early life began in shallow water. But these results raise the possibility that life emerged deep in the ocean.
In the future, Edwards and her team plan to set up a microbial observatory some 15,000 feet below sea level to investigate microbes on and below the sea floor. “It is my hope that people turn their heads and notice that there’s life down there,” Edwards said.

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