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Speciation

Mikaela Berthiaume from MCR Labs

INTRODUCTION

Fungal Speciation identifies the probable cause of a Yeast/ Mold failure in cultured organismal testing. In yeast/mold culture testing, the sample is incubated in a yeast/mold growth medium, and organisms begin to grow if fungal spores are present within the original sample. In some cases, there may be multiple organisms identified in a single sample. 

Speciation also refers to a process within evolution that leads to the formation of new and distinct species. However, many species can look very similar or even identical to one another despite having different genetic sequences. The term cryptic species refers to different organismal species that cannot be visually distinguished.

METHODS

Cells from unidentified yeast and mold colonies are taken from a cultured medium and DNA is extracted from the constituent cells. The DNA is then amplified using polymerase chain reaction (PCR) to generate vastly more copies of that DNA. Those copies are then sent to a third party laboratory that sequences those DNA copies and provides the genetic code. 

Molecular barcoding is the process by which organisms are identified by their unique genetic sequence. A DNA barcode is a unique pattern of DNA sequences that identify living organisms. That genetic code is then compared to the DNA sequences of known microbes. 

DNA extraction- 

This step is where the organismal cells are opened up and DNA is released. That DNA is then cleaned up and separated from cells, organelles, and other organismal debris. Once cleaned up, the DNA can then be amplified.

DNA amplification- 

Polymerase Chain Reaction (PCR) is a fast and inexpensive technique used to copy or amplify segments of DNA. Samples are heated to denature DNA into single strands. Taq polymerase enzymes build two new strands of DNA using primer sets and the original strand as a template. This then creates duplicates of original DNA with one old strand and one new strand each. Each of those strands are used to create two new copies and so on. 

Sanger sequencing- 

In this step, the amplified DNA is analyzed to produce a DNA sequence. A DNA sequence is the string of genetic building blocks (i.e., nucleotide bases) that comprise a particular  DNA molecule,  providing scientists with specific  genetic information.  BLAST- Basic Local Alignment Search Tool (BLAST) is a computer algorithm available for use at the National Center for Biotechnology Information (NCBI) website, among others. BLAST can rapidly align and compare a queried DNA sequence with a database full of sequences, providing the researcher with a list of species-specific genetic matches. This feature makes BLAST a critical tool in ongoing genomic research.

RESULTS

Helping Clients 

When fungi are found in Cannabis crops remediation is often sought out. There are a lot of remediation practices that will reduce most microbes, however not all practices work for all microbes. For example, some are resistant to UV radiation, and others are resistant to bleach. The best way to tell what species you are dealing with in a contaminated crop is by identifying exactly what the culprit is so you can remediate in proper ways. We can also help to observe practices in the operation to see if the contamination is due to human error, products, environmental factors, or others. 

Speciation can also tell whether bioremediation practices have created more of a problem than a help. However, when the proper environment for the original pest to grow is right that means its a good environment for the bio remediator to grow in as well, and as the original pest dies off they provide a food source for the bioremediation organism and they can cause more harm than help if not properly minded. Once results come back we can determine the species that caused the failure in the Yeast/ Mold cultured organism test and compare it to the bio remediation being done in the grow.

DISCUSSION

Tracking Common Species for our Clients

With the data collected we can see if clients have similar or the same species at certain time frames of the year or if the species is brand new to them. This can help to understand why the organism(s) are popping up in the grow and the best remediation practices. Trend data such as this can also help to pin point contaminated products coming from manufacturers. Speciation data can also be used for if a client is to have the same species present in their grow after eliminating it before, other remediation options can be addressed or the client will already know exactly what to do in order to eliminate the problem.

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