David Coil edited Results_and_Discussion_Growth_experiments__.md  about 8 years ago

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We eventually concluded that the design requirements were mutually exclusive; either we could achieve containment for liquid cultures at the expense of aerobic conditions, or we could achieve aerobic conditions at the expense of liquid culture containment. We chose the latter, so our plates were prepared with solid media. Solid media is not traditionally used for OD measurements, and so our results need to be interpreted differently from OD in liquid culture. Using clear agar to maximize transparency, we programmed the plate reader to take OD measurements at nine different locations in each well, each of which was measured twenty five times per observation. The plates were inoculated in a manner intended to create many small colonies (see Materials and Methods). As these colonies grow, their edges intersect with reading points, and the OD for that point increases in a stepwise fashion. As the colony thickens, the OD gradually increases. OD in liquid media is thought to correspond to scattering of light by individual cells, whereas our measurements correspond to the number, diameter, and thickness of the colonies. The intervals elapsed between occultations of the reading points decrease exponentially, and so the average OD across each well behaves very similarly to traditional observations of log-phase growth in liquid media. However, in the absence of correlation with the gold standard of dilution plate counts, this should be considered as a relative measure of growth. This was validated by repeated growth experiments on earth, showing normal growth kinetics of colonies grown with this method, an sample dataset is shown in Supplementary Figure 1. To our knowledge this is the first use of solid media to measure bacterial growth kinetics in this manner. The data from the different plate readers (Tecan and Molecular Dynamics) was compared at 96 hours by plotting the OD600 values against each other. While the concordance was not perfect, there was a very strong relationship between the two machines which provided validation of the data from both Molecular Dynamics machines (ground and space).  By this measure, the vast majority of the bacteria (45/48) behaved very similarly in space and on earth (Table 1). Only three bacteria showed a significant difference in the two conditions; _Bacillus safensis_, _Bacillus methylotrophicus_, and _Microbacterium oleivorans_. However, upon As part of double checking these results, we performed  Sanger sequencing the 16S of  rRNA gene from cultures obtained genes  from the wells on corresponding to each of these species of  the space plates andthe  ground plates, we inferred contamination of the _B. methylotrophicus_ and _M. oleivorans_ wells and therefore discarded those data. Some plates. A few  wells showed a produced  mixed Sanger sequence, suggesting the presence of more than one organism in the well, while others well. In addition, a couple of wells  gave a clear identification as of  a contaminating organism. We therefore inferred that there had been some contamination of the _B. methylotrophicus_ and _M. oleivorans_ wells.  Since the remaining 45 organisms were not tested for contamination, it is possible that some of those represent false negatives. The remaining candidate was _B. safensis_ wells were all clear of any signs of contamination.     This  _Bacillus safensis_, safensis_ strain was  collected at the Jet Propulsion Laboratory (JPL-NASA) on a Mars Exploration Rover before launch in 2004. As part of standard Planetary Protection protocols, all surface-bound spacecraft are sampled during the assembly process and those strains are then saved for further analysis. We obtained this strain as part of a collection of JPL-NASA strains to send to the ISS (Table 1). In this experiment, _Bacillus safensis_ grew to a final density of ~60% higher in space than on the ground, with very little variation between replicates (Figure 1). The genome sequence of this strain, _Bacillus safensis_ JPL-MERTA-8-2 has just been published \cite{26586895} and may contain clues as to why this strain behaved so differently in space. It is perhaps no surprise that most built environment-associated bacteria behave very similarly on the ISS as on earth. After all, the ISS is a home and office of sorts, with environmental conditions very similar to a building on earth with the exception of gravity. The ISS is maintained at around 22 °C with a relative humidity of around 60% and pressure and oxygen concentrations very close to those at sea level on earth. Additionally, this experiment did not provide enough time to study the long-term adaptation of bacteria to the environment on board the ISS.