DOI: 10.5061/dryad.5hqbzkh2k
title: Data from: Phase transitions in yeast and bacterial populations under stress

description: Nonequilibrium phase transitions from survival to extinction have recently
 been observed in computational models of evolutionary dynamics. Dynamical
 signatures predictive of population collapse have been observed in yeast
 populations under stress. We experimentally investigate the population
 response of the budding yeast Saccharomyces cerevisiae to biological
 stressors (temperature and salt concentration) in order to investigate the
 system’s behavior in the vicinity of population collapse. While both
 conditions lead to population decline, the dynamical characteristics of
 the population response differ significantly depending on the stressor.
 Under temperature stress, the population undergoes a sharp change with
 significant fluctuations within a critical temperature range, indicative
 of a continuous absorbing phase transition. In the case of salt stress,
 the response is more gradual. A similar range of response is observed with
 the application of various antibiotics to Escherichia coli, with a variety
 of patterns of decreased growth in response to antibiotic stress both
 within and across antibiotic classes and mechanisms of action. These
 findings have implications for the identification of critical tipping
 points for populations under environmental stress.
description: <b> </b> To investigate the dynamics of
 yeast population growth under stress, two environmental stressors were
 utilized, temperature and elevated NaCl concentration. In both cases,
 <i>S. cerevisiae</i> (strain yWO3) was initially grown at 30
 °C in standard medium (YEPD) containing 10 g/L yeast extract, 20 g/L
 peptone and 2% dextrose. These initial 50 mL cultures were inoculated with
 cells to an OD (optical density) of 0.0001. From this initial
 concentration, the cells typically grew to an OD of 2.5 in 24 hours. All
 OD measurements were taken at 600 nm. To study the response to
 temperature stress, the initial culture, prepared as described above, was
 inoculated into 50 mL of YEPD in 250 mL flasks to a resulting OD of 0.05.
 The samples were then placed in orbital shaking water baths that had
 already reached the temperature of interest.  Sample ODs were then
 measured every 24 hours.  If the sample had grown, the sample was diluted
 back to an OD of 0.05 in a volume of 50 mL YEPD in a new 250 mL flask. If
 the sample had not grown significantly (less than 0.01 OD growth), or if
 the OD of the sample was lower than 0.05, the sample was placed back into
 the water bath for another 24 hours.  Measurements were taken over eight
 24-hour periods. Growth was measured by calculating the number of times
 the population doubled between measurement cycles, or number of
 doublings. For
 the measurement of yeast growth under high salt stress, separate YEPD +
 NaCl media were prepared for each NaCl concentration.  The ratio of yeast
 extract, peptone, and dextrose per liter was unchanged, but salt was added
 at appropriate g/L concentrations. An initial culture in YEPD was
 inoculated into 50 mL of YEPD + NaCl in 125 mL flasks to a resulting OD of
 0.05. The samples were then placed in an orbital shaking water bath at 30
 ºC. As with the temperature studies described above, sample ODs were
 measured after 24 hours.  If growth had occurred, the sample was diluted
 back to an OD of 0.05 in a volume of 50 mL YEPD + NaCl in a new 125 mL
 flask. If the sample did not have significant growth, or if the OD was
 less than 0.05, the sample was returned to the incubator until the next
 measurement period. Measurements were taken over eight 24-hour periods,
 and doublings were calculated. <i>Escherichia coli</i> (MG1655) were grown
 in M9 minimal glucose media overnight, shaking at 37 °C. This bacterial
 culture was used to inoculate 96-well plates containing a dilution series
 of 10 different antibiotics, at a starting OD (600 nm) of 0.005
 (<i>i.e.</i>, 2 µl of culture in 198 µl media). We selected a
 panel of 10 antibiotics across different antibiotic classes with a variety
 of mechanisms of action. Each antibiotic was added at a starting
 concentration of 100 µg/ml and subsequently serially diluted by ¾ to give
 40 different concentrations, ranging from 100 µg/ml to 0.001 µg/ml. There
 were 6 replicates for each antibiotic. 96-well plates were incubated,
 shaking at 37 °C, for 24 hours. The OD (600nm) for each well was measured
 using a Cytation 3 multimode plate reader (BioTek). Doubling times for
 each well were calculated as a function of initial and final OD as they
 were for the yeast data.