High-throughput automation of ecological experiments

Ecological experiments often require high levels of replication for two reasons. First, ecological dynamics are inherently ‘noisy’ because they are the product of a  large number of interacting parts. Second, measurement error is often high relative to effect sizes. Both of these factors mean that high replication is needed to detect significant treatment effects, but experiments are often limited by the number of replicates. One enormous advantage of microbial ecology is that it is possible to conduct experiments with vastly superior levels of replication.

In addition, community ecology often requires experiments that manipulate the composition of communities. However, the number of possible combinations of species is enormous. Automation allows us to sample a much larger number of communities.

Lab robots

We have added several lab robots to our lab.

The workhorse is Darth Hamilton, which is a liquid handling robot. It’s main task is to construct communities from a collection of bacteria. The video shows the robot moving a 96-well microplate into position after reading its barcode. The microplate will hold the experimental communities. The robot then samples bacteria and adds culture media using the pipetting tips before replacing the microplate into a new stack and collecting the next 96-well microplate.

We have been using the pipetting robot to create and manipulate communities. Two small robots are being used to measure the communities. The first is a Biotek stacking robot, which feeds the microcosms into a microplate reader (shown in the video). The second is an Intellicyt Hypercyt robot attached to a BD Accuri C6 flow cytomter. The plate reader tends to be used for conducting functional assays,while the cytometer tracks cell populations.