What is environmental DNA (eDNA)?

All animals shed cells throughout their life either from their skin, in waste products, during reproduction, or as a result of predation. These shed cells are released into the environment and can be collected from soil or water samples. They contain unique, taxon-specific DNA sequences that are can be used for identification. First the DNA must be extracted or isolated from the environmental sample (e.g. water, soil), and then fragments must be isolated and then sequenced using Next-Generation sequencing techniques. Identification of individual sequences are then made by comparing the results to publicly accessible online databases such as GreenGenes or GenBank. Read below for a more detailed explanation of the process.

• The process starts by collecting two liters of pond water from forty locations within each pond. The jars containing the pond water are brought back to the laboratory for filtering. (Environmental variables such as dissolved oxygen, pH, temperature and salinity are collected at each sampling point using an YSI Professional multi-meter probe. This data will be used for later analyses to look for associations between these parameters and what organisms are found in different conditions.)

• Two liters of water are reduced to a couple hundred milliliters of DNA extract via filtering containing the genetic material from thousands of organisms: High-quality Millipore filters are used collect the cells and other inorganic materials such as silt. This usually requires between three and seven filters per pond depending on the amount of organisms and other factors.

• Genetic material is isolated directly from the filters using the PowerWater extraction kit from MoBio. The process includes many steps to break open (lyse) cells to free the DNA, remove cell debris and inorganic materials, and finally clean the DNA for sequencing.
• Isolated DNA samples are sent to a sequencing facility that uses Mi-Seq from Illumina, where the genetic codes are sequenced.
• The raw data is sent back to our lab where it is processed via the QIIME pipeline on the High Powered Computing Cluster at the College of Staten Island, CUNY. This analyses starts by cleaning up the sequences, which is followed by identification using the aforementioned databases. Graphical representations, such as the Principal Coordinate Analysis (PCoA) image shown below, are then created to help visualize the data. Now we can begin to understand the patterns and processes of biodiversity along this urban landscape.

 

Fig 1. PCoA analysis of bacterial communities sample in 2014. Courtesy of Dr. Jessica Joyner.