Biological Research


Soil and Root Health

Fumigation phaseout is forcing farmers and researchers alike to revisit our knowledge and understanding of soil and root health.  Methyl bromide (MeBr) and other fumigants have provided a growing environment in the soil that is essentially free of soilborne pathogens, weeds and nematodes.  In addition, methyl bromide has greatly minimized risk during the growing season.  In MeBr-fumigated fields, strawberries grow and produce in a very consistent manner, mitigating much risk taken by growers who invest an average of $25,000/ac to plant a strawberry crop.  Alternatives must provide a level of reliability equivalent to the investment made.

Soil health can be defined as “the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans (NRCS, 2014)”.

Root health is a response to the interaction of the soil environment and the plant genetic traits, which ultimately translate into overall plant health and productivity.


In California, both conventional and organic growers regularly apply compost.  Compost production occurs at the commercial scale with several large operators offering delivery and even spreading services.  Safe and prescribed practices haven been established by the California Compost Council, which include permits along with regular temperature and turning reporting requirements. While the many benefits of compost to soil are well known, little is known about the differences between different types of compost available to the growers.

We have identified four local sources of compost of uniform quality, available at a reasonable cost to strawberry growers on the central coast: yard trimmings (municipal waste) compost, dairy manure-based compost, spent mushroom compost and vermicompost.

Compost types
Four composts used for this study, from left to right: composted yard trimmings, composted steer manure, vermicompost, and spent mushroom compost.



Compost Characterization

Compost Characterization

Our first step is to characterize the composts based on physiochemical and microbial properties.  All analysis are done on finished compost that is ready for field application.

Compost Physiochemical Properties

Mushroom Compost
Manure Compost
Yard Trimmings Compost
Nitrate-N (ppm)1202346.6502
Total N1.911.52.5
EC (dS/m)4.8284.57.1
Application methodBroadcastBroadcastBroadcastApply to rootzone
OMRI Approved


Total bacterial and fungal abundance are measured by culture-based methods, using dilution plating of each compost.  Mushroom compost had the greatest abundance of both bacteria and fungi while vermicompost had the lowest abundance of bacterial and fungi.  This information only tells us about culturable abundance and does not inform us on diversity or identification of species, which are also important.

Screen Shot 2014-07-27 at 8.57.13 PMBacterial and fungal abundance of four different composts (above).  Total colony forming units are enumerated after several days of incubation on bacterial- or fungal- selective general media.   

Screen Shot 2014-07-27 at 8.47.35 PM

Total microbial activity  (above) of both fungi and bacterial can be measured using hydrolysis of fluorescein diacetate. Means comparison shows highest microbial activity in yard trimmings compost and lowest activity in manure compost.

Interestingly, similar trends were found in our field trials where each type of compost was added to a commercial field in five different locations. In this case, compost (30T/A) was added to four replicate plots, incorporated to approximately 8″ then sampled using a 4″ core sample two weeks after application.

Microbial activity in 5 fields

Microbial activity of field soil amended with compost (above).  Five field trials, described by location, were established in which four types of compost were amended into field soil.  Two weeks after incorporation, soil microbial activity was measured by FDA hydrolysis, resulting in three levels of activity- high, medium and low.  In all fields, compost increased microbial activity compared to the control.  Regardless of the native soil, the effect each compost bestows on microbial activity is similar. In the methyl bromide fumigated field (MB, Central Coast), microbial activity was significantly greater than all other fields.

Disease Suppressive Soil

Disease suppressive soil is a well-known phenomenon in which soilborne diseases fail to develop in spite of high infestation levels.  Qualitative and quantitative changes in the soil microflora are generally regarded as the key suppressive mechanism. Some soils are naturally suppressive, however, suppressiveness can be induced by the addition of soil amendments such as compost. Previous work shows promise for managing Verticillium wilt with compost.  Specifically, reduced wilt on several host crops has been effected by compost, microbial antagonists of V. dahliae have been identified in vitro, and strawberry roots have shown preferential colonization by V. dahliae antagonists.

To evaluate disease suppression, we use two assays described below.

Suppression of Verticillium dahliae

The effect of compost on infection by Verticillium dahliae, the cause of Verticillium wilt, was evaluated by growing strawberry crowns in soil amended with compost and inoculated with V. dahliae. After three weeks, plants were removed and 150-200 cm of roots were placed on a semi-selective medium and evaluated for root infections (image below). Roots grown in vermicompost and steer manure compost had the fewest infections whereas those grown in yard trimming and spent mushroom compost had the most infections. One possible explanation for the observed differences is the extent to which compost elevates the activity of microorganisms in soil that compete with V. dahliae for root niches and/or nutritious root exudates.

Screen Shot 2014-07-27 at 9.36.03 PM
Frequency of Verticillium dahliae strawberry root infections when grown in different composts (above).  

Suppression of Pythium ultimum

In the case of strawberries, Pythium ultimum is part of a disease complex called Black Root Rot.  This complex results in numerous root lesions causing parts of roots and rootlets to die, compromising overall health and productivity of plants. While this disease does not often lead to plant death, the plant stunting and reduction in yield can be severe.  This is predominantly  a problem in non fumigated soil, such as organic fields.  Compost has been evaluated for suppression of P. ultimum in many research trials with positive results; therefore, we wanted to evaluate our four commercial composts.  To do so, cucumbers are used as a surrogate crop since they are  sensitive to P. ultimum and can be grown quickly and easily under greenhouse conditions, unlike strawberry crowns.  Potting soil is amended with 20% compost, spiked with P.ultimum, and sown with surface sterilized cucumber seeds.  This work is still underway.


Potting soil amended with composts (above).  Potting soil is amended with 20% compost and sown with 20 cucumber seeds.  After 2 weeks, surviving seedlings are counted.  From left to right: Vermicompost, control (no added compost), composted yard trimmings, composted steer manure and spent mushroom compost.

Root Development

Scanning rootsRoot health and development are critical to overall plant health and productivity.  The 30-40% productivity gap between fumigated and non fumigated soil is not well understood, but is potentially due to root health. Therefore, we are investigating root development in soils under different production practices, including organic and methyl bromide fumigated.

To measure root development, we take 4″ soil cores, separate the roots from the soil by sieving, generate an image using a computer scanner and analyze the total root length using WinRhizo software.



Screen Shot 2014-07-27 at 9.44.28 PM

Root Development in cultivar Chandler in a commercial field amended with different composts (above).  The treatment “control + N” is a nitrogen control in which we add nitrogen from a non-compost source, like cottonseed meal, to an amount equivalent to the greatest N found in a compost.  In this way, we can attempt to separate whether effects are due to nitrogen levels or other factors. These data were taken in May 2014, approximately 6 months after planting.  Please visit our blog to see a short video of how we sieve roots.


Field Trials: Evaluation of Composts

Midseason results- Evaluation of four composts on strawberry production on a commercial farm in Sacramento, CA.

UCCE Strawberry Field Day Meeting March 27, 2014 Sacramento UCCE Office, led by farm advisor Chuck Ingels.

Sacramento Grower Meeting 3/27/14

Sacramento Grower Meeting p2 3-27-14Sacramento Grower Meeting p 3 3-27-14