DIY extremophiles
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PatrickG
Jul 17, 2011, 3:30:57 PM7/17/11
to DIYbio
I was wondering how many people here are interested in some DIY work
with extremophilic microorganisms? I think there would be multiple
advantages:
1) the "extreme" conditions would preclude the irrational fear of DIY
syn bio and desire to regulate it, since these organisms would likely
never be pathogens
2)There are a multitude of interesting aspects of extremophilic
microorganisms, and a quick check of uniprot shows that many of their
proteins are in fact uncharacterized. Lots of potential to learn
there.
3) There are transformation protocols for a number of extremophiles
I'm not suggesting this to the exclusion of more common microbes.
Obviously, a number of proteins wouldn't really do well in Sulfolobus,
being at 80C, and the well-understood nature of E. coli and S.
cerevisiae, for instance, is a great boon to DIYbio.
With that point out of the way, I ask anyone who's interested in these
creatures: how easy would it be to isolate some of the more well-known
ones? I know there was a paper from the 70s about isolating T.
aquaticus from domestic hot water supplies (I forget the title of the
paper, sorry...), and alkaliphilic bacteria seem to dwell in many
soils, albeit in low numbers. Methanogens do not seem to be in short
supply (though their obligately anaerobic nature would probably make
this difficult). Is there any place where it would be (relatively)
straightforward to isolate hyperthermophiles like Sulfolobus?
I know that was more questions than information, but I'm just
wondering what you think.
Thanks
Patrick
with extremophilic microorganisms? I think there would be multiple
advantages:
1) the "extreme" conditions would preclude the irrational fear of DIY
syn bio and desire to regulate it, since these organisms would likely
never be pathogens
2)There are a multitude of interesting aspects of extremophilic
microorganisms, and a quick check of uniprot shows that many of their
proteins are in fact uncharacterized. Lots of potential to learn
there.
3) There are transformation protocols for a number of extremophiles
I'm not suggesting this to the exclusion of more common microbes.
Obviously, a number of proteins wouldn't really do well in Sulfolobus,
being at 80C, and the well-understood nature of E. coli and S.
cerevisiae, for instance, is a great boon to DIYbio.
With that point out of the way, I ask anyone who's interested in these
creatures: how easy would it be to isolate some of the more well-known
ones? I know there was a paper from the 70s about isolating T.
aquaticus from domestic hot water supplies (I forget the title of the
paper, sorry...), and alkaliphilic bacteria seem to dwell in many
soils, albeit in low numbers. Methanogens do not seem to be in short
supply (though their obligately anaerobic nature would probably make
this difficult). Is there any place where it would be (relatively)
straightforward to isolate hyperthermophiles like Sulfolobus?
I know that was more questions than information, but I'm just
wondering what you think.
Thanks
Patrick
Nathan McCorkle
Jul 17, 2011, 4:34:30 PM7/17/11
to diy...@googlegroups.com
L.A. biohackers are doing something with a hydrogen-phile
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Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
General Oya
Jul 17, 2011, 9:04:43 PM7/17/11
to diy...@googlegroups.com
I read last year, that some researchers out of Washington state were using methanogens for estrogen bio-remediation. I would love to learn more about that process. Our sponser for 2010 igem works mostly with thermophiles and provided our TAq from which we pcr'd out the polymerase DNA using primers designed based from the blast results we found online.
Wasn't there some xenobiology talk from NASA last year about the possibility of various sulfur based life forms within our own solar system (not terra)?
Ryan
Cathal Garvey
Jul 18, 2011, 3:15:34 AM7/18/11
to diy...@googlegroups.com
Cue Mac arriving with the Halotolerant bacteria? :)
There's a kit from one of the educational companies featuring Halotolerant Bacteria/Archaea (which?) which I think comes with a cloning vector. Could be wrong, but if the vector is absent we could still cook one up!
Message has been deleted
Brian Degger
Jul 18, 2011, 2:31:19 AM7/18/11
to diy...@googlegroups.com
Interested for sure, could start with the halophiles, those pink
bacteria seen in salt lakes. Nice article on them in a Scientific
American, will dig up the reference.
Cheers, Brian Degger
bacteria seen in salt lakes. Nice article on them in a Scientific
American, will dig up the reference.
Cheers, Brian Degger
Mackenzie Cowell
Jul 19, 2011, 11:38:58 AM7/19/11
to diy...@googlegroups.com
Arthur Kuan
Jul 19, 2011, 11:42:58 AM7/19/11
to diy...@googlegroups.com
Do you have more information on their growth rate?
thanks.
Dakota Hamill
Jul 19, 2011, 11:51:43 AM7/19/11
to diy...@googlegroups.com
Here is a cool site I found goolging for bacteria in salt marsh pools. There are a bunch of marshes here in Gloucester and these little pools that get left every full moon or so when the tide rises really high, and they are filled with "mats" of alge and bacteria alike. Never knew what they were though..but this site seems to have it all. Bacteria are more towards the middle/bottom, keep scrollin
http://zottoli.wordpress.com/saltmarshes/salt-marsh-pannes-and-pools/
http://zottoli.wordpress.com/saltmarshes/salt-marsh-pannes-and-pools/
Brian Degger
Jul 19, 2011, 2:04:54 PM7/19/11
to diy...@googlegroups.com
Not extremophiles as such, but if you have access to marsh or estuary
mud you can cultivate a community of bacteria. Winogratsky published a
protocol in the early 1900s to convert this mud into a interesting
colorful consortia of bacteria. One that is striking is the purple
sulphur reducing ones. They are slow bacteria, takes 1.5 to 2 months
to mature but worth it.
mud you can cultivate a community of bacteria. Winogratsky published a
protocol in the early 1900s to convert this mud into a interesting
colorful consortia of bacteria. One that is striking is the purple
sulphur reducing ones. They are slow bacteria, takes 1.5 to 2 months
to mature but worth it.
On Tuesday, July 19, 2011, Dakota Hamill <dko...@gmail.com> wrote:
> Here is a cool site I found goolging for bacteria in salt marsh pools. There are a bunch of marshes here in Gloucester and these little pools that get left every full moon or so when the tide rises really high, and they are filled with "mats" of alge and bacteria alike. Never knew what they were though..but this site seems to have it all. Bacteria are more towards the middle/bottom, keep scrollin
>
> http://zottoli.wordpress.com/saltmarshes/salt-marsh-pannes-and-pools/
>
>
>
>
Patrik
Jul 20, 2011, 2:17:59 AM7/20/11
to DIYbio
Carolina has a range of kits for the salt loving Archaea,
Halobacterium sp. NRC-1:
http://www.carolina.com/category/living+organisms/prokaryotes/archaea+and+halobacterium.do
http://www.carolina.com/category/teacher+resources/classroom+activities/halobacteria-+making+microbiology+manageable.do
If you live anywhere nearby a salt flat - near the SF Bay Area, or
Utah's Great Salt Lake, for example - you can probably isolate some
wild Halobacteria or other haloarchaea using Carolina's Halobacterium
medium, which is salty enough that hardly anything else will survive
on it. Or you can probably make your own medium by adding extra NaCl
and other salts to another bacterial growth medium.
Here's a nice student project on growing Halobacterium sp. NRC-1:
http://www2.masters.edu/w/GetHostedFile.ashx?x&Growing+Halobacteria+sp++NRC-1+_3_.pdf&Id=31
Halobacterium sp. NRC-1:
http://www.carolina.com/category/living+organisms/prokaryotes/archaea+and+halobacterium.do
http://www.carolina.com/category/teacher+resources/classroom+activities/halobacteria-+making+microbiology+manageable.do
If you live anywhere nearby a salt flat - near the SF Bay Area, or
Utah's Great Salt Lake, for example - you can probably isolate some
wild Halobacteria or other haloarchaea using Carolina's Halobacterium
medium, which is salty enough that hardly anything else will survive
on it. Or you can probably make your own medium by adding extra NaCl
and other salts to another bacterial growth medium.
Here's a nice student project on growing Halobacterium sp. NRC-1:
http://www2.masters.edu/w/GetHostedFile.ashx?x&Growing+Halobacteria+sp++NRC-1+_3_.pdf&Id=31
Brian Degger
Jul 20, 2011, 9:40:05 AM7/20/11
to diy...@googlegroups.com
Theres an article on halobacteria in American.scientist may-june 2007
and a sidebar on nrc-1
Http://www.americanscientist.org/IssueTOC/issue/961
Cheers Brian
and a sidebar on nrc-1
Http://www.americanscientist.org/IssueTOC/issue/961
Cheers Brian
PatrickG
Jul 20, 2011, 5:34:51 PM7/20/11
to DIYbio
Yeah, a lot of them are slow-growers, but some aren't bad. An extreme
example (I know this would be a poor subject for DIYers) would be
Pyrococcus furiosus, which has a generation time of less than an hour
at optimum conditions, iirc. A number of hyperthermophiles actually
have reasonable generation time, like S. solfataricus, which I think
is around 6h. Methanogens, though interesting, I understand are quite
slow, and also picky about oxygen. Some halophilic archaea can
apparently reproduce in 6-7h (http://www.ncbi.nlm.nih.gov/pmc/articles/
PMC242385/pdf/aem00172-0142.pdf). I'm rambling now, so I'll get to the
point:
1. Part of my question is wondering whether it is feasible to isolate
certain kinds of extremophiles. In particular, I'm wondering if/how
DIYers could isolate an aerobic hyperthermophilic archaeon like those
of the Sulfolobus genus. I know that Yellowstone prevents people from
touching the springs, but could some archaea be in runoff near the
springs/could a sample be taken from that runoff?
2. Sounds like halophilic archaea are a nice way to start, since they
seem easy to get and not terribly difficult to culture. + there are
transformation systems for them.
3.I like the idea of a DIY methanogen culture, say, Methanosarcina
acetivorans. They have a unique and useful metabolism, and are fairly
prevalent, as well as having transformation protocols available.
Nonetheless, I don't know the extent to which DIYers would be able to
construct a good anaerobic culture environment.
I guess I'm just trying to narrow the list down right now: of the
extremophiles, which ones are easiest (I think that question has been
answered with the halophiles, but feel free to disagree), which are
almost completely impossible (probably deep vent archaea) and which
are quite challenging but maybe doable (maybe some thermophiles and
hyperthermophiles?)
Additional thoughts/suggestions/corrections?
example (I know this would be a poor subject for DIYers) would be
Pyrococcus furiosus, which has a generation time of less than an hour
at optimum conditions, iirc. A number of hyperthermophiles actually
have reasonable generation time, like S. solfataricus, which I think
is around 6h. Methanogens, though interesting, I understand are quite
slow, and also picky about oxygen. Some halophilic archaea can
apparently reproduce in 6-7h (http://www.ncbi.nlm.nih.gov/pmc/articles/
PMC242385/pdf/aem00172-0142.pdf). I'm rambling now, so I'll get to the
point:
1. Part of my question is wondering whether it is feasible to isolate
certain kinds of extremophiles. In particular, I'm wondering if/how
DIYers could isolate an aerobic hyperthermophilic archaeon like those
of the Sulfolobus genus. I know that Yellowstone prevents people from
touching the springs, but could some archaea be in runoff near the
springs/could a sample be taken from that runoff?
2. Sounds like halophilic archaea are a nice way to start, since they
seem easy to get and not terribly difficult to culture. + there are
transformation systems for them.
3.I like the idea of a DIY methanogen culture, say, Methanosarcina
acetivorans. They have a unique and useful metabolism, and are fairly
prevalent, as well as having transformation protocols available.
Nonetheless, I don't know the extent to which DIYers would be able to
construct a good anaerobic culture environment.
I guess I'm just trying to narrow the list down right now: of the
extremophiles, which ones are easiest (I think that question has been
answered with the halophiles, but feel free to disagree), which are
almost completely impossible (probably deep vent archaea) and which
are quite challenging but maybe doable (maybe some thermophiles and
hyperthermophiles?)
Additional thoughts/suggestions/corrections?
> On Mon, Jul 18, 2011 at 2:31 AM, Brian Degger <brian.deg...@gmail.com>wrote:
>
>
>
>
>
> > Interested for sure, could start with the halophiles, those pink
> > bacteria seen in salt lakes. Nice article on them in a Scientific
> > American, will dig up the reference.
> > Cheers, Brian Degger
>
>
>
>
>
>
> > Interested for sure, could start with the halophiles, those pink
> > bacteria seen in salt lakes. Nice article on them in a Scientific
> > American, will dig up the reference.
> > Cheers, Brian Degger
>
> > On Monday, July 18, 2011, General Oya <general...@gmail.com> wrote:
> > > I read last year, that some researchers out of Washington state were
> > using methanogens for estrogen bio-remediation. I would love to learn more
> > about that process. Our sponser for 2010 igem works mostly with thermophiles
> > and provided our TAq from which we pcr'd out the polymerase DNA using
> > primers designed based from the blast results we found online.
> > > Wasn't there some xenobiology talk from NASA last year about the
> > possibility of various sulfur based life forms within our own solar system
> > (not terra)?
> > > Ryan
> > > On Jul 17, 2011 1:34 PM, "Nathan McCorkle" <nmz...@gmail.com> wrote:>
> > L.A. biohackers are doing something with a hydrogen-phile
>
> > > I read last year, that some researchers out of Washington state were
> > using methanogens for estrogen bio-remediation. I would love to learn more
> > about that process. Our sponser for 2010 igem works mostly with thermophiles
> > and provided our TAq from which we pcr'd out the polymerase DNA using
> > primers designed based from the blast results we found online.
> > > Wasn't there some xenobiology talk from NASA last year about the
> > possibility of various sulfur based life forms within our own solar system
> > (not terra)?
> > > Ryan
> > > On Jul 17, 2011 1:34 PM, "Nathan McCorkle" <nmz...@gmail.com> wrote:>
> > L.A. biohackers are doing something with a hydrogen-phile
>
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