Halophiles!

dexter

ROOT
Registered Senior Member
Hey, I'm starting a research project on archean halophiles, and was wondering if anyone had any interesting information they would like to share. I'm in the process of isolating a strain obtained from the salt evaporation ponds in SF, CA. I'm having some problems finding the right medium for them to grow in, but we have several mixed cultures growing. Any information would be most appriciated!:D
 
I presume you are doing this at college level. I'm guessing it's some sort of undergrad research project. In that case, I predict you already know more on this subject than 99% of the people who post here (myself included). The occasional poster CharonZ has demonstrated expert microbiological knowledge.
 
Are you doing agar shakes or plates to isolate them? And did you already tested whether your mixed isolates really contain archaea of interest?
Also posting the composition that you used as well as further basic parameters of the ponds might be helpful.
 
CharonZ - We used agar plates and broth tubes. Growth on the plates was not noticable until yesterday (yay!) by red colonies. Until then we used broth containing 28% NaCl, peptone, casamino acids, FeCl3, Yeast Extract and some other metals and such(I dont have the actual recipe on me, but thats the main components as I recall).

The original cultures were taken from some salt evaporation ponds in Southern California by a CSU Long Beach microbiologist.

We are assuming that the mixed isolates contain the archaean halophiles pretty much becasue of the NaCl concentrations in which they grew. at near saturated levels, I don't know what other organisms could survive. They stained gram negative, and when the plated culture was seen under a dark field microscope, they were spirillium in shape. We ran a gram stain on the new plate growth, but I made the fatal mistake(for the bugs) to put the cells in a drop of regular water, which I am assuming caused lycis, so the gram stain was a bust, and stained gram-postive, but true cells could not be seen, just clumps of matter and such. I am assuming this has something to do with the fact that they don't have PG in their cell walls, but I am not certain.

Half the plates were incubated in 37C dark room, and half the tubes incubated in 37 dark room on a shaker. the others were left in the light at room temp.

The plated growth originated from the 37C dark room.

The new cultures did not contain multiple types of cells, instead it was only the spirillium, and some rod type. The NaCl saturated broth tubes produced the most variety, but the postage stamps were only found in the original culture we made at 28% NaCl. The next saturated cultures only produced long rods, and shorter square rods.


Also, I just streaked some isolation plates from the agar culture that finally grew. The semester is over next week, but I innoculated a large saturated flask in hopes of creating a large culture for further study next semester.


Sorry for the scatter-brained-ness of this post, I just wrote down small things that I'm remembering off the top of my head, and some things come inbetween them.

If you have information, I would love to hear it. I'm presenting the project tomarrow, but I'm still interested in the halophiles. Though the project did not produce any significant results, due to time constraints, I am hoping to further my study of them in the comming months, hopefully with an isolation :)
 
I am going to go and check on them in an hour or so, so I will keep you updated.
 
You think about shotgun sequencing the halophiles straight from their pond, then compare them to what you cultured?
 
You think about shotgun sequencing the halophiles straight from their pond, then compare them to what you cultured?

:confused:

That's not going to help dexter isolate (ie. seperate and grow) a specific strain from a mixed culture.
 
You think about shotgun sequencing the halophiles straight from their pond, then compare them to what you cultured?
Yeah, if you got the funds, technical equipment and manpower for a metagenome project, go for it :p
For identification purposes you'd go for the 16s rRNA only.

Back to isolation.
So the medium is a undefined complex one (peptone, casos and yeast extract). This of course means that the main selective factor is, as you described, the NaCl. Now if you do not care what archaea you isolate one should at least for instance make a FISH to determine whether the bacteria are archaea (Gram-stains are not diagnostic enough) as there are also halophilic bacteria. If you can narrow down what you want you could use or create a specific minimal medium to have more selection.
What I am not quite clear about is whether the colonies on the plate (you made dilutional series, right?) contain only one or several species?

In the latter case one could used solidified defined minimal media to dilute them into it.
 
I tried to sequence the 16s RNA, but because it was a mixed culture, it did'nt provide any information.

What is a FISH?

Diagnostic tests that I am looking to do if I get an isolation are an amino acid utilization test, and a carbohydrate utilization test.

I do not have access to the ponds that the bugs were taken from, I am in NorCal, and they are down south.


We didnt dilute them either, as we didnt have enough time and they were taking too long to grow. Apparently classes before us have never had as much sucess with halophiles as we did, so that is good news.

I did check the cultures today, and no new growth could be seen, I will check them again next week, but after that I'm going to be moving for the summer. I am going to try and get a large culture growing in about 250 mLs of a broth, hopefully they will show pigment too :)

DarksidZz. . .. No, it doesnt, though for our poster we were going to design the logo as Halofiles, and have the graphics of the X-files and Halo mixed together, but that would have been unprofessional.
 
FISH (Fluorescence in situ hybidrisation) is a technique in which you make a fluorescence labelled probe via PCR which is specific for archaea in this case (you can even try to use species specific probes, e.g. 16s rRNA) and then you hybridise this probe with fixed and pre-treated cells on a slide. Under the microscope (you need a fluorescence mic, of course) you'll see those cells giving a signal, to which the probe is binding. That way you can directly identify the cells.

Tests of aa and sugar utilisation will only be diagnostic if you already narrowed the species down with highly specific media, though.

In order to get a pure culture you have to do serial dilutions until each colony only harbours one particular cell type. Some prokaryotes are syntrophic, though. and do not get easily separated.

Also, what primer did you use? Were they specific for archaea?
In general one should have a highly enriched or even pure culture before proceeding. One of the few approaches that actually makes sense in highly mixed cultures is FISH.
Other than that enrich them with dilution agar plates first and then do specific pcrs (either archaea or bacteria).

On top of my head I can't think of any halophilic spirilla.
 
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