Fungi in Vermicompost

Over the past year and half Aggrego Data has started offering fungal sequencing along side bacterial sequencing. This was always the plan, but trying to research and provide insights into two whole domains of life at once was a bit overwhelming. I'm proud to say that we now have pretty good handle on a broad diversity of both bacterial and fungal communities found in vermicompost and soils. Between both bacteria and fungi we have around 1,150 literature references that we use to characterize and describe all of these organisms. It continues to be updated as we identify unseen organisms in new samples we receive. Also, a shoutout to Sean Bremner, who has been doing most of the fungal literature collection and summarization.

What fungi are not in vermicompost (AMF)

I'm going to start with what I have not seen in vermicompost, and that is arbuscular mycorrhizae fungi (AMF). They would be easy to identify in sequencing data because all species belong to a single phyla of fungi, Glomeromycota. These are the most well known beneficial fungi as they are found globally in association with about 80% of all plant species. Arbuscules are the tree like structure that form inside of plant root cells (seen below, right) that allow for rapid nutrient exchange between the fungi and plant.

AMF are essentially an extension of the plants root system, transporting nutrients like nitrogen and phosphorus and providing pathogen protection. They also produce glomalin, a recalcitrant iron containing protein that acts as a super glue, helping with soil aggregate stability and water infiltration.

Pictures of stained arbuscular mycorrhizae fungi colonizing lettuce root. (Courtesy of Takeshi Sentoku @amf_sentoku on X )

It's not surprising that these organisms are absent from vermicompost because they are obligate syntrophs of plant roots. This means they are entirely dependent on plant roots for growth and reproduction and even lack genes to degrade organic matter like most other fungi. It's even said that if you leave soil fallow for too long with no plants growing the AMF population could be depleted after a time.

Fungi Found in Vermicompost

I'm going to take you through a fungal community from a vermicompost sample seen below which is fairly representative of the samples I've tested so far. Pretty much all of the samples are dominated by the phyla Ascomycota which is not surprising simply because this phyla contains the largest amount of fungal species.

Organic Degraders

The majority of fungi found in vermicompost I would not describe as plant growth promoters, but rather complex organic degraders. These guys specialize in breaking down lignin and chitin.

Example fungal community from a commercial vermicompost sample.

Chaetomiaceae

The family Chaetomiaceae account for 61% of the sequences (dark red). These fungi are This family also contains well known thermophilic fungi so they might survive a thermophilic precomposing process.

Given these characteristics ,it's not surprising to find these organisms usually dominating the fungal community of worm castings. There are some plant growth promoting fungi with in this family. especially in the genus Chaetomium (10%).However, at the species level we see organisms like Humicola ampulliella (11%), Chaetomium longiciliatum  (10%), and the genus Staphylotrichum (30%); there is no specific published literature demonstrating plant growth promoting properties.

It's not that these organisms are bad, at the very least they still likely provide disease suppression and organic degradation in soils. In many cases there just was not much information at all about these specific species and we might just need to wait for more research to full understand their benefits related to plants.

Fusarium

The Fusarium genus is probably the most interesting group of organisms that is commonly found in the vermicompost samples we have tested so far. This genus currently contains 431 species and 3558 unclassified isolates and hybrids. These organism are notorious plant pathogens causing root rot, crown rot and blight; but fear not they are more than likely plant growth promoters or neutral organisms.

Fusarium spp. A-c Top and reverse colony of Fusarium species. d Appearance of pycnidia in MEA. e, f Chlamydospores g Appressorium h-q Conidia. Scale bars: d = 2.5 mm, e-q = 10 μm.(https://fungalpedia.org/glossary/fusarium/)

In our example sample above we the genus Fusarium at 7% abundance. We usually find this genus contains the species species F. variasi (5%), F. oxysporum (2%), and F. equiseti (0.05%).

F. variasi does contain pathogenic strains but it has also been correlated with increased phosphorous uptake in plant indicating a mutualistic symbiosis with the plant. It's thought that is solubilizes iron bound to phosphorous using siderophores (special iron chelating molecules) which makes both iron and phosphorous plant available.

F. oxysporum is one of the better known fungal plant pathogens, but it is a ubiquitous soil-borne fungus. It is now considered a "species complex", that includes both pathogenic and non-pathogenic strains which are difficult to distinguish between. Importantly, the majority of isolates found in soil are non-pathogenic. These widespread non-pathogenic strains are often recovered from asymptomatic plant roots and can colonize plant tissues as endophytes without causing disease. Non-pathogenic strains offer benefits to plants, primarily by acting as biocontrol agents against pathogenic fungi, (e.g., inhibiting mycelial growth or reducing disease incidence and severity,). Some non-pathogenic strains have also been shown to promote plant growth and yield.

Similar to the other two species, Fusarium equiseti exhibits a complex, dual nature regarding plant growth. It is recognized as a phytopathogenic fungus causing various diseases, including wilt in plants like pepper, tomato, and chickpea, as well as root rot and seed decay in others. However, it also functions as a natural root endophyte and plant growth-promoting fungus (PGPF). Specific isolates can act as biocontrol agents, for example, effectively controlling Fusarium wilt of spinach or stimulating growth and reducing root rot in pea. This highly variable impact depends heavily on the specific fungal isolate, the host plant, and the environmental conditions.

For transparency, Aggrego Data classifies these types of organisms as both potential pathogens and plant growth promoters in our fungal reports.

Penicillium

The organisms from the penicillium genus is found pretty much everywhere. It is one of the most common spores found in residential air, they are responsible for the majority of food spoilage, and is best known for producing the antibiotic penicillin discovered in 1829. A few species are cultured commercially for agricultural inoculants and other can be plant pathogens. Again, lot going on here for a single genus.

Computer illustration of Penicillium roqueforti. (Katernya Kon/ Science Photo Library)

In terms of what we've seen in vermicompost, the most abundant and common spieces from this genus are P. oxalicum and P. roqueforti which we see at 7% and 6% in our sample above.

P. oxalicum

This species is a ubiquitous fungus found in diverse environments like soil and air. In soil, it's a key phosphate-solubilizing fungus, releasing insoluble phosphorus by secreting organic acids.  It also aids in bioremediation, tolerating and reducing heavy metals (lead, chromium) and degrading contaminants like the anti-microbial Triclosan. For plants, P. oxalicum acts as a potent plant growth promoter, enhancing nutrient uptake and growth. It's also a biocontrol agent, inducing systemic resistance against diseases (e.g., downy mildew, tomato wilts). While it often lives as a beneficial endophyte in plant tissues, it can also act as a pathogen, causing diseases like stem and fruit rot.

P. roqueforti

Penicillium roqueforti (pcitured above) shows significant promise as a plant growth-promoting fungus, particularly in soils contaminated with heavy metals. Research indicates it can enhance stress tolerance and induce resistance in plants by restricting heavy metal transfer (Ni, Cd, Cu, Zn, Pb) from soil to plant tissues. This fungus also improves nutrient uptake (Mg, K, Na, Ca) and promotes overall plant growth via auxin production (shoot/root length, biomass, chlorophyll). Interestingly, it is also used to make blue cheeses like Roquefort and Gorgonzola. There is no evidence of it being a plant pathogen.

Aspergillus

 Aspergillus is the last genus of fungi I am going to talk about that is commonly seen in vermicompost. It is in the same family as Penicillium (Aspergillaceae) and similarly are found globally as mostly as common molds with 837 documented species. Some of these species are found to be plant growth promoting fungi in soils but others are opportunistic plant pathogens.

Agar plates and microscope images of Aspergillus fumigatus

Aspergillus fumigatus

Aspergillus fumigatus (1% of this sample) is a highly versatile fungus vital for nutrient recycling in compost and soil, thriving as a dominant, heat-tolerant decomposer. It is considered a powerful plant growth-promoting fungus as it significantly boosts plant development by producing vital phytohormones like IAA and gibberellins and enhances nutrient availability via phosphate solubilization, siderophore production, and nitrogen fixation.

Unlike most of the other fungi we have talked about this species does not seem to have a risk of plant pathogenesis. However, it is known to cause infections in immunocompromised individuals.

Some closing thoughts-

When I first started looking at fungal communities, on the surface, I thought it was much simpler than bacterial communities. There appears to be much less fungal diversity compared to bacteria, however, there is a lot of fungal complexity past the genus level with hundreds of species in a genus. Even beyond the species level of identification organisms can be quite different.

There is still a lot of work to be done to discern between potential pathogens and plant growth promoters. In some cases it maybe genetic factors we can identify, but other factors like environmental conditionals and plant health also seem to determine the nature of fungi/plant relationships.

There will be more to come about fungi as we collect and analyze more data. This is really just a small sampling of the more common organisms. If you have any questions please ask.