Tools, tips, and terrible traditions for raised beds – Part 1

Raised beds a month after planting. Adult beverage not harvested here.

Many of us are sheltering at home during the COVID19 outbreak, and that might mean you’re spending more time in the garden. It certainly seems to be true based on my Facebook feed. And given that even more people are showing interest in growing their own food, I thought some practical posts on raised beds dos and don’ts might be fun. John Porter did a nice review of some of the misperceptions about raised beds last year, and that’s worth reading as well. This week’s post will be on siting and materials needed for building a raised bed. At the end of the post is a list of online resources with more information.

Trees to the south will shade vegetable gardens throughout the growing season.


To grow most vegetables, you need direct sunlight at least six hours per day, and more is better in terms of productivity. That means full, unfiltered sunlight, so that your seeds and plants get the entire light spectrum. You’ll need to take into account seasonal changes, like the sun’s angle and the appearance of deciduous canopies, before choosing your site.  If part of your bed will unavoidably be in the shade, simply choose plants that will tolerate part- or full-shade conditions for that location.

Building materials

Construction of raised beds. Carpenter contracting not available.

We use pressure-treated hemlock and Douglas fir for our beds, which measure 8′ by 22′ (at the outside dimensions.). Modern pressure treatment uses alkaline copper quaternary, which is nothing like the toxic chromium-arsenic cocktail from earlier times. You don’t have to use wood, of course – other materials will work but do educate yourself on any potential leaching issue into the soil.

Underneath the beds is….nothing. If our underlying soil was contaminated with heavy metals or some other material, we would put down a membrane first to keep our raised bed soil separate from the contaminated soil. But we have no issues, so it’s soil next to soil, meaning we have great drainage.

Planting media

Native topsoil stockpiled from construction project.

The best material for your raised bed is actual native topsoil (if you can find it). If you don’t have enough of your own, see if anyone locally is giving away “free dirt.” People who put in decks, ponds, and other hardscape structures often don’t realize their discarded dirt is real topsoil. Do be cautious with this potential windfall. Ask about pesticides or other chemicals that may have been used in the original landscape. And you should do an initial soil test to see your baseline nutrient values. It’s easier to incorporate amendments BEFORE you fill your beds.

There are exceptions to the native topsoil recommendation – for instance, if your soil is contaminated with heavy metals from industry or agriculture, you shouldn’t use it for growing edibles. In this case, you need to use a commercial topsoil, and isolate it from the underlying soil as described earlier. Commercial topsoils can be heavily amended with compost and other organic material, meaning you have much less actual soil and will constantly need to refill your beds as the organic matter decomposes. Try to find a mix with the greatest possible percentage of topsoil.

Read the label! Is there actually soil in potting “soil”?

The worst choice of all are soilless media. This includes nearly all bagged potting “soils” at garden centers. Read the contents panel carefully – does it say the word “soil” anywhere? If it’s all organic material, you are going to have to fill your beds every year. This is both expensive and time consuming. Plus you could very well have excessive levels of some nutrients that will build every year as you add more.

As you make your decision about what to fill your raised beds with, consider what you will be growing, If you are only growing summer crops, it will be easier to amend the bed every year. If you have a winter crop, or perennial herbs, you can’t incorporate more material without destroying the existing rhizosphere and your plants. Perhaps that means you need two raised beds, or at least have a divided system.


A U-shaped or keyhole design.

This part is really up to you! Raised beds should be high enough to work comfortably, big enough to hold what you want to grow, and narrow enough to be able to reach all the way across (for one-sided access) or halfway across (two-sided access).

We wanted a design where we could include a critter fence. Once in a while a deer might wander through our property, and rabbits certainly do. The hardware cloth fence keeps larger animals out and also provides a great trellis for beans and other climbers.

Gated garden and critter fence.

We opted for a U-shaped system, with a gate on one end. The inside edges of the beds are topped with 2×6 boards that can be used as a bench. We did run stabilizing boards between interior and exterior posts. They are buried and don’t really interfere with the plants. (Note to self – next time put those stabilizing boards in BEFORE filling with soil.)

What’s next?

Next time I’ll discuss some of my favorite tools for using in raised beds and possibly other places. And we’ll touch on the importance of soil testing before you add organic matter or other fertilizer to your beds. In the meantime, be sure to check out these resources:

Are raised beds for you? This comprehensive fact sheet goes into more detail.

Home vegetable gardens – an overview.

How much organic material is too much? Don’t overdo – read this first!

A root’s life

Roots are the unsung heroes of plants! But unfortunately your every day hard working root gets little respect from gardeners. “We are so taken for granted” whined Radix– “Its just so hard, we are all down here in the dark, nobody see’s us, we get no admiration, yet we work so hard!”. Radix is your every day “working root” mostly ignored by gardeners. Even though the seasons change, and leaves come and go, Radix is growing most all the time! Gardeners love the color of flowers, the texture and shape of foliage, the architecture of tree tree branches and admire all the things plants do above ground. They beautify the world, provide us food, and provide oxygen for us to breathe. We heap our admiration on above ground functions of plants, but without Radix, and all the other roots, the above ground parts would perish.

Healthy roots growing under wood chip mulches.

Growing plants is about growing the whole organism. We may pick the fruit, admire the flowers, or rest under the shade, but none of it would be possible without proper care of root systems. Roots have varied functions—they provide anchorage so the plant can stand upright; they absorb minerals and water; and they store energy in form of starch. Plant shoots grow in the realm of light and much of their adaptations revolve around catching sunlight. Their atmosphere is mostly nitrogen and oxygen. Roots grow in the realm of soil and darkness, their atmosphere is oxygen restricted and dominated by carbon dioxide and even toxic gases like sulfur dioxide, and methane if soil conditions become saturated. Just like all parts of plants, oxygen is required by roots to respire or utilize chemical energy for their growth. Poor Radix can choke if the oxygen supply is limited.

Shoots live in a herbivorous world. Plants get eaten by animals. Because they have buds of all kinds they can grow back, leaves may contain alkaloids and other molecules that reduce herbivory, and plants can arm themselves with spines, thorns and prickles, but roots live in a microbial world. While microbes can grow on most plant surfaces, the root system is bathed in microbes (the soil food web). Not only do roots have to defend themselves underground but they have specific alliances that let them do that! As you know from some of my other blogs, root pathogens can kill all ages of plants from seedling to mature oak trees. The happens when pathogens (which are opportunists) are not well regulated by soil microbes, or when plant root systems are stressed in some way. Large populations of soil bacteria, fungi, nematodes and arthropods limit the development of opportunistic pathogens. These organisms are supported by soil carbon or organic matter which is essential to their abundant reproduction in soil. This carbon is best supplied to root by mulching with freshly chopped Arborist chips.

To examine root health, expose the cortex with a knife. It should be white, an unhealthy root will be discolored. Many roots are black on the outside and this is normal as they have melanin in their epidermis as a protectant against microbes.

Roots store carbohydrates made in leaves as starch. This stored energy can be used for their growth or redistributed through the plant later. In order for stored starch to be used, it must be converted back to glucose (by enzymes) and then broken down through chemical respiration. These processes take oxygen which is limited in soil as a function of depth. The deeper you go the less oxygen. This is why trees and most plants have roots in the upper foot or so of soil. This upper foot of soil is sensitive and fragile. It can be compacted by foot traffic or equipment and lose oxygen content. Weed barriers, fabrics, and sheet mulching deprive soil of gas exchange, and the amount of carbon dioxide increases at the expense of oxygen under these barriers. Too much water can fill soil pore spaces causing saturation that usually contain oxygen and decrease the amount of available oxygen since it does not dissolve well in water. All of this also applies to the soil microbial communities which also require oxygen to grow and thrive.

A healthy soil contains plant roots (top) and an abundance of micro organisms. These soils will be porous, contain higher levels of organic matter and mycorrhizal fungi (white portion at the bottom of image)

So how do we respect Radix and all the other hard working roots? Promote soil health by avoiding tillage and cultivation. Use Mulches made from fresh tree trimming chips, avoid compacting soils with machinery, and do not shock soils with excessive application of manure, fertilizer, or water which can perturb the microbiology of a soil. I also suggest you learn to admire roots for all that they do for plants in your garden. Check in with Radix every now and then by digging down and looking at root systems. See if they are growing. Try to learn the seasonality of peak root growth so that you avoid practices that may harm roots during their critical growth periods. Be alert to the symptoms of root rot on garden plants especially at the tops of plants such as leaf drop, shoot dieback and wilting.

Potting Soil Poison

Gardeners often struggle to grow plants in containers. You may feel that you have a really black thumb at times when newly planted seedlings fall over dead or fail to thrive. The problem may not be disease or poor gardening acumen but rather your container media otherwise sold as “Potting Soil”. A trip to one of the big box stores or a larger retail nursery will offer gardeners many choices of bagged potting soils. They are marketed to give you the impression they will grow anything and everything. But do they?
Over the last couple of decades I have done comparative potting media trials where I plant small plugs (usually impatiens) three per six inch container. I go out and find every retail brand of potting mix I can find and plant them all up and then follow them for about two months. I’ve been thinking of revisiting the studies and seeing if anything has changed. I also want to test the assumption that you can’t predict the grow ability of a potting soil by reading the ingredient label as some research suggests. While there can always be a surprise with any given product, I think that from my many trials I can make some suggestions to improve the outcome of your gardening adventures in containers.

Soil on the left has no nutrients same soil on the right with 2 grams of ammonium sulfate added on the surface of the medium one time.

Growing media is not the same as soil. Since media are placed in containers, often plastic ones, they need to be very porous. Porosity of up to 50% is not uncommon in container media. The bulk of the media needs to hold water and minerals for plant growth. Usually an organic material that has a high cation exchange capacity is used. The darling of potting mixes has been Peat Moss. Since peat moss harvesting is damaging to the environment (see previous blog by Linda CS), many gardeners may want to avoid media with peat moss. Bulking agents that do not hold much water or nutrients are also added to “lighten” or aerate the medium. Horticultural perlite (expanded volcanic glass) is the most common. Sand is also sometimes used but it adds weight to the bag and is not preferred by manufacturers. Some media use bark or other wood products to provide greater porosity.
There are usually about 18 to 20 different media on the market at any given time and the results of growing plants in them is predictable. About 10 of the media will not grow anything very well, 5 give ok results and about 5 of the products will grow a nice plant. A lot of the reason for success or lack thereof is about nitrogen chemistry. If no fertilizer is added, the medium will likely not grow well. You can add your own fertilizer and make about  ½ of these poor growing media work. One quarter to one half a teaspoon (approximately 2gm) of ammonium sulfate usually peps up most media that are ok but lack nutrients.  This is an amount used in a standard height 6inch (15cm) diameter plastic container.  Larger containers and plants will require incrementally more fertilizer to achieve growth goals. 
Some media will not grow even when fertilized. This is because they may contain manures, or composts and manures that have added too much salt to the medium. Adding fertilizers to these products only makes them less growable. Sometimes these potting soils will improve with leaching but then fertilizer will need to be added back later to make up for what was leached away. Generally a salty potting mix is worth avoiding.
So how can you tell if you are getting a good or bad mix. You can start by reading the ingredient list. And you will need to decode that list to help you make some decisions. What manufacturers call things can be very misleading. Look for a medium that has fertilizer added and lists what kind of fertilizer was used. These media usually grow without help. Avoid media that use manures, they are not suitable container media ingredients.

Some potting soils claim they can grow plants bigger than others, some claim to be all organic and some claim to be friendly to the earth. This is all marketing. Look for a simple ingredient list that is fortified with a nutrient charge (fertilizer). Begin there. You may want to sieve the medium to remove large particles if you are growing seeds, add more bulking agent (bark, sand, perlite, pumice) for plants that need increased porosity such as orchids, bromeliads and cactus. Don’t be afraid to modify potting mixes to suit the needs you might have. If plants don’t grow, consider adding more nutrients. After growing for some time (months to years), many media will breakdown, and the plant will need to be repotted in a new medium.

Standing up for (and lying down on) the environmentally sustainable lawn

If you’ve been reading this blog for a while, you might remember that I got rid of our lawn (getting rid of your lawn post) at our Seattle house . It took too much water to keep it green in the summer, and the resulting ornamental landscape was more ecologically diverse and aesthetically pleasing for such a small site.

On the way to replacing the lawn with landscape
And the same landscape a few years later.

But that was then, and this is now. In 2017 we moved back to the family farm, which has a full acre of landscape – including lawn. Although we are slowly reducing the vast expanse of lawn, we will keep part of it because (1) we are on well water and there is an irrigation system and (2) because we are allowing the lawn to become a diverse tapestry of different plant species – an ecolawn, if you will.

Farmhouse landscape with an acre of lawn!

When I was growing up, my father fought unsuccessfully to keep the moss and weeds out. I happen to LOVE the moss and the fact that it grows here has nothing to do with poor drainage or anything else. It grows here because the environmental conditions support its growth. I love the spongy feel of the underlying moss, and it reduces the amount of mowing necessary because it’s limited in height. And no fertilizers or pesticides are needed.

Mossy lawns are lovely for walking…and laying down on.

Speaking of mowing…I hate gas powered mowers. They’re smelly and noisy, they contribute to air pollution, and when something goes wrong you have to take it to small engine repair. These excursions are infrequently successful but always expensive. So imagine my delight is discovering newer battery-powered mowers! All you have to do is swap battery packs. They are quieter, there are no emissions, they don’t smell, and they have an electric engine! No small engine repairs, and they are also lighter for this reason.

A newer technology, battery-operated mower with rechargeable battery

I was even more excited to find compatible leaf blowers. We have tons of Oregon white oak leaves, and we blow them into the beds. We do NOT leave them on the lawn, because they interfere with some of our non-grass lawn inhabitants. They are perfect on the beds because their curly, rigid structure prevents compaction and they keep weeds out while allowing water and oxygen to penetrate.

Keep the leaves off the lawn and over the beds.
Our container violets have escaped into the lawn; covering them with leaves could kill them.

Finally, our ecolawn allows me to see and appreciate the reproductive structures of our mycorrhizal fungi. I don’t even pretend to know the species and whether they are edible. I just love the fact that they appear every fall after we’ve stopped mowing.

Some of our lawn mushrooms…
…and some others…
…and others.

Sometimes lawns aren’t appropriate, as we found in Seattle. But sometimes they are – and as long as they are cared for in an environmentally sustainable manner, they shouldn’t have to be something we apologize for.

Fruit Tree Pruning Basics

Last week I helped to train Master Gardeners about pruning fruit trees. January and February are the months that we recommend fruit tree pruning in Southern California.  In colder climates, pruning may not occur until later when freezing temperatures are minimized and there is less chance of damage to new growth. While trees don’t “need” pruning to bear fruit, pruning practices can enhance fruit production, promote earlier fruiting bearing buds, and increase fruit quality if done in an informed way. In many respects, modern fruit trees have been bred for big fruit, and pruning might need to be done to prevent limb breakage, reduce the number of fruit and position it in the tree fore ease of harvest. Misinformed pruning can lead to disease or loss of bearing wood. “Fruit tree” is a broad category, but for this blog, I am referring to deciduous trees (not subtropicals such as citrus, avocado, mango etc.). Two main categories are common: Pome fruits such as apples and pears and Stone fruits such as cherries, plums, apricots, peaches, almonds and pluots.

The first thing to figure out when pruning any tree grown for fruit production is where the fruit will be formed. This requires examining and understanding buds, twigs and the age of growth that is produced. Second we need to understand the tree’s responses to pruning and how that will affect future fruit production. Finally an understanding of negative consequences of pruning is essential.

Peaches produce fruit on last year’s growth

Apples and pears produce fruit on spurs

Why prune you ask if trees will produce without pruning? Pruning shapes a tree, and helps to create fruiting buds that are conveniently placed for harvest-this keeps fruit pickable with less time on ladders. Pruning gives an opportunity to remove fruiting buds thereby invigorating remaining buds and increasing size and quality of the fruit that will form with less fruit thinning later. Pruning also gives an opportunity to remove diseased, damaged, tangled or infested branches.  While various training styles can be used for structural pruning of young fruit trees the open vase or modefied central leader systems are preferred and descriptions of them can be found in extension leaflets.  For my own trees I usually do not prune them the first year after planting in order to encourage a stronger root system.  In the second and third years I pick scaffold branches or train branches on the central leader.

Fruit is produced on various aged twigs or branches depending on tree species. Peaches produce fruit on growth from the previous year or one year old wood. Since peaches grow vigorously fruiting wood ends up on the outside of a tree. Heading back (or heading) cuts (reducing last year’s branches by at least half their length) will remove ½ the fruit and stimulate buds lower in the tree that will make more fruiting wood. For this reason peaches are usually pruned “hard” to stimulate maximum amounts of fresh fruiting wood. Apples, Pears, Plums, Cherries and Apricots produce most of their fruit on small side branches called spurs. Apples and Pears may also produce fruit from the terminal bud.

Young trees often make many long whips and these are usually headed back (heading cuts remove the terminal bud) to stimulate spurs in the following years. Once the overall shape and size of the trees are set, less pruning is required as spurs may produce fruit over decades of time. As trees mature spurs build up so removing densely clustered spurs on mature trees with thinning cuts (removing an entire branch, spur or twig) will increase the size and quality of fruit formed on the remaining spurs.

Pruning is often used on newly planted trees to form the structure of the tree. When forming the branch structure do no indiscriminately head back every branch as this will stop the growth of the branch that is headed. New growth will only resume from buds that are released to grow. Think carefully about what you want to grow and what you want to slow-down in growth. Pruning is always a growth retarding practice. Branches are best spaced up and down and around a central leader. In other training systems for stone fruits one heading cut when the tree is just a whip will create an open vase shape where all the branches arise from a single point on the trunk. While this is considered a branch defect in shade trees, it is a convenient training system for fruit trees if you don’t let the tree get too large and manage the fruit loads that are produced. Trees trained to a modified open center where branches are spaced on a central leader have stronger branch attachments and can bear greater fruit.

This apple is extensively sunburned from over pruning

As trees age and grow they require regular training with heading cuts to shorten vigorous branches of peaches or thinning cuts to remove whips, water sprouts or other unwanted branches.  Be careful not to over-prune especially in summer or sunburn can result.  When fruit sets in the spring or early summer it can be thinned by hand.  This form of pruning will increase size of the remaining fruit and quality.   Summer pruning is sometimes practiced on very vigorous trees to slow their growth and invigorate buds for the following spring.  Prune with care in the summer espeically on green barked trees like apple and pears to avoid sunburn.

Woodpeckers: Friends or Foes?

[This blog post has been provided by Bec Wolfe-Thomas, an administrator for the Garden Professors blog group on Facebook.]

Pileated woodpecker. Photo by Josh Laymon

Woodpeckers (Picidae) frequently get a bad rap from gardeners. It’s often their impression that the birds irreparably damage trees, but this is untrue. Most woodpeckers are insect eaters; they can hear insects under the bark and in the wood of trees. They then target their drilling with uncanny precision to get their meal. This removal of insect pests, such as emerald ash borer, benefits the tree.

Emerald ash borer larva. Photo by Pennsylvania Department of Conservation and Natural Resources.

And what about the feeding holes left in the tree? This is an exciting bit of tree physiology! Trees are able to compartmentalize or isolate the wounds. After the woodpecker has made a hole to retrieve the insects within, the tree starts compartmentalizing the wound. How long it takes for a tree to compartmentalize a wound and close it depends on species and climate factors.

Compartmentalization of decay in trees (CODIT). Photo from Wikimedia.

Below are photos of woodpecker holes in various states of compartmentalization, from freshly drilled to completely compartmentalized and closed holes. Woodpeckers help keep trees healthy by preventing large pest infestations. And while the small feeding holes might be an aesthetic concern to gardeners, they’re only temporary. They will eventually be compartmentalized and closed, and the tree will be healthier in the long run by having fewer pests.

This woodpecker hole is partially compartmentalized; you can see the edges are rounded, no longer rough. Photo by Bec Wolfe-Thomas.
This wound has fully compartmentalized and all that is left is a pucker on the trunk. Photo by Bec Wolfe-Thomas.

[Please note the larger holes excavated for nesting will compartmentalize but will not close over time.]

Flammability of Landscape Plants–Why the lists are BAD!

California had the worst fires in the last two years of its existence as a state. Hundreds of thousands of acres of brush and forest burned. More importantly thousands lost their homes as fires moved across urban/rural interfaces to destroy communities. The entire town of Paradise, California was burned to the ground. Here in Ventura County, the Thomas Fire was the state’s largest fire by the time it was done, and hundreds lost homes. No other time in history have we been so focused on what will burn, why it will burn, and what we can do to have a “firewise” landscape.

In 2017 The Thomas Fire in Ojai, California was the largest brush fire in the history of California fire fighting. It was surpassed the following year by the Camp fire in Northern California.

Fire authorities around the world have advocated creating defensible spaces around homes that are clear of ignitable vegetation. Some authorities have mandated by law that mulch, pine needles and other debris be removed as a fire prevention measure near structures. There is a general recognition that any plant can burn. Even well irrigated plants will rapidly desiccate and become flammable in the face of strong wind and a heavy fuel load that is inflamed nearby.

Flammability of landscape around homes is dependent on several factors. Vegetation placement can obstruct or allow for fire fighters ability to reduce damage to a home. While it is natural to assume that avoiding flammable plants is a part of this process, there is no standard method for testing plant flammability. Many lists of firewise plants have unknown origin or are just guesses. Flammability can be assigned four dimensions: ignitability, sustainability, combustibility and consumability. These factors refer to time till ignition; time a material will burn; rapidity or intensity of burn and quantity of material that will burn. The components of combustion are influenced by moisture content, percentage of carbon, percentage of volatile compounds; surface area to volume ratio and other factors. The varied factors are usually not all studied at the same time and are not all equally important to plant flammability. Thus assessing flammability even within the context of a controlled study will only partially assess a material’s likelihood of burning under various conditions. Hence most of the lists are not that helpful.

While fresh wood chip mulches are consideder by some fire authorities to be a fire hazard, there is little published evidence of this and a single element like mulch can not be tied to flammbability of the landscape.

Behm et. al. showed that variations in flammability between plant species exists, and also that species within the same genus can vary widely in their flammable nature. Thus lists should not assume species in the same genus all have the same flammability. There is some thinking that flammability is an evolutionary trait that some plants exploit to their benefit, i.e. they are made to burn, such as the California Chaparral plant communities. Simply burning fuels in a laboratory setting does not take into account many of the factors associated with fuel burning intensities. Species differences notwithstanding, the amount of dead plant matter (dead twigs and leaves) vs. live matter, the arrangement of leaves, mulch and adjacent species all play a role in the flammability of the landscape itself which cannot be studied in a lab setting. Landscapes are “fuel bed complexes” with multiple elements that are not replicated in studies. For instance, small leaves from some shrubs ignite easily, but when burned as litter, develop low heat release rates because of poor ventilation.

Testing live plant materials alone is misleading because the flammability of an intact shrub is caused by the interaction of live matter with “necromatter”. Dead tissues are thermal catalysts which ignite live material. The ratio of necromatter to live matter influences flammability and is generally not well studied. Fire modelling also has a role in understanding what will burn. Both wind and slope increase the spread rate and the fireline intensity of burnable plants. Fire behavior characteristics on a given plant also are affected by both its physical and chemical characteristic — tissue mineral and water content have impacts on flammability. This bodes poorly for firesafe plant lists because lists do not consider plant physical or chemical attributes and if moisture levels are low it will burn regardless of its structure and geometry or its status on a list. Sometimes though a dense wall of well hydrated vegetation can save homes such as the avocado orchards that held back fire in the Thomas Fire in Montecito, Ca.

While lists don’t satisfy scientific rigor they are great for policy makers and homeowners who want to know what to plant. Unfortunately many lists are just compilations of other lists, none of which were based on research. Sometimes lists confuse one desirable characteristic with another, such as native plant lists that tout drought tolerance. Many drought tolerant plants are not fire resistant especially after a long dry period, indeed they often evolved to burn under such conditions.

For those that live in fire prone areas, fire resistant plant lists will always be an attractive or even required element of landscapes. Lists will not save a structure in the face of high winds and adequate fuel or embers. A defined defensible space around buildings, and maintenance of plantings that removes dead matter, maintains irrigation, and maintains proper distance from combustible surfaces will be more effective than choosing landscape plants from flammability lists.

Fernandes, P.M. and M. G. Cruz. 2012. Plant flammability experiments offer limited insight into vegetation—fire dynamic interactions. New Phytologist 194: 606-609

Behm, A.L., M. L. Duryea, A.J. Long, and W.C. Zipperer. 2004. Flammability of native understory species in pine flatwood and hardwood hammock ecosystems and implications for the wildland –urban interface. International J. of Wildland fire 13: 355-365.

White, R.H. and W.C. Zipperer. 2010. Testing and classification of individual plants for fire behavior: plant selection for the wildland-urban interface. International J. of Wildland Fire 19:213-227.

Soil or dirt? It’s really up to you

Dig up dirt. Treat like dirt. Dirt poor. Replace the word “dirt” with “soil” and you get phrases that make no sense. This is a roundabout way of explaining that “dirt” and “soil” are not the same things, either in idioms or in the garden. Yet many of us effectively turn our soils into dirt through poor garden practices.

This is dirt. (Photo from Wikipedia)

This is soil.

For the purposes of this post, we’re going to use a single criterion to distinguish between soil and dirt: one is a living ecosystem and the other is not. A thriving soil ecosystem contains sufficient water, oxygen, and nutrients to support bacterial, fungal, plant, and animal life. Regardless of soil type, about half of the volume in a living soil should be pore space and the other half soil particles. Half of the pore space should be filled with water and the other half with air. When we make choices about activities that affect garden and landscape soils, we need to be proactive in preserving both the particle-pore balance as well as connectivity between the soil and the atmosphere.

All soils have pore spaces regardless of their texture.

Pore size varies with particle size.

The only way pore space can be reduced is through soil compaction. So don’t do it.

  • No driving. If equipment must be brought in, put down a thick layer of wood chips to protect the soil, or at least plywood.

Not really the way to do park renovations.

These amenity trees quickly became liabilities, thanks to soil compaction during construction. {Photo courtesy of Jim Flott)

  • No naked soil. Bare soils are compacted soils. Mulch!

Basically dirt.

Wood chips covering real soil.

  • No rototilling. It grinds your living soil into dirt. Disrupt the soil as little as possible when you plant.

I have no words.

  • No stomping, pressing, or otherwise compacting the soil during planting. Let water and gravity do that work for you.

Let’s just press that pore space out of existence.

Mud it in! Let water and gravity settle new transplants.

The only way soil and atmosphere connectivity can be disrupted is by covering the soil with low permeability materials. So don’t do it.

  • No soil layering. Don’t create abrupt layers of soils with different textures. It interferes with water and gas exchange.

Soil horizons change gradually in natural soils.

Poor surface drainage indicates a perched water table caused by abrupt changes in soil texture (photo courtesy of Rich Guggenheim).

  • No sheet mulches. I’m sure you’re tired of hearing me say that and I am tired of saying it. Sheet mulches have less permeability than chunky mulches. That means oxygen and water have more difficulty getting through. Period.

The less porous the material, the more slowly gas diffuses through it. Read more about it in our recent article

Chips are great. Why ruin them with cardboard underneath?

Landscape fabric is even worse than cardboard, but the weeds love it.

And plastic? Dont even THINK about it.

Do use lots of groundcovers, chunky mulches, and hardscape in areas where there’s considerable foot traffic. They all protect the soil and are important parts of a well-designed, sustainable landscape.

Soils love all sorts of mulches.

Inorganic mulches protect soil, too.

If you just can’t get enough about soil science for gardens and landscapes, do check out this new publication by Dr. Jim Downer and myself.

Fertilizer—Friend or Foe to disease causing organisms?

Gardeners that read this blog understand that minerals are absorbed mostly by plant roots as ions, and are essential for plant growth and development. Some minerals are required in parts per hundred, and are macro-nutrients while others are only required in parts per million or parts per billion, and are considered micronutrients. As long as enough of the 16 most essential minerals are available, plants grow and reproduce in a healthful way. When not enough of one of the essential elements are available, a deficiency occurs, and plants

Nutrient deficiency symptoms in new growth of Camphor tree

may present deficiency symptoms. Mineral nutrient deficiency symptoms are considered abiotic disorders. There are, however, cases where excess or deficiency of elements can be predisposing to disease caused by pathogens. Most some mineral elements do have a role in the development of disease caused by some pathogens but this is largely demonstrated in agriculture and often most home gardens do not suffer nutrient caused plant diseases.
Diseases can be either biotic with a living pathogen driving the disease or abiotic where a physiological condition is caused by the environment and host interactions. Mineral nutrients also are often implicated in abiotic disease.


Blossom end rot in tomato fruit

Perhaps the most famous one is blossom end rot of tomato. This disorder is seen by gardeners around the country and is widely attributed to calcium deficiency. Expanding fruit are a tremendous “sink” for nutrients like calcium and it was thought that if not enough calcium was available in soil the disorder would occur. It is accepted that localized Ca deficiency (in fruit) may play a role in the initiation of blossom end rot, but there are many other factors that lead to the full blown condition, some of which are not fully understood. The fact that blossom end rot (BER) occurs in calcic soils in California underpins the complexity of this disorder.  In many cases, simply adding calcium to soils does not correct the problem. Research in California suggest that the plant hormone abscisic acid (ABA) regulates water flow, the development of water conducting tissues, and calcium uptake in tomato. Researchers found that ABA treated tomatoes were cured of blossom end rot.  For gardeners, making sure plants are fertilized, and avoiding varieties susceptible to BER is the best course of action.

Soil-borne pathogens are perhaps most affected by minerals dissolved in soil solution. Minerals can act in specific ways (specific ion effects) or as total ion effects (osmotic strength or concentration) having direct impact on pathogenic propagules or on the host itself. In a biological disease relationship there are several possibilities:
• Specific ions harm or favor the pathogen.
• Specific ions harm or support the host.
• Ionic strength changes the root environment making the host weak and susceptible.
• Ions change the pH of the soil solution making it more or less fit for a pathogen or the host.
• Ions change the soil physical environment making it more or less fit for a pathogen or the host.

Root rot of annual color plant is a common find in many garden centers

While it is often espoused that the well “fed” or fertilized plant is resistant to disease, it is rarely borne out in published research on ornamental plants. Keeping a good nutritional level in nursery stock will not necessarily protect plants from many of the virulent pathogens that are capable of causing disease. Excess fertilization may lead to luxury consumption by the fertilized plant and can produce succulent growth that will exacerbate of such diseases as powdery mildew. It is well known that seedling diseases caused (damping off) are more severe with increased medium salinity and it was later discovered that increased soil salinity also increases susceptibility of ornamental plants to Phytophthora root rot diseases. Phytophthora is the most common pathogen associated with rotted roots in most gardens.

Plant mineral nutrition supports plant health in two basic ways (1) formation of mechanical barriers (cell wall strengthening) and (2) synthesis of defense compounds that protect against pathogens. The role of specific elements and their compounds is complicated and unique to each disease/host system. Certainly deficiencies of molecules such as calcium and potassium can interrupt either defense mechanism and if nutrients are supplied enough to prevent deficiencies there is little role of nutrients in preventing disease.
Root rot is a disease of thousands of ornamental plants and a serious problem in many gardens. Root rots caused by Phytophthora spp. occur in a range of nutritional and pH ranges. Nitrogen has been shown to lessen root rots and this is likely due to conversion of nitrogen into ammonia gas in soil which acts as a fumigant. Many studies found no relationship of nitrogen source to root rot disease development.  Calcium increases disease resistance to root rot in avocado and other plants. While it is understood that calcium has direct effects on plant membranes, root cell membrane leakage, cell wall thickness, and many other host factors, there are also direct effects on the pathogen in soil. Calcium ions reduce the production of disease spores and disrupt their ability to swim and find susceptible roots. When soils and soil less media are low in soluble calcium, when calcium is easily precipitated out of solution, or when the pH is high and limestone minerals decrease the availability of calcium, root rots will be able to infect.  Increases of sodium ions in soils and soil less media can also increase Phytophthora caused diseases.

Some non-essential elements have become popular as disease suppressants. Research has shown Silicon increases resistance of plants to powdery mildew, root rots and to stress in general. Silicon is implicated in strengthening cell walls as well as in defense protein production in plants. But not all plants are capable of utilizing silicon, so its role in plant defense is limited to those species (mostly grasses) capable of metabolizing it. Silicon has been erroneously recommended for widespread disease prevention. Its actual utility is likely very narrow. Much more study is necessary to understand silicon’s role with ornamental plant-pathogen systems. Gardeners will find little use for silicon as a disease prevention too.

Plants extract minerals from container media and garden soils—the process is complicated; it is mediated by the substrate/soil, water chemistry, temperature and the applied minerals (fertilizers) as well as by plants. Gardeners should apply fertilizers that can supply a constant low level nutrient charge or rely on nutrients provided in mulches. Fertilizing decisions are best guided by having a low cost soil analysis by a University lab. Supplying extra soluble calcium may be helpful in managing root rots, especially where heavy rainfall is normal and soils may be highly leached. Preventing salt build up (by leaching irrigation) in high salinity soils (low rainfall places) and that can occur when media dries out, will also help plants avoid infection by root rot organisms. It is good to remember that fertilizers never cure diseases, but there may be a role in preventing disease when plants are nutrient deficient.
Baker K.F. 1957.  The UC System Producing Healthy Container-Grown Plants. University of California Division of Agricultural Sciences Agricultural Experiment Station Publication #23.

Cherif M., Asselin A., Belanger R.R. 1994. Defense responses induced by soluble silicon in cucumber roots infected by Pythium spp. Phytopathology 84:236-242.

Datnoff, L.E., Elmer, W.H. and D. M. Huber eds. 2007. Mineral nutrition and plant disease. APS Press The American Phytopathological Society, St. Paul, MN. 278pp.

Downer A.J., Hodel D.R., Matthews D.M., Pittenger D.R. 2013. Effect of fertilizer nitrogen source on susceptibility of five species of field grown palms to Fusarium oxysporum f. sp. canariensis. Palms 57: 89-92.

Duvenhage J.A., Kotze J.M. 1991. The influence of calcium on saprophytic growth and pathogenicity of Phytopthora cinnamomi and on resistance of avocado to root rot. South African Avocado Growers Yearbook 14:13-14.

Faufeux F., Remus-Borei W., Menzies J.G., Belanger R.R. 2006. Silicon and plant disease resistance against pathogenic fungi. FEMS Microbiology Letters 249:1-6.

Kauss H., Seehaus K., Franke R., Gilbert S., Dietrich R.A., Kroger N.. 2003. Silica deposition by a strongly cationic proline-rich protein from systemically resistant cucumber plants. Plant J. 33:87-95.

Lee B.S., Zentmeyer GA. 1982. Influence of calcium nitrate and ammonium sulfate on Phytophthora root rot of Persea indica. Phytopathology 72:1558-1564.

Ma, J.F.  2011. Role of silicon in enhancing the resistance of plants to biotic and abiotic stresses. Soil Science and Plant Nutrition 50:11-18.

Macdonald J.D., Swiecki T.J., Blaker N.S., Shapiro J.D. 1984. Effects of salinity stress on the development of Phytophthora root rots. Cal Ag 38:23-24.

Messenger B.J., Menge J.A., Pond E. 2000. Effects of gypsum on zoospores and sporangia of Phytopthora cinnamomi. Plant Dis 84:617-621.

Powell C.W., Lindquist R.K. 1997. Ball Pest and Disease Manual (2nd ed). Ball Publishing Batavia Publishing. 426 pp.

Span T.M., Schumann A.W.  2010.  Mineral nutrition contributes to plant disease and pest resistance. University of Florida Publication #HS1181.

Tonetto de Freitas, S., K.A. Shackel and E. J. Mitcham. 2011. Abscisic acid triggers whole-plant and fruit specific mechanisms to increase fruit calcium uptake and prevent blossom end rot development in tomato fruit. J. of Experimental Botany 62:2645-2656.

Daylor, M.D. and S. J. Locassio. 2004. Blossom-end rot: A calcium deficiency. J. of plant Nutrition 27: 123-139.

Zentmeyer G.A. 1963. Biological control of Phytophthora root rot of avocado with alfalfa meal. Phytopathology 53:1383-1387.

Hydroponics, Aquaponics, & Aeroponics, Part Deux

Last month I shared some basic info on the major techniques for growing plants without soil, namely hydroponics, aquaponics, and aeroponics.  With such interest in these topics, I thought it would be good to dive a little further into the technologies used.  I’ll provide a bit of basic information about each type of system used for production and provide some resources for further technical reading if you’re interested in learning more. For some simple diagrams of the systems, check out this link (we don’t know if we can “borrow” the images, so we didn’t copy them over).


“Deep” water may be a bit of a misnomer, as it usually brings to mind thoughts of mysterious sea creatures living in the dark depths of the ocean.  Technically, the “deep” water can be just a few inches, as it is deep in reference to other methods.  This is perhaps the simplest and least expensive of the systems and can be a great entry point for beginners.

For deep water culture, the nutrient solution is held in a large container with some sort of floating support holding the plants.  The container is at least a few inches deep and holds a relatively high volume of water.  There are some containers that are designed for deep water hydroponics, but repurposed containers will work as long as they are food safe (meaning that they do not leach or break down).  Large plastic totes or even plastic buckets can be used.  As for supporting structures for plants, Styrofoam is the most common.  There are cell trays made of Styrofoam that are commonly used in production of small crops (or for growing transplants, which is a common use of this technique).  Foam boards with holes to hold pots can also be used.  Back when I was in grad school we developed hydroponic systems in my plant propagation class using foam insulation boards floating in large plastic totes.

One thing that you have to keep in mind for deep water culture is the need to incorporate oxygen into the system.  We often talk about the issue of overwatering houseplants and how it can damage roots  due to hypoxic, or low oxygen, situations.  Imagine how roots growing only in water would create situations for poor root and plant growth.  In all the other systems water flow helps incorporate oxygen into the water.  In deep water, there is no moving water and therefore no air incorporation.  The most common tool used for this, especially for small systems, is an aquarium air pump and air stones that help create bubbles in the system.

One benefit of this system is that it has a low level of risk when it comes to system failure.  There are few moving parts to break down and loss of electric doesn’t result in roots drying out due to loss of water flow.


Ebb and Flow troughs in an aquaponics system. Note the floating styrofoam rafts. (I did research in this system during my master’s program.)

These systems, also called flood and drain systems, are one step of complexity above the deep water systems by introducing water flow.  Plants can either float as in deep water culture or be held in media that fills the container.  While many containers can be used, the most common are longer channels that promote water flow from one end to the other.  This system also introduces a reservoir of some sort that holds excess nutrient solution and a pump to deliver it to the container.  The level of water in the container is controlled by a raised drain pipe where solution exits the system back to the reservoir.

The DIY system I build using gutter with the Rwandan students (mentioned in the first installment on hydroponics) is ebb and flow.  The drain from the gutters is a few inches high within the channel, so the water raises those few inches before it drains out.  Some producers use long channels the width of those floating cell trays to grow plants in a relay fashion, planting them on one end and move them along as new rafts are added until they are harvested on the other end.

This system is common not only in hydroponics, but aquaponics as well.  Instead of a nutrient solution reservoir, the water from the tank(s) holding the aquatic stock (commonly fish, but could also be crustaceans like shrimp) is pumped into the plant channels and flows back into the system.  Systems may be based on continuous flow into and out of the system, but most commonly a timer is used to have multiple periods of flow and rest mainly as a means to reduce power usage.


This system evolved one more step above ebb and flow by limiting the volume of water used in the system.  Here, water is pumped from the solution reservoir to shallow channels where plants are held in pots or blocks of inert media such as rockwool.  Roots are not submerged in water, but instead grow within a thin film of solution that flows almost continuously through the system.  These channels have a slight slope where the end with the drain is a little bit lower than the end where the water enters.  The slope can be adjusted slightly to affect the speed of the water through the system.

This system is becoming common in production of leafy greens and herbs because it uses a much smaller volume of water.  But that small volume of water also presents a risk.  If there is a power failure or a clog in the tubing that delivers water to the system the roots can very quickly dry out and crops die, especially in situations of high heat and light.


Dutch bucket method for trellised crops

Perhaps one of the most commonly used systems across the world due to their simplicity, drip systems could be compared to a drip irrigation system used in the field.  Drip emitters are used to supply nutrient solution to plants in containers containing an inert media such as peat, coir, perlite, or grow stones. The containers can be pots, buckets, or bags/blocks of the media and are most commonly placed on the floor of the greenhouse or growing location with gutters to collect the solution that flows through the containers. A common method is using long, narrow bags filled with coir or other media referred to as the slab method.  Another common method, called the Dutch bucket method, uses buckets with drain holes in the bottom, commonly placed on a greenhouse floor.  Water trickles down through the media and roots and leaves the system through the bottom of the container.

Systems vary in the collection of the used solution.  Some may collect the solution that flows into the gutter and collect it in a reservoir to be reused, however some systems may allow the solution to flow out as waste.  These differences depend on the needs of the producer, available resources, and local regulations.

One of the comments that we got on my first article was about people growing container plants could technically consider it a form of hydroponics.  That might be a bit of a stretch, but you could technically consider growing container plants in soil-less media as drip or flow through hydroponics if you provide all of the nutrients through soluble fertilizers in the water.


Typically used for small scale production, wick systems are one of the simple ways to grow plants without soil in terms of technology.  In this system, a passive wick uptakes nutrient solution from a reservoir and pulls it into the media (usually absorbent itself).  This wick could be a true wick, like a string made of absorbent material that inserts into an individual pot or it could be a mat made of absorbent material that pots or trays sit atop.

I’ve seen this commonly used perhaps not strictly in hydroponics, but for watering individual plants like African violets where yarn or twine is inserted into a drain hole in the pot and sits in water.  Technically this could be hydroponics if the media doesn’t contribute nutrients to the plant and they are all contained in the water instead.


This is probably the simplest of the methods and is used primarily by small scale producers and home growers.  It is similar to the deep water method in that there is no flowing water, but it is even simpler because there isn’t even an air bubbler.  In this method, plants are grown in large containers or buckets and the structure that supports them is fixed to the top of the container rather than floating.  As the growing solution is used up, the level of solution in the container decreases.  This creates a zone where the roots are exposed to air, providing the oxygen that the roots need.  The solution is kept at a level where at least the bottom portion of the roots are submerged in the nutrient solution.


Probably the most complex or technical system, aeroponics supplies water and nutrients to plants through a mist or aerosol emitted through pressurized nozzles.  The roots hang in a chamber without media and are misted every few minutes with nutrient solution.  The excess solution drops to the bottom of the chamber and is reused.  This system uses very small amounts of water, which can be beneficial for growing in dry areas but also creates a potential risk if the system or power fails.  Just like the NFT system, any prolonged period with out water will quickly result in plant damage or loss.  Beside power loss, this systems is also prone to clogged emitters, since the pressurized nozzles rely on very tiny openings to pressurized the solution.

Keep in mind that several systems that are sold for home or small scale production that are labeled as aeroponic, such as AeroGarden and Tower Gardens, don’t technically use aeroponics to grow since the solution isn’t applied as a mist or aerosol.  I would say they operate more like a vertical NFT system where water flows over the roots as it travels down the chamber.


Hydroponic Greenhouse Production Resources – UMass Extension

Introduction to Hydroponics – Johnny’s Seed

All You Need to Know to Choose a Hydroponic System – Upstart Farmers

How to Start Growing with the Kratky Method – Upstart Farmers