Monday, February 15, 2016

Primary vs. Secondary Decomposing Mushrooms

Shaggy manes, a great example of secondary decomposers
There are many different kinds of mushrooms out there, classified by their source of food. Parasitic mushrooms attack living organisms. Mycorrhizal mushrooms form a symbiotic relationship with plants, trading nutrients for sugar. But when it comes to the world of mushroom cultivation, the real species of interest are the saprophytes, the mushrooms that decompose dead tissue. But even those come in several different varieties. There are primary, secondary, and tertiary decomposers. Tertiary decomposers are mushrooms that live in soil, scraping out a living on the little scraps of nutrition they can find here and there. Very few are of culinary significance. Primary and secondary decomposers, on the other hand, are the species that compose the majority of our culinary mushrooms.

When a tree falls in the forest, it is the primary decomposers that move in and start the process of turning the body of the tree back into soil. Think about the trunk of a tree. While the tree is alive, there isn't much living inside the tree, besides the tree, of course. Plus, it is made of solid wood (weird how that works, eh?) and most living creatures can't penetrate through to get to the energy stored in the wood. Fungal species are quite adept at it, though, and among the mushrooms, there is still lots of competition for any new food source. Once the primary decomposer detects an available food source, it throws all its energy towards occupying it. Growth is very rapid and it grows a huge amount of tissue in a fairly dense concentration.

Once it has colonized what it can grab, the primary decomposer produces a flush of mushrooms, then proceeds to decompose as much of the food source as it can.
Chunk of wood that has been fully decomposed by white rot
fungus, still looks like wood
However, primary decomposers are not particularly complete in how much they decompose. Most are either brown rot fungus, which means they decompose the cellulose and leave the lignin behind, or white rot fungus, which means they decompose the lignin and leave the cellulose behind. Either way, the wood still looks pretty much like wood when the fungus is done with it. It is just a whole lot softer and lighter.

The secondary decomposer moves in and picks up where the primary decomposer left off. It certainly feeds on the cellulose and/or lignin that is left over, but it also decomposes the other compounds present in the tree.

The biggest difference between the two is the type of environment they prefer to grow in. The primary decomposer is adapted to the inside of a freshly fallen log. They prefer an environment with little to no competition. They produce ideally on pasteurized sawdust, straw, or something similar. Secondary decomposers are a little different. In nature, once the primary decomposers have finished, insects, soil bacteria, and all kinds of other organisms have started invading. It provides a richer micro-ecosystem. This is the preferred habitat of the secondary decomposers. Some won't even produce mushrooms in sterile substrate. Several even prefer a well-composted substrate that still has some woody/fibrous components to it.

The same piece of wood as above, just squeezed to show
how soft it is. It is ready for a secondary decomposer
As for how to tell the difference, just look at the growing requirements. If the mushroom will fruit off of just sawdust, vertical or horizontal surface, it is probably a primary decomposer. If it requires a casing layer and only fruits from a horizontal surface, it is probably a secondary decomposer. Examples of primary decomposers are shiitake (Lentinula edodes), oyster (both Pleurotus and Hypsizygus species), reishi (Grifola frondosa), and pioppino/black poplar (Agrocybe aegerita). Examples of secondary decomposers are button/portobello (Agaricus brunescens), king stropharia (Stropharia rugoso-anulata), and shaggy mane (Coprinus comatus).

Considering my current projects, what are the implications of this information? Well, the main thing is that when mixing mushrooms and gardening, the information about what habitat the mushrooms like is very important. So when you are doing it in aquaponics, like I am, there need to be some minor adjustments to how you do it. For example, if you are doing traditional aquaponics, using media, primary decomposers are going to be your best bet. But rather than sawdust/woodchip blocks, which is the usual preferred method, partially buried logs would be best. The worms would gobble up the blocks too soon, whereas they would do no appreciable damage to the logs.

On the other hand, if you are doing aquaponics with soil, both primary and secondary decomposers can be used. The primary decomposers will still do better in logs, but the active soil in an aquaponics system can be really beneficial for secondary decomposer mushrooms. Plus, they would add additional filtration for the water.

A little over a year ago I created a woodchip bed in my aquaponics system using king stropharia mushrooms. The results were better than expected. They obviously thrived in that environment. I intend to keep experimenting as often as I can manage. I think there are great combinations out there yet to be discovered.


  1. This is awesome! I wanna try this once I get the system up and running. I wanted to ask you if you could make a short video walkthrough of your setup, I understand it's a basic CHOP system but would still appreciate a more thorough representation. I also have a question regarding additional mushroom beds; since they are still in the loop with the rest of the system do you drain them to one central sumptank or they have their own?
    I also wanted to ask if you used a water siphon for draining and also what type of fish is working in your system.

  2. Video is probably not a bad idea. Not sure when I will get to it, though. As for multiple beds, I have two. Both share a main tank and a sump tank. For larger systems, you could go either way. I am currently considering building a larger system with 4 beds. At this point, I want to do either 2 or 4 main tanks, but all would share the same sump. That would keep all of them on the same water system and help average out demand.

    And no, I don't use siphons. They are a dubious idea for traditional aquaponics and a fairly terrible idea with soil. They would plug in a matter of days. Mine has a direct drain with a filter and a cage and it still has trouble with occasional plugging.

    As for fish, I have blue tilapia.

  3. Awesome post! I'm a longtime reader and marine biologist, and your systems fascinate me. One question - are secondary fungus also mycoryzal? If not, what do they eat? Or can they exist simultaneously with primary desomposers on the same log? Or do you add wood that a primary decompose is already done with to the soil?

  4. That is actually a pretty good question. The easy answer is no, they decompose the remaining organic matter in the log. The harder answer is...maybe. Certain mushrooms, likey elm oysters (Hypsizygus ulmarius), which is a primary decomposer, have been shown to increase the growth of plants in their general area. The question is, do they do so because of the increased availability of local nutrients, or do they do so because they have worked out a sort of mycorrhizal arrangement with the plants for direct barter? I think more research is necessary, for sure.

    As for most of the secondary decomposers, there is still plenty of complex organic molecules in the leftover wood after the primary decomposers get to it. They just go afte a wider variety of compounds than the primary decomposers do, and they probably help break down the bodies of the primary decomposer fungus as well.

    As for existing simultaneously, not really. Mushrooms are pretty possessive about their food sources and have a variety of techniques to keep what is theirs. Most mushroom growers will sequence the mushrooms. When the primaries are done, they pasteurize and then inoculate the secondaries.

  5. Thanks for the response! So, in an aquaponics system, are you adding both logs for the primary decompsers, and a secondary to the soil?

    I'm sort of fascinated by this, as many of the best mushrooms are mycoryzal and not saprobic, or at least have different growth stages that are mycoryzal. I'm thinking here of, say, morels, which are real tough to cultivate. But like you say, what happens if you grow them in a soil based aquaponics system?

  6. Yeah, basically. Currently my system isn't big enough to support large logs, but the "finished" logs I have tossed in have almost universally produced more mushrooms. I grew king stropharia mushrooms (an avowed secondary decomposer) last year and they did great. So as I move forward, I am really looking forward to trying more combinations.

    The problem is that I live in the Phoenix area. Our late fall to mid spring weather is perfect for growing mushrooms, but our summer weather is not conducive to most varieties, being very hot and very dry. So I have a limited ability to experiment.

    I agree that many of the best varieties are mycorrhizal, but I wonder about the ability to cultivate those in a system like this. Most form associations with tree in a fairly specific environment.

    I agree with you assessment on morels, though. I need to do more research, but there is certainly a possibility there. Morels are a tough one, but there are two of their growth requirements that would fit well with my system. The first is that they tend to fruit really well following floods. My system is flooded regularly. The second is that they tend to fruit really well following fires. I am going to start experimenting with biochar. Maybe they will respond to biochar similarly to how they respond to fires. It is all worth finding out.

  7. Ed, I am hooked to your blog. So much system thinking going on in it. Being an Industrial Engineer, I love seeing new ways to elevate system reliability, durability and increased efficiency accompanied with symbiotic relationships. You have inspired my soon to be aquaponics project to a totally new level.
    Thanks for your insightful blog.
    Keep up the good work...
    Shafak from istanbul

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