Compost in Seed Starting Mix: Recipe for Success….or Failure?

A recent question posted to the Garden Professors blog Facebook group (a place where you can join and join in conversation of garden science) asked about the potential for compost added to seed starting media to cause failure in germination.  It is a good question, and one that seems to have several different camps – from garden hero author folks swearing by it in their (non-peer reviewed) books, to fact sheets saying it isn’t a good idea.

I’ve always promoted that the best practice for seeds starting is using a sterile media to avoid such problems as damping off.  Many of the problems I’ve heard associated with compost and seed starting are that improperly finished compost can introduce disease microorganisms to the media or cause phytotoxicity, it can make the mix too heavy and thus create anaerobic conditions that starve emerging seedlings of oxygen or cause decomposition, and there is the potential for residues of herbicides in composts using farm waste, manure, or lawn clippings as a feedstock. But does compost really pose a risk to seed starting?  I decided to take a very quick spin through the literature to weigh the possibilities.  Here are some of the potential issues and what a quick glance at the literature says.

Keeping the Germs out of Germination

Compost, even finished compost, has a high microbial activity.  For the most part, the fungi and bacteria in compost are good guys that pose no threats to plants, they decomposers or neutral.  But incorrectly managed compost can also harbor fungi such as Pythium and Rhizoctonia that cause damping off or even other diseases such as early and late blight if diseased plants were added to the compost and sufficient heat levels weren’t maintained.  Composts that don’t reach 140°F and maintain that temperature for several days to kill off potential pathogens run the risk of introducing diseases into seedlings.

Many promote the use of compost and compost products for potential antagonistic effects on bad bacteria.  We’ve discussed compost tea and the lack of conclusive evidence that it has any effect on reducing disease here many times before, and this article found that there is no significant effect of compost tea on damping off.  Some other articles, such as this one, did find that commercially prepared composts added to media did suppress damping off.  However, it is to be noted that these are commercially prepared composts, which have a strict temperature requirement and often require testing for pathogen and bacterial populations.  Many home composters aren’t as proficient at maintaining temperatures suitable for pathogen elimination.

Even if the compost is pathogen free, introduction into a germination media could potentially increase the population of pathogens already present in the media (or that land on it from the air) by providing a source of food for bacterial and fungal growth.  The sterile mixes aren’t just sterile from a microorganism perspective, they’re also sterile from a nutrient perspective as well to help inhibit potential pathogen growth.  The seeds come with their own food, so it isn’t needed for initial germination – the seedlings should be moved to a more fertile mix once they’ve established their first set of true leaves.

Image result for damping off
Damping off, source hort.uwex.edu

You may be saying- “but we also direct sow seeds outdoors, where there’s lots of pathogens present in the soil.”  While this may be the case, damping off is still a definite problem in direct sowing and the loss of investment in materials, lights, and time is generally much lower (and less painful) than in indoor seedling production.  This is especially the case for large operations or for home gardeners who grow lots of stuff from seed.

This is the main issue that leads to the best practice recommendation to use a sterile seed-starting mix that doesn’t contain compost.  If a mix contains compost, it should be from a commercial enterprise that follows best practices or  pasteurized.

Maturity isn’t just for wines, cheeses, and people

Continuing to talk about proper composting, improperly finished compost that hasn’t properly matured (finished composting) can also lead to problems with seed germination.  Unfinished compost can still have woody material included, which has a high C/N ratio and also contain/release phytotoxic compounds during the decomposition process. The presence of decomposition microorganisms in a high C/N ratio means that there is still decomposition happening, which requires nitrogen for the process.  With absence of nitrogen in the media, the nitrogen from the seed or the seedling can be leeched out, effectively causing mortality after or even before germination.  The tender seedling serves as a source of N for the decomposing fungi.

We’ve had this discussion before when it comes mulch.  While mulch is perfectly fine on top of the soil, if it gets mixed into the soil there could be potential implications on N availability.

A germination bioassay is one tool commonly used to test for compost maturity.  Quickly germinating (and inexpensive) seeds are germinated on the compost (or on filter paper soaked with an extract from the compost in some commercial operations).  The rate of germination vs germination failure can give some insight into the maturity of the compost.  This paper discusses the use of the technique for commercial sawdust compost used for potting media.

You can use a bioassay of your own to test for compost maturity (or herbicide persistence, discussed later) for applications in your garden.  Sow an equal number of inexpensive, fast-germinating seeds like radish or lettuce sown on the compost with a control sown on moist paper towel in a bag.  Compare the number of germinated seeds and thriving seedlings after several days to see if there is an issue with the compost.

Keeping Things Light

One other quality required for seed starting media is a good level of porosity (pore spaces) for the media to hold air.  Air (oxygen) is important as it is needed by the roots for respiration.  If the media is too heavy or holds too much water you run the risk of hypoxia, or lack of oxygen, in the roots.  This can result in root die off and subsequent seedling failure.  Most seed starting media are composed of very light materials such as peat moss, coir, vermiculite, or perlite for this very reason.  Compost, by nature, is a more dense material with less porosity and has a higher water holding capacity.  Therefore incorporation of too much compost can create the potential risk of compaction or excessive water holding in the mix.

When Persistence Doesn’t Pay Off

Most herbicides break down during the composting process through a variety of physical and biological interactions.  However there have been reports of some herbicides that are persistent after the composting process, resulting in a residue that could damage plants grown using the compost (see this paper for some examples).  Many of the reports show the damage manifesting in mostly large applications of compost to gardens.  However, the more fragile nature of germinating seeds and young seedlings make them especially susceptible to herbicide residue damage.  For further discussion (and examples of bioassays used to detect herbicide residues), check out this paper.

So the potential for pathogens, risk of improperly matured compost, effect on porosity, and potential for herbicide persistence present some significant risks to germination if they are incorporated into seed starting media.  These are the risks that cause many sources to promote using sterile seeds starting media, and I think the advice is well founded.  While some may not experience these possible issues, the potential is still there.

Understanding mysteries of plant diseases

(Post 1 of 3 in this blog series)

Gardeners, especially those new to gardening may find they have a “black thumb.” Plants die for no reason! “Oh well chuck it in the greenwaste recycling can and start again.” Or… “Oh I can’t grow cyclamens!… They always die in my garden for some reason.” For many gardeners it is mysterious why some plants fail to thrive or die suddenly. Plant disease processes are complicated, and it requires some knowledge of botany (anatomy and physiology), genetics, and microbiology to really understand what is happening. Also, since microbes are microscopic and most pathogens are microbial we can’t always see them at work, especially before symptoms develop. Symptoms are plant responses to the action of a disease agent. In this post I will try to describe the different kinds of diseases, and where they come from.

There are two broad categories …
of plant disease possible in gardens: biotic  diseases and abiotic diseases. Biotic diseases have a disease agent called a pathogen. The pathogen can be microbial, or a nematode or a virus, or a parasitic seed plant. Bacteria and fungi are the most common microbes. It is debatable weather viral particles are living, so also debatable weather or not they are considered microbes. Of the biotic pathogens, fungi cause  most diseases in gardens.  Many pathogens rely on environmental conditions to favor their lifestyle, this is particularly true of bacteria which like moist, warm environments.

The other category of disease is the abiotic category. Abiotic diseases have no pathogen. An environmental condition such as an excess or lack of an environmental condition causes physiological changes in plants that develop symptoms. Extremes of temperature, light, humidity, soil or water chemistry, soil physical conditions, air quality, and pesticide residue can all lead to abiotic diseases. Since there is no pathogen there is no epidemic, and abiotic diseases are not infectious. So spread, occurrence and movement of abiotic diseases are usually different than biotic disorders

So how does disease happen?
I have heard many gardeners make sweeping statements like “overwatering killed my plant” or “It just died of neglect” or “insects killed it”. Plant pathologists describe the disease process with a cartoon called the disease tetrahedron. It describes the interaction of four things: the pathogen, the environment, the host and time. Of course it is only a triangle for abiotic diseases since there is no pathogen.

For disease to occur there must be an active pathogen present that is virulent (has genes to cause disease). The pathogen must have enough inoculum present to begin the disease process. A single spore rarely leads to a successful disease (although it can in some systems).  Most importantly the pathogen must have the right genetics to recognize its host.

Next the environment must be conducive to the pathogen and its development and/or  harmful or stressful to the host. The environment can cause the host stress while favoring the pathogen.  An example would be oxygen starvation in flooded roots. The environment must favor the pathogen’s build up and dispersal of its inoculum (infective propagules such as spores, cells or seeds). Often splashing rain during the warming spring period is important for their spores to reach a susceptible host.

Finally for disease to happen, the host must be susceptible to the pathogen and possibly predisposed in some way to its attack.  Pathogens also have phenotypic synchronicity, that is the ability to produce inoculum at the same time as the host is producing susceptible plant tissues (leaves, buds or stems).

The final facet of the tetrahedron is time. Diseases do not occur instantaneously (even though we may only notice them instantly) – it takes time for them to develop.  Disease life cycles or life histories describe how pathogens survive, reproduce and disseminate themselves through the environment over time. The tetrahedron can be used to understand the factors that lead to disease but also can be used as a way to stop or control diseases (more on that in another post).

So where do diseases come from and where are they going?
Abiotic diseases are caused by environmental extremes.  Another way to look at them is that they occur when there is a violation of the adaptations of the host.  In this regard when we grow plants not well adapted to our climate or environment they can be harmed. A good example is my papaya tree. Right now it has been harmed by low temperatures. Growing a papaya in Ojai, CA is a violation of its adaptations.

Jim’s papaya tree is intolerant of Ojai winter temperatures–a violation of its adpatatons

If abiotic factors don’t cause actual symptoms, sometimes they are able to weaken the host so that a pathogen can enter, and begin disease formation.  So abiotic conditions are often predisposing factors for the development of biotic pathogens. Many of the root rot pathogens such as Phytophthora or Armillaria

Wet soils and fine texture (clay) predispose trees to root rot. Note the “root snorkels’ did not prevent the problem

require a predisposing abiotic factor such as drought, saturated soils, high salinity or compaction to facilitate disease development.

Many canker diseases such as those caused by Botryosphaeria are predisposed by drought conditions

So where do pathogens come from?

I like the hospital analogy. Where do you go to get sick? A hospital! They certainly have a difficult time controlling the spread of disease there because that is where sick people go. So where do sick plants come from? Often a nursery!  Nurseries import plants from wholesale sources, propagate from their own stock, sometimes reuse their container media, and grow many hosts in a concentrated place over time. There is no better place for diseases to occur than in nurseries.

This is especially true of root diseases because roots are inside the container and often not observed at the time of purchase

Inspect nursery stock for healthy roots before purchase

(but you always should inspect roots of all purchased plants from six packs of garden flowers to boxed trees). Also, some nurseries suppress diseases with fungicides that do not eradicate the pathogen, so when fungicides wear off (after you purchase your plant), disease can develop from now unsuppressed pathogens. Nurserymen relax! I’m not saying that all nurseries sell diseased plants (at least knowingly), but consumers should take extra care when selecting plants and when bringing new plants to their property.

While landscape mulches don’t likely spread viable pathogens they can change soil moisture status enhancing collar rots if irrigation is not adjusted. This tree was also planted deeply, another predisposing factor for disease

Once pathogens establish in the landscape, they may continue to harm new plants. Some pathogenic spores blow in on wind or inoculum moves in water courses along streams or other water paths. Animals, people and equipment can move infested soil onto a property.   Once diseases have run their course, pathogens often survive as saprophytes in the diseased tissues. They overwinter or over-summer in debris on the ground. So sanitation is critical in disease control (more on this in another post). Fruiting bodies can be moved in the greenwaste stream but there is very little research showing that disease is initiated by contaminated greenwaste, even though some pathogens may survive there. We do know that when greenwaste is chipped, it dramatically reduces pathogen and insect survival. Stockpiling wastes for as little as seven days will reduce chances pathogen survival by an order of magnitude. Certainly our favored arborist chips are very unlikely to have viable pathogens especially when sourced locally.

Understanding that diseases are not usually caused by gardening practices but by a pathogen or an environmental factor is the first step in diagnosis and control. In my next post I will talk about disease diagnosis and detection…

 

Your New Year’s resolution : No “alternative facts” or “fake news” in 2019!

From the Bad-Ass Teacher’s Association – a group after my own heart.

Welcome to 2019! In keeping with the tradition of a new year, I’m hoping you will join me in resolving to promote good gardening science among your friends, relatives, colleagues, and customers. One of the most important tools you’ll need is a collection of resources that are not only science-based, but are relevant to gardens and landscapes (not agricultural production). With that in mind, here’s my list of authors and institutions who are credible resources.

First off, of course, I’ll have to start with the Garden Professor faculty. While this blog is a great archive of information from all of us, some of us have also published books and articles, recorded podcasts, webinars, and DVDs.

Print and digital media – individual authors
Dr. Jeff Gillman has a nice list of books to consider, in addition to those by Joseph Tychonievich and one by Dr. Holly Scoggins. And I’ve got my collection of books and DVDs as well. Dr. Lee Reich, while not officially part of our GP faculty, has published more books for the home gardener than any of the rest of us.

So many good books!

These are popular publications rather than peer-reviewed journal articles. But the authors have solid credentials and years of experience in teaching and research. That makes them reliable sources of information, and while no one is infallible, these authors are active learners and educators. You can be sure that they present the information in their disciplines as accurately and objectively as possible.

Print and digital media – university Extension publications
Ideally, university Extension publications undergo stringent peer review and are updated regularly. In reality, not all Extension publications are equal in quality. I’m on the faculty at Washington State University and one of my jobs is to keep our Home Garden series of articles current (http://gardening.wsu.edu/). I can confidently say that the fact sheets and manuals on our site have been through peer review and are as accurate as possible. Some are getting near the end of their shelf life (five years at WSU) and need to be revised or removed.

Many of these peer-reviewed publications are relevant outside of Washington State.

Are there other universities that have peer-reviewed, current, and relevant Extension publications for gardens and landscapes? If so, please add them to the comments and I will check them out. (To save time and aggravation, please check these out yourself first. Don’t just list them and wait for me to go through them with a critical eye.)

Social media, including blogs and Facebook

The Informed Gardener website – where it all began.

I first got into social media with the construction of my Informed Gardener web page. The white papers, podcasts and other materials housed here are all science based, but they have not been through peer review. Many of them have been adapted into peer-reviewed Extension fact sheets but all of them represent a collection of relevant information that remains accurate despite being dated. Hey, there’s only so much I can do…

The Garden Professor blog – 10 years old!

The Garden Professors blog was born in 2009, followed in 2011 with our Facebook page and discussion group. Both of these have the distinction of being the first (and possibly only?) exclusively science-based gardening groups on Facebook.

The Garden Professors page, where new tidbits are shared daily.
The Garden Professors discussion group, where anecdotes and home remedies are left at the door.

 

 

 

 

 

And yes, I’ve probably left someone or something out
By now you’re probably saying “What about Dr. X’s Facebook page or Professor Y’s blog?” This post is admittedly narrow, because I only know the people that I know. I’d like to expand the recommendations in this post to include other discipline experts who have information directly relevant to the mission of the Garden Professors. (This means we are NOT including information more relevant to farming or other types of agricultural production.)

So feel free to add your suggestions as comments, keeping in mind the criteria I mentioned above. Hopefully what we can create together is a really nice resource list for all us to use.