At a very early stage of our project we noticed that standardization in the phototrophic community needs to have an overhaul to enable reproducible experiments. As we started doing growth curves we used to determine the light intensity via a planar quantum sensor sensitive only to photons with a wavelength between 400nm-700nm; coming from an angle of approximately 120°. Because of the way we setup our incubator, the illumination was coming from two different light sources, which needed to be measured individually. While our first attempts included measuring the intensity by facing the quantum sensor at the lights respectively and then converting these values by a factor accounting for spherical flux of light. We then came up with the idea to search for a scalar radiometer that has a detection surface of nearly 4π steradian, can only measures photosynthetic active radiation. With the help of this method we used to determine the exact amount of µmol photons/m² that can be used for photosynthesis. (400nm-700nm).

After we determined the light intensity via this method the doubling time of our strain reduced drastically from two hours to 90 minutes. We believe that the standardization of measuring light intensity has a huge impact in the field of phototrophic biology. What we often time stumbled upon when we were looking for literature on our iGEM project was that the information on light intensity in these papers were often inconsistent. Oftentimes the only values on the intensity were given in the unit µEinstein, but the needed details on how that number was measured, was missing. So some people would measure the intensities with a planar device, others would determine them via a spherical quantum sensor.

During our skype call with James Golden he emphasized that a lot of experiments are simply not reproducible, because there is no way to tell how much light one has to expose their organisms to. Additionally, we got the feedback of Dr. Nicolas Schmelling that even professional cultivation devices from companies which are specialized on building them, cannot deliver consistent and even illumination.

To go even further, we think that the spectrum of the respective lamp should also be considered when talking about standardization. The light spectrum of our two lamps look as illustrated by Fig. 1. Even though the standardization of the light quality seems to be a very hard task it should still be included in scientific works in order to give as much information as possible about the experimental setup.

We measured an equidistant grid of points at which we measured the average amount of photons (10 seconds) to minimize fluctuation. These data points were then interpolated with the help of a b spline surface to predict the amount of µmol photons at any given point of the incubator. This method is described in more detail on our model page. We believe that the standardization of measuring light intensity has a huge impact in the field of phototrophic biology and immensely helps to create reproducible experimental setups.

We could show that light intensity had a big effect on reporter gene expression. This displays the importance of standardization especially if one want to characterize parts such as promoters RBS terminator or engineer even more complex designs like genetic circuits or synthetic metabolic pathways. We propose a standardization of the light measurement process and inclusion of information, such as the way of measuring, light source and proper light intensities in every publication for phototrophic organisms.

When working in Synthetic Biology, reporter genes such as fluorescence proteins are indispensable elements to characterize BioBricks. For a good characterization a suitable reporter is required. But reporters can be more than just merely a detection tool for transcriptional activity but they can also give a deeper insight into cellular conditions beyond the genetic context. We provide a diverse set of reporters not only for the purpose of describing genetic tools but also for the sensing of a variety of parameters which are crucial for cyanobacteria.

For our project it was indispensable to establish a measurement workflow that is not only applicable to UTEX 2973 and other cyanobacterias but also has a high throughput. While we worked on our Marburg Collection 2.0 with 55 parts we came to the conclusion it was also necessary to develop a measurement method that were suitable to such a large collection. Therefore we elaborated different workflows - containing different cultivation vessels and parameters - and revised them after evaluating the results. In the end we were able to establish a workflow specially designed for our methods to cultivate and characterize the parts from our Marburg Collection 2.0, that is tailored to Synechococcus elongatus UTEX 2973.

Experimental Procedure

The results of our part characterization were obtained by fluorescence and luminescence measurements. But before the light could be measured we had to elaborate a cultivating and measuring workflow.

For the cultivation-workflow we tested different well plate formats and growing parameters for the best growing conditions. Due to the size of the Marburg Collection 2.0 (55 parts) and space limitation in our incubator, our first thought was using well-plates. We started with 96-well-plates and found out that it was impossible to cultivate Synechococcus elongatus UTEX 2973 in incubator with 130 rpm. The rpm of the incubator was limited because cultures in flasks had to be incubated at the same time, presenting risks of falling over at higher rpm. At 130 rpm we found a compromise between cultivating flasks and well-plates in the same incubator. After revising the workflow over and over we came to the conclusion, that it is favorable to cultivate the UTEX 2973 in transparent 24-well-plates ,because, in contrary to 96-well-plates, there was enough movement in the wells to prevent the cells from forming a pellet/cloud.

Additionally, it was necessary to use transparent wells to ensure every well with similar light conditions. Concerning the light conditions, we evaluated that the cells showed good growth in the wells at low-light conditions (around 500 µE). The evaporation of medium played an important role in cultivation using well-plates thanks to their relatively small volume and large surface area.

It was also essential to know the volume in the wells for measuring in the plate reader. Therefore we compared different seals for the well plates and in the end we came to the conclusion that using a semipermeable foil is the best solution. The evaporation could be minimalized and the cells were able to get enough CO2 thanks to improvement in air circulation. By using a foil it was possible to cultivate the cells for 2-3 days without losing significant amount of media.

As described before we used the following workflow as shown in Fig. 1 to cultivate and measure our parts. The cultivation started by picking colonies from BG11-agar-plates that were used at the end of the triparental conjugation. For every part we picked 3 different colonies and inoculated them in 1.0 mL BG11-media with 0.5 µl Spectinomycin. Thus in the first 24-well-plates we could inoculate 8 different parts with 3 biological parallels. When the cultures grew to OD₇₃₀=0.6-0.8 they were inoculated to 1.0 mL of OD₇₃₀=0.1 into the wells A1-3 (part 1) and A4-6 (part 2) of another 24-well-plate. At the same time the Well B6 was inoculated with 1.0 mL of a OD₇₃₀= 0.1 UDAR culture that was used as a blank while evaluating the results. When all the cultures in the second 24-well-plate reached OD₇₃₀=0.6-0.8 they got inoculated twice in the same well-plate. It was done by inoculating the wells A1-3 into the wells C1-3 and D1-3 creating technical parallels of the same part (analog for A4-6 and the UDAR inoculating to B4 and B5). When the wells C1-D6 (and the UDAR) reached an OD₇₃₀=0.6-0.8 the cultures were transferred into a 96-well-plate. Every well of the 24-well-plate was measured three times. Following this workflow we were able to measure three biological parallels and two technical parallels for every biological parallel. It enabled us to have a good statistical database and gives our results a stronger meaning/significance. While working with this workflow it was essential to keep the cultures in their exponential phase because it would significantly speed up the growth by reducing the lag-phase to an absolute minimum.

Concerning the measurement part we decided to transfer the cultures into black/white luminescence is measured in white ones. We measured in 96-well-plates because it enabled us to measure every part three times by consuming only 600 µl of the 1.0 ml 24-well-cultures. Further we could measure eight parts in only one plate. (four 24-well-plates lead into one 96-well-plate for measurement)

Fluorescence measurement

After transfering the cultures into the 96-well-plate the fluorescence of the parts was measured. More precisely, the activity of the parts was determined by the expression of the sYFP. The sYFP fluorescence served as an indicator and the sequence for the sYFP was in the same cassette as the considered part. For our measurement we created a program that measured the OD₇₃₀ and the fluorescence of the wells with the following settings:

OD measure with plate reader: Settings: 730 nm, 3 measuring points (circle)
Fluorescence Settings: Excitation 488 nm, Emission 518 nm size 2x2 (circle), frame 1200 μm strengthener:optimal

In order to measure the OD in each well we determined the absorption at 730 nm. Further we measured multiple points in each well, where 3x3 points (circular) with a gap of 1350nm to the border of the well showed consistent results with small standard deviations. We used the same settings of the multiple measurement for the fluorescence measurement. While using sYFP as signal for our part measurement we have set the emission wavelength to 515 nm and the excitation wavelength to 527 nm, fitting the exact wavelengths of the sYFP.

“Strength and growth come only through continuous effort and struggle.” - Napoleon Hill

Although the quote was certainly never meant in this way, it is quite fitting to our project, as the growth of our Synechococcus elongatus strain UTEX 2973 was one of the key aspects throughout the year. Our goal to create the fastest phototrophic chassis was fueled by our unwavered dream of accelerated research on the multitude of mechanisms and possibilities that phototrophic organisms have to offer. We were quick to learn that this goal was not as close as we might have thought. On our way we encountered countless obstacles, some easier to overcome than others - one of the most resilient ones being the growth conditions we had to provide. Actually reaching the technical values we wanted was not the main issue, no, the hardest part was finding the holy grail of growth conditions, the perfect combination of parameters to cultivate our strain in.

Digging through literature we found various setups that were seemingly the “optimal growth conditions” for S. elongatus UTEX 2973 and it was apparent that in order to find the optimal conditions, we ultimately had to try all of them out by ourselves. So we set one of our biggest projects in motion, recording numerous different growth curves with many different parameters.

Before calibrating key parameters like CO2 concentration, light intensity and temperature, we conducted some smaller trials on various other criteria, such as lid type, flask size, flask type and culture volume, as those are not heavily affected by the other parameters. Through these experiments, we could clearly identify a set that enabled the best growth for our chassis: plastic lids on 250ml erlenmeyer flasks with three chicanes and 50ml culture volume. Having fixed these initial parameters we set sail to the sea of endlessly variable growth conditions in hope to discover the true needs of S. elongatus UTEX 2973.

As phototrophic chassis primarily require light and CO2 for their growth, those were the two parameters we were most interested in, but due to the UTEX 2973 strain being reportedly tolerant to higher temperatures than most other S.elongatus strains (Tan et al., 2018), this was another aspect to be tested. As time was scarce, we parallelized our measurements, meaning that while different temperatures or CO2 concentrations were put on trial we were able to compare the growth under different light intensities. At this point it is important to mention that the light intensities in our incubator were not always set the same way: in the beginning we measured the light distribution with a planar light measurement device, using a conversion chart we acquired from Prof. Dr. Annegret Wilde from Freiburg to convert the values to theoretical spherical values, but after our insightful talk to Prof. Dr. James W. Golden (read here what else we learned from him) we hurried to get hold of a spherical measurement device to make sure we could accurately set the light intensities - and the difference was striking: the doubling time of our cultures increased by a huge amount which was an important step into the right direction for us.