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Robert Karl Stonjek
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 Posted: Tue Jul 22, 2008 6:33 pm Post subject: News: Microbes beneath sea floor genetically distinct |
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Microbes beneath sea floor genetically distinct
Tiny microbes beneath the sea floor, distinct from life on the Earth>s
surface, may account for one-tenth of the Earth>s living biomass, according
to an interdisciplinary team of researchers, but many of these minute
creatures are living on a geologic timescale.
"Our first study, back in 2006, made some estimates that the cells could
double every 100 to 2,000 years," says Jennifer F. Biddle, PhD. recipient in
biochemistry and former postdoctoral fellow in geosciences, Penn State. "Now
we have the first comprehensive look at the genetic makeup of these
microbes." Biddle is now a postdoctoral associate at the University of North
Carolina, Chapel Hill.
The researchers looked at sediment samples from a variety of depths taken
off the coast of Peru at Ocean Drilling Site 1229. They report their
findings in today>s (July 22) online issue of the Proceedings of the
National Academy of Sciences.
"The Peruvian Margin is one of the most active surface waters in the world
and lots of organic matter is continuously being deposited there," says
Christopher H. House, associate professor of geoscience. "We are interested
in how the microbial world differs in the subsea floor from that in the
surface waters."
The researchers used a metagenomic approach to determine the types of
microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet
beneath the ocean floor. The use of the metagenomics, where bulk samples of
sediment are sequences without separation, allows recognition of unknown
organism and determination of the composition of the ecosystem.
"The results show that this subsurface environment is the most unique
environment yet studied metagenomic approach known today," says House. "The
world does look very different below the sediment surface." He notes that a
small number of buried genetic fragments exist from the water above, but
that a large portion of the microbes found are distinct and adapted to their
dark and quiet world.
The researchers, who included Biddle; House; Stephan C. Schuster, associate
professor; and Jean E. Brenchley, professor, biochemistry and molecular
biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular
biologist at the Center for Astrobiology, UCLA, found that a large
percentage of the microbes were Archaea, single-celled organisms that look
like Bacteria but are different on the metabolic and genetic levels. The
percentage of Archaea increases with depth so that at 164 feet below the sea
floor, perhaps 90 percent of the microbes are Archaea. The total number of
organisms decreases with depth, but there are lots of cells, perhaps as many
as 1,600 million cells in each cubic inch.
" These microbes influence the Earth>s long-term carbon cycle and also these
microbes may be quite ancient," says Biddle.
If the rest of the world is like the Peruvian Margin, then at least one
tenth and as much as a third of the Earth>s biomass could be these tiny
microbes living in the mud. However, this population lives at an unusual
rate. Single-celled organisms usually consume food for energy and then
rather than grow larger, simply divide and reproduce themselves. While the
Bacteria Escherichia Coli, as an example, doubles its numbers every 20
minutes, these Archaea double on the order of hundreds or thousands of years
and consume very little energy.
"In essence, these microbes are almost, practically dead by our normal
standards," says House. "They metabolize a little, but not much."
According to House, organisms metabolizing at such slow rates is what we
could expect to find in other areas of our solar system because such
environments have much less energy available than on Earth. Perhaps, similar
organisms may be in hydrothermal vents beneath the ice of Europa -- the
second moon of Jupiter -- or in subsurface aquifers of Mars.
"We do not expect the microbes in other places to be these microbes
exactly," says House. "But, they could be living at a similar slow rate."
Biddle notes that these microbes could survive major Earth impacts by
asteroids, so the subsea floor could be a refuge for life during extinction
events. Now this study shows they may be a reservoir of novel genetic
material as well. Her future research will focus on understanding the
lifestyle of the microbes.
"For example, how do they die?" asks Biddle. "It is a simple question that
we cannot answer."
Source: Penn State
http://www.physorg.com/news135878602.html
Posted by
Robert Karl Stonjek |
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Tom Hendricks
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| Posted: Thu Jul 24, 2008 9:42 pm Post subject: Re: News: Microbes beneath sea floor genetically distinct |
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On Jul 22, 1:33 pm, "Robert Karl Stonjek" <rston...@bigpond.net.au>
wrote:
[quote]Microbes beneath sea floor genetically distinct
Tiny microbes beneath the sea floor, distinct from life on the Earth>s
surface, may account for one-tenth of the Earth>s living biomass, according
to an interdisciplinary team of researchers, but many of these minute
creatures are living on a geologic timescale.
"Our first study, back in 2006, made some estimates that the cells could
double every 100 to 2,000 years," says Jennifer F. Biddle, PhD. recipient in
biochemistry and former postdoctoral fellow in geosciences, Penn State. "Now
we have the first comprehensive look at the genetic makeup of these
microbes." Biddle is now a postdoctoral associate at the University of North
Carolina, Chapel Hill.
The researchers looked at sediment samples from a variety of depths taken
off the coast of Peru at Ocean Drilling Site 1229. They report their
findings in today>s (July 22) online issue of the Proceedings of the
National Academy of Sciences.
"The Peruvian Margin is one of the most active surface waters in the world
and lots of organic matter is continuously being deposited there," says
Christopher H. House, associate professor of geoscience. "We are interested
in how the microbial world differs in the subsea floor from that in the
surface waters."
The researchers used a metagenomic approach to determine the types of
microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet
beneath the ocean floor. The use of the metagenomics, where bulk samples of
sediment are sequences without separation, allows recognition of unknown
organism and determination of the composition of the ecosystem.
"The results show that this subsurface environment is the most unique
environment yet studied metagenomic approach known today," says House. "The
world does look very different below the sediment surface." He notes that a
small number of buried genetic fragments exist from the water above, but
that a large portion of the microbes found are distinct and adapted to their
dark and quiet world.
The researchers, who included Biddle; House; Stephan C. Schuster, associate
professor; and Jean E. Brenchley, professor, biochemistry and molecular
biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular
biologist at the Center for Astrobiology, UCLA, found that a large
percentage of the microbes were Archaea, single-celled organisms that look
like Bacteria but are different on the metabolic and genetic levels. The
percentage of Archaea increases with depth so that at 164 feet below the sea
floor, perhaps 90 percent of the microbes are Archaea. The total number of
organisms decreases with depth, but there are lots of cells, perhaps as many
as 1,600 million cells in each cubic inch.
" These microbes influence the Earth>s long-term carbon cycle and also these
microbes may be quite ancient," says Biddle.
If the rest of the world is like the Peruvian Margin, then at least one
tenth and as much as a third of the Earth>s biomass could be these tiny
microbes living in the mud. However, this population lives at an unusual
rate. Single-celled organisms usually consume food for energy and then
rather than grow larger, simply divide and reproduce themselves. While the
Bacteria Escherichia Coli, as an example, doubles its numbers every 20
minutes, these Archaea double on the order of hundreds or thousands of years
and consume very little energy.
"In essence, these microbes are almost, practically dead by our normal
standards," says House. "They metabolize a little, but not much."
According to House, organisms metabolizing at such slow rates is what we
could expect to find in other areas of our solar system because such
environments have much less energy available than on Earth. Perhaps, similar
organisms may be in hydrothermal vents beneath the ice of Europa -- the
second moon of Jupiter -- or in subsurface aquifers of Mars.
"We do not expect the microbes in other places to be these microbes
exactly," says House. "But, they could be living at a similar slow rate."
Biddle notes that these microbes could survive major Earth impacts by
asteroids, so the subsea floor could be a refuge for life during extinction
events. Now this study shows they may be a reservoir of novel genetic
material as well. Her future research will focus on understanding the
lifestyle of the microbes.
"For example, how do they die?" asks Biddle. "It is a simple question that
we cannot answer."
Source: Penn Statehttp://www.physorg.com/news135878602.html
Posted by
Robert Karl Stonjek
[/quote]
I would love to know if these microbes have UV protection in their
genetic makeup.
It would be astounding if they did not. It would suggest an origin
without UV protection
or the need for it. |
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Lorentz
Guest
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| Posted: Fri Jul 25, 2008 5:00 pm Post subject: Re: News: Microbes beneath sea floor genetically distinct |
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On Jul 22, 2:33 pm, "Robert Karl Stonjek" <rston...@bigpond.net.au>
wrote:
[quote]The researchers, who included Biddle; House; Stephan C. Schuster, associate
professor; and Jean E. Brenchley, professor, biochemistry and molecular
biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular
biologist at the Center for Astrobiology, UCLA, found that a large
percentage of the microbes were Archaea, single-celled organisms that look
like Bacteria but are different on the metabolic and genetic levels. The
percentage of Archaea increases with depth so that at 164 feet below the sea
floor, perhaps 90 percent of the microbes are Archaea. The total number of
organisms decreases with depth, but there are lots of cells, perhaps as many
as 1,600 million cells in each cubic inch.
I am not sure that Archae should be considered as distinct from[/quote]
prokaryotes, the other superkingdom of bacteria. Sure, their ribosome
DNA is distinct from the other bacteria. However, the ribosome DNA is
inherited separately from their chromosomal DNA, and from their
plasmid DNA. The chromosomal DNA of the prokaryote bacteria and
archaebacteria are probably not so distinct. Lateral gene transfer
probably effects the chromosomal DNA separately from the ribosomal
DNA, and may even be different from the plasmid DNA.
I have no reference except a lecture I once attended in the
Smithsonian. There the researcher claimed that the chromosomal DNA of
archaebacteria and prokaryote bacteria in the deep sea showed signs of
high levels of mixing, unlike the ribosomal DNA. However, this makes
sense. We know that plasmids are routinely exchanged between bacteria.
The ribosomes aren>t that mobile. So the ribosomes may be more
"inbred" than the chromosomes. So Woelers classification of the
"superkingdom" archae may not be as fundamental as he claimed.
Or perhaps we should look at it the opposite way. Maybe ribosomes
are more fundmental to the evolutionary process than is currently
recognized. If archaebacteria are more common in extreme environments,
maybe it is because their ribosomes are sturdier than their
chromosomes. So maybe we should straight out be classifying organisms
based on the ribosomal DNA sequences instead of their chromosomal DNA
sequences.
Consider eukaryotes (animals, plants, fungi, and protozoa). What
about differences in their ribosome DNA? Or how about differences in
their mitochondrial DNA? Within plants, what about differences in
chloroplast DNA? Maybe there are significant differences on the
species level.
It seems to me that apart from "genecentric" bias, there seems to
be a big bias toward chromosome genes. We have to rember that not all
genes are chromosomal.
[quote]
" These microbes influence the Earth>s long-term carbon cycle and also these
microbes may be quite ancient," says Biddle.
Thie chromosomes or their ribosomes? If you say that[/quote]
archaebacteria are predominant in deep ocean sediments, then one is
speaking about ribosomes. Maybe the chromosomes aren>t so ancient.
Maybe gene transfer between chromosomes has been occurring between the
deep ocean sediments organisms and the upper ocean organisms. Maybe we
should talk about "ancient" in terms of separate gene networks. |
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