Category Archives: Uncategorized

Pathogen-Reducing Compost

January 14, 2020

Benefits of compost are widely known: 1) enhances water holding capacity, soil structure, organic matter, drainage, and nutrient holding capacity of soil, 2) provides a source of beneficial microbes, 3) decreases both inputs (to your garden) and outputs (from your garden), a plus for sustainability, and, 4) reduces fertilizer and pesticide use.

However, did you know that well-made compost has the ability to reduce pathogens and enhance plant growth?

An extensive research study of 120 bioassays, involving 18 composts and seven pathogens, found positive disease suppression in 54 percent of the treatment combinations, a disease stimulating effect only rarely (3%), and no effect in 43 percent of the treatment combinations (Termorshuizen et al., 2006).

Other studies have shown that “backyard” compost is superior to the commercial product, possibly due largely to richer and varied starting materials, plus a more relaxed thermophillic phase (wherein temperatures are sanitizing but lower than those recorded in commercial composts). Backyard composting presented higher counts of bacteria, actinomycetes, and fungi. It also shows higher percentages of isolates producing extracellular enzymes which allow the breakdown of tough substrates, including polyethylene!

Although the studies show the efficacy of compost, no one has come up with the perfect recipe or management strategy to combat a particular soil pathogen. This is because the soil microbial community is so dynamic and complex. Quality control tools are also lacking.

Still, we know from research that microbial organisms in compost are able to reduce pathogens my means of: direct antagonism (antibiotic production and direct parasitism), predation, competition for resources, enzyme production, and, induced resistance in plants – through signaling networks and hormones.

Sun, Jan 19, 2-4. work party
Sat, Feb 1, 10-12, Work Party
Sat, Feb 1, 1-3, PRUNING CLASS
Sun, Feb 16, 2-4, Work Party
Sat, Mar 7, 10-12, work party

Note, compost is more effective as a pathogen prevention method than when used as a management strategy for some existing soil or plant pathogen. Elaine Ingham, veteran soil scientist, points out that compost and soil should be colonized with a sizeable and diverse body of microbes. “There are only so many seats at the table. If the good guys are already there, the bad guys are turned away.”

Image Credit: Zosia Rostomian & Jill Banfield, Creative Services, Berkeley Lab

Who are these microbial actors who play such a beneficial role in a garden? It’s bacteria, fungi, protozoa, and nematodes, none of which can be seen with the naked eye. There are millions of microbes in a gram of compost and hundreds of thousands different species. In fact, it’s the diversity of players that makes good compost a pathogen suppressor.

Commercial composts can differ widely in their suppressive effects and can vary as to which pathogens are diminished. However, commercial composts can meet the objective of adding organic matter to the soil. In contrast, the special compost that you can produce with backyard composting, using correct temperature, moisture, aeration and curing processes, will yield a compost that you can use sparingly as an inoculum throughout your garden. It will jump-start good soil biology and maintain nutrient cycling, creating an environment fostering pathogen-suppressive soil.

Next up – A template on making a thermal compost.
Also, watch the calendar for a hands-on thermal composting class, coming in early May, 2020



Hadar & Papadopoulou, 2012 – Suppressive Composts: Microbial Ecology Links Between Abiotic Environments and Healthy Plants DOI: 10.1146/annurev-phyto-081211-172914

Vaz Moreira et al., 2008 – Diversity of Bacterial Isolates from Commercial and Homemade Composts. DOI: 10.1007/s00248-007-9314-2

Welgarz et al., 2018 – Microbial diversity and nitrogen-metabolizing gene abundance in backyard food waste composting systems DOI: 10.1111/jam.13945

Fayolle , L., 2006 –  Eradication of Plasmodiophora brassicae during composting of wastes

Cangelos, G, 2014, Dead or Alive: Molecular Assessment of Microbial Viability DOI: 10.1128/AEM.01763-14

Your Hori-Hori Could be Harboring Clubroot

November 26,  2019

I meet weekly with the DirtLife group at Sound Bio Lab. Other members are scientists who are also interested in soil. We are designing a community-based science project so we surveyed the Seattle P-Patch gardeners, via their listserve. Fifty responded. Gardeners are interested in microbial diversity, effective composting and concerned about soil-borne fungal pathogens, especially clubroot.

A few months ago we began reading peer-reviewed research articles on these topics. We will develop a project that will:

Make use of the lab resources available at SoundBio
Provide a tangible benefit to Seattle urban farmers
Integrate SoundBio and community volunteers in carrying out the project

In the meantime, after reading well over a dozen research articles, I thought I would share mentioned cultural practices that are important to minimize the impact of clubroot (Plasmodiophora Brassicae or P. Brassicae) and its spread. For details about this pathogen see the Club Root Summary doc on our Library page.

At FECO, we have adopted most of the preventative measures listed below.

Prevention of clubroot

Don’t plant brassicas within 7 years after an infection. P. Brassicae resting spores can live 20 years, but have a half-life of 4 years. See OSU Pub 9148 pdf in the Library Page. It lists crops and weed hosts.

Rotate brassica crops (only effective for soil and root pathogens like P. Brassicae that are biotrophic and have a narrow range of hosts).

Favorable conditions for the pathogen include warm, wet soils (optimal temperatures between 68ºF and 80ºF) and the infection period is most likely within six weeks after planting. June and July sowings, if clubroot is present, can increase incidence and severity of the disease.

Keep plants healthy; they have incredible defense mechanisms.

Develop disease-suppressive soils by introducing organic matter (OM). The benefits accumulate across successive years leading to improved soil health and structure.

Try clubroot-resistant cultivars but they may or may not work. Studies show that P. Brassicae can rapidly erode the resistance of a newly-developed resistant cultivar. In other words, it quickly morphs into a new pathotype that conquers the resistant cultivar.

You can try adding calcium carbonate (“liming”) to reduce the likelihood of resting spore germination. This is a very complex, and a bit controversial, issue. At soil pH higher than 6.5, iron and zinc are less available to plants.
A group of farmers from Alberta (where canola is grown) were surveyed and they did not follow appropriate protocols. In the Library is an OSU Pub 9057 that outlines how to incorporate lime – based on soil type, and also how to monitor pH before and after application. Soil pH lab tests, including the important pH buffer test, only cost $5.20 at Northwest Agricultural Consultants.

Sat, Dec 7, 10-12, Work Party
Sun, Dec 15, 2-4, Work Party
Sat, Jan 4, 10-12, Work Party
Sun, Jan 19, 2-4, Work Party

Cultural Practices

Infected transplants are the most prevalent source for the spread of pathogens into an uninfected area. Flats of transplants from greenhouses should not be placed on the soil to harden off. Reused trays are reported to be a high risk for pathogen contamination.

Knock off soil from all tools, boots, gloves at the location where you were working the soil.

Brush off and/or wash any remaining mud or clinging soil.

If you know the disease is present, disinfect tools etc with a 2% concentration of sodium hypochlorite bleach (mix an amount of regular 6% household bleach with twice that amount of water). Note: You can’t disinfect a tool with soil on it. Soil cannot be disinfected this way.

Consider pavers or tiles in beds when it’s necessary to step into the garden bed.

Avoid excess watering and ensure good drainage.

Use mulches to physically isolate above ground plant parts from contact with the soil.

Plant cover crops. When incorporated into the soil, residues from some cover crops release chemicals that either directly inhibit pathogens or enhance soil microbe populations that can compete with pathogens.

Infected plant disposal

Dig those infected plants out! Digging is better than pulling, to get most or all of the root system. Use a sack so spores can be contained.

I must have read 11 articles that said, “Dispose of infected soil and plants properly.” Isn’t that helpful. I had to hunt for this information:

Infected plants can be thermally composted with temperatures of 122ºF for 7 days or 140ºF for one day, if the pile is maintained at 50% moisture (squeeze a handful of compost and drops of water should exude).

You can put the plants in your yard waste because it goes to a facility that uses thermal composting. However, be aware of the risk of leakage from your plot to the compost facility.

Infected plants can be put into your pressure cooker with water, then cooked on high for 30 minutes. After this has cooled, open the lid, stir, then repeat the cooking. That’ll get ’em.

Soil, shaken from the roots of infected plants, plus soil from brushing/washing off tools, can be buried 12 inches. The hole should not be where flooding will occur and it should remain undisturbed. (You will have to dig a new hole next year.)

Research indicates that good cultural practices can serve well to fight this and other soil-borne pathogens, and these practices are well within our control.

If you have a history of success with other sanitation/cultural practices, please share them via the comments section.


Koike, S, 2003, Vegetable Diseases Caused by Soil-borne Pathogens, Pub 8099

Gossen, B.D., 2012, Effects of temperature on infection and subsequent
development of clubroot under controlled conditions

LeBoldus J.M., 2012, Adaptation to Brassica Host Genotypes by a Single-Spore Isolate and Population of Plasmodiophora brassicae (clubroot) › doi › pdf › PDIS-09-11-0807

Burnett, F., 2013, Management of clubroot (Plasmodiophora brassicae) in winter oilseed rape

Buriel methods – disposal practices – plants and animals
Texas A&M Agrilife Extension

Preventing Clubroot – Agricultural Sanitization
2019, Government of Alberta

L. Fayolle, 2006, Eradication of Plasmodiophora brassicae during composting of wastes

Are Those Freckles?

October 18, 2019

Not Freckles. Dimples? Not dimples. Bitter pit. It’s a bothersome disorder, common in  Honeycrisp apples. In the cells of this apple, there is more air space and more pores than in normal apples. The pits are manifestations of clumps of dead cells. The scanned photo of an apple shows fewer veins in the calyx (bottom) of Honeycrisp, which is why bitter pit tends to show up near the bottom.

Lee Kalcsitis, WSU Assistant Professor, Tree Fruit Physiology, writes: Honeycrisp naturally have bigger cells than most apples. That seems to predispose them to structural degradation associated with bitter pit. And trees that have access to extra water allow those cells to grow even bigger, while limited water during the later stages of fruit growth can keep the fruit cells a little smaller and more stable.

Sun Oct 20, 2-4, Work Party
Sat Nov 2, 10-12, Work Party
Sun Nov 17, 2-4, Work Party
Sat Dec 7, 10-12, Work Party

Calcium binds up pectins which translates to the glue that holds the cells together. That glue helps to resist bitter pit but it breaks down as the apples mature. The glue breaks down faster in fruit with less calcium.

However, calcium is one of the most immobile nutrients. When leaves pull up water from the roots, calcium also travels up. Since the leaves transpire more water than fruit, they get the bulk of the calcium. (Cork spot in pears and tomato end rot have the same issue in that the calcium may be in the soil but it’s not necessarily in the fruit tissue where it is needed.)

The strategy for commercial growers is to withhold water, without stressing the tree, and apply calcium sprays. Still, results of these techniques are highly varied. Crop load is also an important factor because, if there are a small number of fruit, they will be large and more susceptible to bitter pit. On the other hand, too many apples can cause fewer blooms the following season.

My strategy: eat them when they are ripe! (Storage time increases the pitting.)


additional resources:
Calcium Absorption during Fruit Development in ‘Honeycrisp’ Apple Measured Using 44Ca as a Stable Isotope Tracer. L Kalcsits, G van der Heijden, M Reid, K Mullin – HortScience, 2017

Advanced sensing techniques for analysis of elemental concentrations associated with bitter pit in apple. Zúñiga CE, Jarolmasjed S, Kalcsits LA, Sinhal R, Zhang C, Dhingra A, Sankaran S*. 2017. Postharvest Biology and Technology 128, 121-129.