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Selfsim
2013-Nov-07, 09:19 PM
Rare new microbe found in two distant clean rooms: (http://phys.org/news/2013-11-rare-microbe-distant-rooms.html)


A rare, recently discovered microbe that survives on very little to eat has been found in two places on Earth: spacecraft clean rooms in Florida and South America.

This population of berry-shaped bacteria is so different from any other known bacteria, it has been classified as not only a new species, but also a new genus, the next level of classifying the diversity of life. Its discoverers named it Tersicoccus phoenicis.

Some other microbes have been discovered in a spacecraft clean room and found nowhere else, but none previously had been found in two different clean rooms and nowhere else.
...
Microbes that are tolerant of harsh conditions become more evident in clean room environments that remove the rest of the crowd.
...
"Tersicoccus phoenicis might be found in some natural environment with extremely low nutrient levels, such as a cave or desert," Vaishampayan speculated. This is the case for another species of bacterium (Paenibacillus phoenicis) identified by JPL researchers and currently found in only two places on Earth: a spacecraft clean room in Florida and a bore hole more than 1.3 miles (2.1 kilometers) deep at a Colorado molybdenum mine.… So much for the idea of relying on Viking's sterilisation procedure as being a primary basis for assuming that no terrestrial organisms could have been transported to Mars, (resulting in apparently positive LR results), eh?

More significantly, how can the possibility of accidental panspermia in future missions be ruled out, should an undiscovered genus be discovered during exo-exploration?

I wonder whether the current-day GCMSs (and maybe even Viking's LR approach) are sensitive enough to detect such hitch-hikers?

I wonder what happens to these microbes when they're exposed for extended periods to say, a martian (or even spacecraft-bound) environment?

Perhaps clean-rooms should be located in Antarctica?

Jeff Root
2013-Nov-07, 11:57 PM
Clean rooms aren't expected or intended to be sterile.
Spacecraft that are sterilized for landing on Mars are sterilized
after being placed inside the aeroshell, and are not exposed
to the clean room environment after that.

I liken the LR result to dropping an Alka Seltzer tablet into a
glass of water.

-- Jeff, in Minneapolis

Selfsim
2013-Nov-08, 01:09 AM
Clean rooms aren't expected or intended to be sterile.
Spacecraft that are sterilized for landing on Mars are sterilized
after being placed inside the aeroshell, and are not exposed
to the clean room environment after that.So, you think spacecraft sterilisation removes sufficient microbes as to not be detectable by the instruments sent to detect 'em eh?


I liken the LR result to dropping an Alka Seltzer tablet into a
glass of water.Huh??

Don J
2013-Nov-08, 04:14 AM
CLEANING AND STERILIZATION STANDARDS

NASA’s current planetary protection requirements for Mars missions are derived from the procedures applied to the Viking landers. Missions not carrying life-detection experiments must be cleaned to ensure that the spacecraft’s total bioload does not exceed 300,000 spores and that the density of spores on the spacecraft’s surfaces does not exceed 300 m-2.Missions with life-detection experiments must undergo additional procedures to ensure that the total bioload does not exceed 30 spores. The effectiveness of the various procedures currently used by NASA and its contractors to meet these bioload standards is determined by the use of reference organisms, including Bacillus subtilis (var. niger), Bacillus pumilis, and Bacillus stearothermophilus. Bacillus spp. (endospore formers) were originally selected as a microbiological indicator of sterilization success on the basis of their enhanced resistance to heat, desiccation, and radiation.

ACHIEVING THE STANDARDS

The twofold approach to the control of forward contamination used by the Viking mission—careful cleaning of the spacecraft, followed by active bioload reduction through heat sterilization (see Box 1.1 in Chapter 1)—forms the basis for the procedures currently in use. All missions are carefully cleaned and then those with life-detection experiments undergo sterilization.

The Viking landers were assembled in clean rooms (see Box 4.1 for a description of current clean-room procedures). During assembly, microbial assays (see Chapter 5) were conducted to establish that the average and total burden of spores on the lander’s accessible surfaces were 300 m-2and 300,000, respectively.1 Current practice requires that those parts of the spacecraft not meeting the requisite bioload standards be washed with isopropyl alcohol and/or a sporicide (ethanol, 65 percent; isopropanol, 30 percent; and formaldehyde, 5 percent) to reduce their bioburden. Decontaminated surfaces are then retested for their contaminating microbiological burden.

Once the landers had been assembled and sealed inside their bioshields, the bioload was further reduced by dry heating the whole spacecraft to at least 111.7 °C for some 30 hours. This procedure was credited with reducing the lander’s bioburden by a factor of 104. Future spacecraft can be designed to maximize accessibility of their components for pre- and post-assembly bioload reduction. However, some components are hermetically sealed before
assembly, so cleaning/sterilizing procedures must be conducted before sealing to prevent recontamination. The sterilization procedures commonly applied in a variety of applications to sealed and unsealed components are listed in Table 4.1. It is worth noting that many of these procedures can have negative impacts on spacecraft performance and may increase mission cost.
Source:
http://www.nap.edu/openbook.php?record_id=9895&page=17

Selfsim
2013-Nov-08, 05:28 AM
Why, thank you for that Don J! :)

Goodness me! ...

i) ... Ethanol, isopropanol, formaldehyde, ethylene dioxide, hydrogen peroxide plasma, methyl bromide ...
Some nice looking organics to react with martian based soil based peroxides in a pyrolitic chamber under heating, there Don. :)
I wonder if anyone has ever seriously looked into the effects of these 'cleaning products' on the experiments/detectors once they reach their destination(s)?

ii) Tersicoccus phoenicis (http://en.wikipedia.org/wiki/Tersicoccus_phoenicis):
According to microbiologist Parag Vaishampayan of NASA's Jet Propulsion Laboratory and lead author of studies about the microbe, "We want to have a better understanding of these bugs, because the capabilities that adapt them for surviving in clean rooms might also let them survive on a spacecraft. This particular bug survives with almost no nutrients.".. which appears to apply to Paenibacillus phoenicis as well.

iii) I wonder whether these bacteria are capable of reproducing and growing once making it through spacecraft 'sterilisation'? I suppose the only spacecraft(s) to have ever gone through such a procedure were the Viking ones? (Ie: because they were the only life detection missions thus far, eh?)

Yep it all looks good on paper (and in theory) ... then there's practice ...

Don J
2013-Nov-08, 07:47 PM
Why, thank you for that Don J! :)

Goodness me! ...

i) ... Ethanol, isopropanol, formaldehyde, ethylene dioxide, hydrogen peroxide plasma, methyl bromide ...
Some nice looking organics to react with martian based soil based peroxides in a pyrolitic chamber under heating, there Don. :)
I wonder if anyone has ever seriously looked into the effects of these 'cleaning products' on the experiments/detectors once they reach their destination(s)?

Blank runs done during the travel to Mars would have revealed the remaining concentration of the cleaning product(s) used to clean and sterilize the pyrolitic chamber or the GCMS or the other life detection equipments..


ii) Tersicoccus phoenicis (http://en.wikipedia.org/wiki/Tersicoccus_phoenicis):.. which appears to apply to Paenibacillus phoenicis as well.

iii) I wonder whether these bacteria are capable of reproducing and growing once making it through spacecraft 'sterilisation'? I suppose the only spacecraft(s) to have ever gone through such a procedure were the Viking ones? (Ie: because they were the only life detection missions thus far, eh?)

Thousand of tests were done to ensure that the total bioload does not exceed 30 spores.It is very unlikely that these remaining 30 spores were doing the party(reproducing) during their trip to Mars. They were more occupied to trying to survive rather than making a party.
http://www.nap.edu/openbook.php?record_id=9895&page=17

Selfsim
2013-Nov-09, 01:49 AM
Blank runs done during the travel to Mars would have revealed the remaining concentration of the cleaning product(s) used to clean and sterilize the pyrolitic chamber or the GCMS or the other life detection equipments.. .. and their concentration relative to the low levels of soil organics, when combined with soil perchlorates and heat .. results in what exactly?

Also, (as we've discussed previously), the low level organic based cleaning products, in isolation may seem very slight .. but when combined with soil samples and heated, the levels could quite easily have unexpected results. This is the lesson from Curiosity/SAM .. a lesson not known to be an issue during the Viking LR results re-analyses studies ...


Thousand of tests were done to ensure that the total bioload does not exceed 30 spores.It is very unlikely that these remaining 30 spores were doing the party(reproducing) during their trip to Mars. They were more occupied to trying to survive rather than making a party.
http://www.nap.edu/openbook.php?record_id=9895&page=17Well, I think the OP is suggesting that Tersicoccus phoenicis might have different partying habits to bacteria used as the model for setting the standards …
NASA’s current planetary protection requirements for Mars missions are derived from the procedures applied to the Viking landers. Missions not carrying life-detection experiments must be cleaned to ensure that the spacecraft’s total bioload does not exceed 300,000 spores and that the density of spores on the spacecraft’s surfaces does not exceed 300 m-2.Missions with life-detection experiments must undergo additional procedures to ensure that the total bioload does not exceed 30 spores.This really doesn't mean much unless the acceptable contamination level is compared with the sensitivity of the detection apparatus .. and the procedures adopted in the detection experiment. In isolation, these numbers mean very little.
The effectiveness of the various procedures currently used by NASA and its contractors to meet these bioload standards is determined by the use of reference organisms, including Bacillus subtilis (var. niger), Bacillus pumilis, and Bacillus stearothermophilus. Bacillus spp. (endospore formers) were originally selected as a microbiological indicator of sterilization success on the basis of their enhanced resistance to heat, desiccation, and radiation.So, I wonder what might happen to the bioload standards if they were to base them on the rumoured, notoriously party-prone Tersicoccus phoenicis and Paenibacillus phoenicis? (I have no idea, by the way …)

Don J
2013-Nov-09, 02:41 AM
.. and their concentration relative to the low levels of soil organics, when combined with soil perchlorates and heat .. results in what exactly?

Also, (as we've discussed previously), the low level organic based cleaning products, in isolation may seem very slight .. but when combined with soil samples and heated, the levels could quite easily have unexpected results.

As a remember the Viking GCMS have not detected organic compounds even if it should have... based at least from meteorites and cosmic dusts contribution.


This is the lesson from Curiosity/SAM .. a lesson not known to be an issue during the Viking LR results re-analyses studies ...

You talk about the MTBSTFA leak which affect Curiosity.Why are you still training it as if it concerned Viking?Also remember that Curiosity was not cleaned and sterilized based on the recommended protocol.



Well, I think the OP is suggesting that Tersicoccus phoenicis might have different partying habits to bacteria used as the model for setting the standards …This really doesn't mean much unless the acceptable contamination level is compared with the sensitivity of the detection apparatus .. and the procedures adopted in the detection experiment. In isolation, these numbers mean very little.So, I wonder what might happen to the bioload standards if they were to base them on the rumoured, notoriously party-prone Tersicoccus phoenicis and Paenibacillus phoenicis? (I have no idea, by the way …)
They could have the possibility to partying in an environment where there is heat ,moisture(ambiant) and a atmosphere like that is the case in the clean room but during the trip to Mars good luck.

Selfsim
2013-Nov-09, 04:26 AM
As a remember the Viking GCMS have not detected organic compounds even if it should have... based at least from meteorites and cosmic dusts contribution.Sure the GCMS didn't ... but the LR test detected something, no?


You talk about the MTFSB leak which affect Curiosity.Why are you still training it as if it concerned Viking?Also remember that Curiosity was not cleaned and sterilized based on the recommended protocol.Its not so much the MTBSTFA contaminant I'm referring to. (This, for sure, is specific to the SAM Curiosity experiment design). The detection of MTBSTFA in the SAM reaction chamber highlights that terrestrial organic contaminants can influence the reactions which happen upon heating in the pyrolysis chambers in any remote GCMS experiment under certain conditions. The 'certain conditions' linking both Viking and Curiosity are the martian soil conditions, specifically the reactions which occur when perchlorates are heated with extant soil contents AND terrrestrial organic contaminants. Tenax was also shown in SAM to have influenced the ion column separation stage of the experiment. Viking may not have had Tenax, but it did make use of palladium, which is an entry point into lots of organic chemistry.

The common point from both Viking and Curiosity to learn from, is that terrestrial contaminants (cleaning products, deliberately included materials, etc) all influence the sensitive detectors ... and when there are free ions floating around, different unanticipated reactions can occur. Who is to say that Viking's LR results didn't encounter such unexpected reactions (which could look like metabolism?). The in-flight and blank run testing done by Viking didn't include the martian soil components which may have contained the catalyst for reacting with Viking's terrestrial contaminants .. which also now, could have possibly included low spore counts, (whatever that means), of the 'party-microbe' ..


They could have the possibility to partying in an environment where there is heat ,moisture(ambiant) and a atmosphere like that is the case in the clean room but during the trip to Mars good luck.Well maybe not in transit .. but in the case of the LR experiment, wasn't nutrient and some heat added to promote active metabolism?

Don J
2013-Nov-09, 05:49 AM
Sure the GCMS didn't ... but the LR test detected something, no?

Yes,the LR was conceived to detect metabolism.


Its not so much the MTBSTFA contaminant I'm referring to. (This, for sure, is specific to the SAM Curiosity experiment design). The detection of MTBSTFA in the SAM reaction chamber highlights that terrestrial organic contaminants can influence the reactions which happen upon heating in the pyrolysis chambers in any remote GCMS experiment under certain conditions. The 'certain conditions' linking both Viking and Curiosity are the martian soil conditions, specifically the reactions which occur when perchlorates are heated with extant soil contents AND terrrestrial organic contaminants.

In another thread i have provided a reference where Levin made it clear that perchlorates were not present at the 2 Viking landing sites because if present it would have be detected during the control tests (destined to kill microorganisms )heated at 160 degree celsius.


Tenax was also shown in SAM to have influenced the ion column separation stage of the experiment. Viking may not have had Tenax, but it did make use of palladium, which is an entry point into lots of organic chemistry.

Again, the Viking GCMS have not detected organic compounds.As for the organic chemistry the Viking GCMS have effectively detected chloromethane and di-chloromethane while analysing the Martian soil samples -but no chloromethane and di-chloromethane was detected during the blank runs .So you cannot say that Earth contaminants ie(cleaning products) reacting with the palladium was the cause.


The common point from both Viking and Curiosity to learn from, is that terrestrial contaminants (cleaning products, deliberately included materials, etc) all influence the sensitive detectors ... and when there are free ions floating around, different unanticipated reactions can occur.
Who is to say that Viking's LR results didn't encounter such unexpected reactions (which could look like metabolism?). The in-flight and blank run testing done by Viking didn't include the martian soil components which may have contained the catalyst for reacting with Viking's terrestrial contaminants ..

The catalyst ie perchlorates was not present at the 2 Viking landing site.



which also now, could have possibly included low spore counts, (whatever that means), of the 'party-microbe' ..

Low spore counts =30... how much of them may have survive the trip to Mars?



Well maybe not in transit .. but in the case of the LR experiment, wasn't nutrient and some heat added to promote active metabolism?
They have tested that with sterile soil ie Lunar dust and the LR response to metabolism was negative.And remember the control tests with Martian soil samples heated at 160 degree celsius (destined to kill microorganisms)which all
presented a negative metabolic response after nutrient was added...

All LR datas from Viking lander VL1 and VL2 ...
Viking Lander Labeled Release
Experimenter's Notebook
http://pds-geosciences.wustl.edu/viking/vl1_vl2-m-lr-2-edr-v1/vl_9010/extras/index.htm

ETA -another method used to -test- a control sample...
Also of interest is Viking Lander 1 Cycle 4 control test not using heat at 160 degree celsius but rather a Martian soil sample taken from the same location that Viking Lander 1 Cycle 3 was stored in the dark during 140 Sol (many months) open to the Mars atmosphere...see details

The sample was collected on Sol 91 and stored in the Biology hopper in the dark, open to the Mars atmosphere, and at temperatures between 10° and 26°C until analysis ie (injection of nutrient) started on Sol 230.

Viking Lander 1 Cycle 4 -control sample- ( in the dark during 140 Sol)
http://pds-geosciences.wustl.edu/viking/vl1_vl2-m-lr-2-edr-v1/vl_9010/extras/v1cycle4.htm

Compare the results with Viking Lander 1 Cycle 3
http://pds-geosciences.wustl.edu/viking/vl1_vl2-m-lr-2-edr-v1/vl_9010/extras/v1cycle3.htm

Collecting samples:
http://pds-geosciences.wustl.edu/viking/vl1_vl2-m-lr-2-edr-v1/vl_9010/extras/collsoil.htm#VL1%20Sample%203