Since these samples were collected in a vacuum, doesn't it make sense to keep them in a vacuum, at least for science that requires the smallest possible amount of contamination?
Nitrogen gas is for most purposes chemically and organically inert, particularly in the absence of oxygen.
It's also abundant, cheap, and non-toxic, so long as the surrounding environment has sufficient oxygen that leaks don't put personnel at risk. Glovebox construction and use is also much easier than with vacuum.
A positive-pressure nitrogen environment will also limit infiltration of oxygen or other contaminants, something which cannot be said of vacuum chambers.
Past experiences (see Nasa SP-88 below) show that vacuum handling provides few if any benefits and numerous risks and complexities.
Nitrogen-flooded environments can be made arbitrarily large, again a characteristic that's not true of vacuum chambers.
A StackExchange question addresses this topic in more depth:
As per the article, however, a nitrogen atmosphere does not preclude growth of Bacillus, many species of which can tolerate a pure nitrogen atmosphere quite readily.
That said, bacillus can survive hard vacuum too through sporulation, so short of analysing these samples in-situ, it’s going to be really hard to prove an ET origin for any microorganisms.
Where specifically are you getting that information?
From TFA:
The nitrogen atmosphere, in which the sample was stored during this time, can be a bactericide for some, but not all, Bacillus species owing to the reduced water activity associated with the dry atmosphere (Munsch-Alatossava & Alatossava, 2014). The bactericidal effects of such atmospheres are not restricted to Bacillus, and thus provides no diagnostic information.
That is: nitrogen should generally kill bacteria, but may not in the case of some Bacillus species. That's quite some distance from saying the bacteria would thrive in that environment, and I'd presume other factors (light, food supply, some means for oxidation) would be necessary, most of which could be reasonably constrained within a sample-examination environment.
Origin determination might be made through C14 or other dating --- any extant in situ bioactive materials would presumably be comprised of primordial carbon with effectively no C14 signature, as opposed to any recently-deposited or growing organisms.
One challenge seems to be that there was very little Bacillus present, 11 to 147 individuals, which seems to have made DNA analysis impractical and would likely challenge isotopic analysis as well.
NB: Not my area of expertise, just close reading, general understanding, and some research-fu.
Since these samples were collected in a vacuum, doesn't it make sense to keep them in a vacuum, at least for science that requires the smallest possible amount of contamination?