TITLE: FUNDIS Fungal Tissue Sampling for PCR
AUTHORS: Harte Singer

[DESCRIPTION]
How to sample dried fungi for PCR amplification

[STEPS]
SECTION: Tissue Sampling
9. Find a suitable place to conduct tissue sampling. A hard, nonporous surface that can be wiped clean with rubbing alcohol is ideal. Turn off any fans and close any windows so there is minimal air movement. Wash your hands and gather your materials and mushrooms for sampling. 
SECTION: Tissue Sampling
10. Set up one of the PCR tube racks and with very clean hands, remove each strip of PCR tubes from its package and close each of the lids before placing the strip into a row of the empty PCR tube rack. 
SECTION: Tissue Sampling
11. Using a sharpie, label the hinges of each PCR strip using the pattern depicted in the photo. Also label the first tube in each strip from 1-12 going from the top to bottom as depicted. Additionally, you can label the last tube in each strip with the plate number, so if this was plate number 5, the last tube on the right of each strip would be labeled 5. This is not depicted in this photo. 
 

SECTION: Tissue Sampling
12. Dip your tweezers into the alcohol and then wipe them using a piece of clean kimwipe. You don't need a whole square and can just rip off a small piece, but make sure to wipe the tweezers thoroughly and repeat this until you are confident they are clean. Alcohol will not destroy DNA, it just helps remove the debris on the tweezer. Most mushrooms don’t make a ton of debris, but be extremely careful with puffballs or any mushroom with a lot of powdery spores that tend to become airborne. It is best to save these specimens for the end of sampling to avoid potentially cross-contaminating  
 
 
SECTION: Tissue Sampling
13. Set tweezers down such that the tines do not come in contact with anything while you grab the mushroom.
SECTION: Tissue Sampling
14. Remove the lid from the tube rack, then remove the first strip of 8 tubes from the tube rack and place it in the second rack for sampling. The first tube on the left will have 1 written on it and the first hinge will be marked. 
SECTION: Tissue Sampling
15. Grab a box/bag of mushrooms and enter the accession number into the data entry sheet in the first corresponding cell.  Write the tube number back side of the voucher slip (i.e. 1-1, 1-2 … 12-8). 
SECTION: Tissue Sampling
16.  Open the box/bag of mushrooms and either reach in with the tweezer or take out the mushroom and place on a clean surface away from your tubes. Carefully remove a small piece of tissue. You will only need a piece about 1x1mm.  Hymenium tissue works best.  Gills, pores, gleba, apothecia etc. This tissue has a high density of DNA. It is critical that you only take clean tissue.  Any dirt, plant matter, or other contaminants will negatively impact the results. Take care not to cause too much damage to the specimens.  Just take your time and take as little as you can. Too much tissue will  negatively impact the results. Make sure you do this operation away from your tube rack to minimize the chance of cross contamination. The amount depicted in these photos is about the maximum amount of tissue you want to use
 
  
  
 
 
 


SECTION: Tissue Sampling
17.  Place the tissue into the open tube and release it, or gently tap/wipe the tines inside the tube. Remove the tweezer and place it aside to be cleaned and close the cap.  Static electricity can make samples stick to the sides of the tubes or make the bits of mushroom behave in a way you dont expect. Be mindful in your movements. 
 
 
SECTION: Tissue Sampling
18. Clean your tweezers and proceed with the next specimen.
SECTION: Tissue Sampling
19. Place each completed strip back in its row in the original tube rack and remove the next strip of tubes for sampling. 
SECTION: Tissue Sampling
20. 
SECTION: Sampling guide
1. Gilled Mushrooms - Sample a very small piece of the gill.
 

SECTION: Sampling guide
2. Mushrooms with pores - Sample a very small piece from the pore tissue

 

SECTION: Sampling guide
3. Cup fungi - Sample from the inner surface of the cup - the part that generally faces away from the substrate. Sometimes there will be a stalk and sometimes there isn't.
 

 

 

SECTION: Sampling guide
4. Inverted Cup Fungi - Sample from the exterior of the tissue on the end of the stalk
 

 

SECTION: Sampling guide
5. Truffles - Sample from the interior of the mushroom. Typically there will be one or more samples that are sliced in half.
 

 

SECTION: Sampling guide
6. Puffballs - These are similar to truffles in appearance, but contain a soft, often powdery interior. Sample the inner material, but be very careful to avoid releasing a puff of spores. It is a good idea to save these for last to avoid cross contamination. Avoid breathing spores. 
 

SECTION: Sampling guide
7. Crusts - These are mushrooms that are flat against a substrate. They can have many textures such as pores, teeth, or they can be smooth. In general, you can sample any part of these, but be careful not to dig into the substrate. Sample by scraping a bit of material off with the tweezers if the surface is completely flat. 
 

 

SECTION: Sampling guide
8. Bird's Nests - These are little cups that contain "eggs" called peridioles. Try to break apart a peridiole and sample that material.