Metagenomics Of The Deep Mediterranean

Metagenomics is a revolutionary approach to study microbes. Rather than
isolating pure cultures, the power of high-throughput sequencing is
applied
directly to environmental samples to obtain information about the genomes
of the prokaryotic cells present in a specific habitat studied. The ocean
is
an ideal subject of this approach because of its enormous microbiota,
whose biomass equals that of all other living organisms on earth is mostly
microbial, and also because most of these microbes are extremely
fastidious to cultivate.



Craig Venter pioneered these studies and has sampled the surface of the
World oceans, but has only scraped the surface. Only one study carried out
in
Hawaii Ocean Time Series (or HOT) station has analyzed the metagenome of
different depths down to 4000m showing the enormous diversity hidden
there.
This article describes the second study of the bathypelagic region, in
this case at a station located over the Ionian abyssal plain, a flat deep
basin
occupying most of the space between Sicily and Greece in the Eastern
Mediterranean. The deep waters of the Mediterranean are special in being
free
from the intrusion of polar waters that feed most the bottom of the global
ocean. The Ionian sample comes from 3000 m deep and is submitted to a
continuous pressure of 300 Kg/cm2 but contrastingly to most deep ocean
habitats this has a relatively warm temperature of nearly 14ВєC.



In general, a remarkable number of similarities were found with the deep
meso-pelagic Pacific and a convergence at the level of taxa found and
types
of metabolism with the soil microbiota is starting to be perceived. The
authors use the term "invisible soil" paraphrasing the "invisible
forest" coined by Paul Falkowski to refer to the hidden but gigantic
primary productivity found in the photic zone. The diversity of metabolic
enzymes involved in resilient organic compounds degradation was very high.
However, many microbes could complement their heterotrophic metabolism
with
chemolithotrophic energy supplies and, specifically in the Mediterranean,
the oxidation of carbon monoxide, probably released by tectonic activity,
could be important. There is also evidence that the microbes rarely live
isolated. The free living planktonic lifestyle is probably not very
popular
in this extremely depleted environment. Quorum sensing genes indicate that
instead, microbes tend to aggregate in particles and they could become
luminescent maybe to attract and be eaten by animals. This strategy could
provide the cells with a sporadic visit to the nutritious oasis of an
animal
gut. Overall, this paper shows that the deep ocean possesses a rich and
mostly unknown microbiota that deserves much more studies.



A recent analysis of a metagenomic library from the deep Mediterranean
shows a surprising high number of quorum sensing or lux genes that are
only
expressed when bacteria live in colonies. The deep ocean might be too
depleted in resources for microbes to live independently. Instead the
association to detritus particles might give them a rich microenvironment.
Now, some of the genes detected have been positively identified as luxA,
directly involved in bioluminescence.



Why would deep sea bacteria be luminescent? One possible explanation is
that they become attractive to animals that at these depths are very
photosensitive. Being swallowed by one of these creatures would give the
bacteria a temporary oasis of nutrient-rich conditions before another long
dip in the abyssal black.



Dr Rodriguez-Valera's paper, entitled, "Metagenomics of the Deep
Mediterranean, a Warm Bathypelagic Habitat," appears in the online,
open-access
journal PLoS ONE on September 19.




Citation: MartГ­n-Cuadrado A-B, LГіpez-GarcГ­a P, Alba J-C, Moreira D,
Monticelli L, et al (2007) Metagenomics of the Deep Mediterranean, a Warm
Bathypelagic Habitat. PLoS ONE 2(9): e914.
doi:10.1371/journal.pone.0000914

plosone/doi/pone.0000914




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