Book Review: Microbe Science for Gardeners by Robert Pavlis

Front cover of Microbe Science for Gardeners by Robert Pavlis. Photo, New Society publishers

Book Review: Microbe Science for Gardeners: Secrets to Better Plant Health, Robert Pavlis, New Society Publishers, September 2023. 192 pages, 6 x 9 inches, charts, diagrams and photos. $22.99.

Robert Pavlis is an engaging and reliable science writer, who owns Aspen Grove Gardens, a six-acre botanical garden with 3,000 plant varieties in southern Ontario. I have previously reviewed Soil Science for Gardeners, Plant Science for Gardeners, and Compost Science for Gardeners. Robert explains science in concise, minimally technological English, with researched and trialed information. In this, his newest book, Robert describes the all-important symbiotic relationships between plants and microorganisms below and above ground. A gram of fresh leaf may be home to a hundred million bacteria.

Aspen Grove Gardens. Photo from the Garden Myths website

In Microbe Science for Gardeners, we learn how we can encourage beneficial microbes and discourage those that damage our crops. We can increase our knowledge of strategies that prevent fungal, bacterial and viral diseases, and cure them. Robert Pavlis is well-known for myth-busting. No farmer likes to find their time or money has been wasted on wishful thinking with a slim hope of good results. With information from this book, we can better understand how various gardening and farming practices affect the microbes living with our plants. Is it good, bad or interesting, to till, use mulches, rotate crops or grow perennials?

This is a good point at which to say Pavlis is not a committed organic gardener. He sees compounds and ions from the plant and microbe point of view, as independent from their source. Pros and cons relate to the ingredients, not their manufacturer. There is plenty of good info and advice for organic growers. The book is studded with sidebars of Microbe Myths. Many of us will find one of our microbe beliefs shattered!

Microbes under consideration include bacteria, fungi, yeasts, nematodes, protozoa, viruses and more, such as archaea, actinomycetes, cyanobacteria and algae. And the microbe communities and microbiomes where different species support each other, such as lichens. Readers are almost certain to find some lesser-known and newly investigated gems of soil biology here, as well as be enthralled by the microscopy photos of tiny creatures we don’t see while thinning carrots.

Plants actively farm the microbes nearby, modifying the space to become more habitable. The microbes make nutrients available for the plants. The role of certain fungi covering roots and effectively increasing the surface area of those roots, increasing the nutrient-seeking range, is fairly well-known. Gardeners adding too much nitrogen fertilizer will cause the microbe system to slow down, creating a dependency on added fertilizer.

Most soils contain adequate phosphorus, although it may be in a form that requires certain microbes to make it available. Beware of adding phosphorus – do a soil test first. Fungi gather and distribute phosphorus to plants, but as with other nutrients, if too much is applied by the gardener, this inhibits growth. Remember, brassicas do not colonize fungi.

Good finished compost can still provide nitrogen 5 years later, as it finishes breaking down. Part of its contribution is via the microbes that feed on the compost, die and break down. There is much we don’t yet know about microbes, and many kinds we have not even identified yet. Recent estimates are that microbes compose 70%-90% of life on our planet.

Microbes are essential to plant growth. Some promote plant growth in ways such as bringing in nutrients and organic matter, fixing nitrogen, producing plant hormones, vitamins and antibiotics, furnishing dissolved minerals and breaking down toxins. There are 558 yeast strains found under chestnut trees. Seventy-seven of them produce a growth-regulating hormone important to roots (15 at a high level).

All carbon energy originates with plants and algae that make food using the energy of the sun. The rest of us get energy by eating those foods. Respiration releases some carbon (as CO2) back into the atmosphere, to be recaptured and used by plants. As microbes digest dead organic matter in compost piles, the process releases CO2. Nutrients are cycled around the life forms that can use them. Nitrogen is another very important nutrient, with its own energy food web.

Those who make compost are familiar with working with the carbon to nitrogen ratio. The bacteria and fungi doing the actual composting need a particular C:N ratio to live. By starting a compost pile at a 30:1 ratio, we allow for the initial release of CO2. Bacteria have a low C:N ratio (5:1 on average). When protozoa and nematodes eat bacteria, the excess nitrogen is released in forms that can be used by plants.

We gardeners also influence microbes. Soil compaction reduces oxygen levels and increases CO2. Aerobic microbes cannot thrive. Tilling does not much affect bacteria, but does rip up fungal hyphae. Tilling introduces more oxygen into the soil. Microbes in the topsoil decrease. Some pesticides harm microbes, others do not. Some microbes use glyphosate (Roundup) as food, leaving benign compounds. This is why glyphosate has a short half-life in the soil. Maintaining a steady moisture level in the soil is important for microbes.

The presence of bacteria on and inside plants is likely essential to the life of the plants. All bacteria are single-celled organisms, most are aerobic and get their energy directly from carbon sources. Most can only move themselves a distance of 5 micrometers in their whole lifetime. Only a few cause diseases.

Bacteria can only ingest small molecules, so to obtain food from plant material consisting of large molecules, they excrete enzymes that can break large molecules down to small molecules such as sugars, and then into ions. If any of the ions hit the cell wall of the bacterium, it can ingest them. Despite this inefficient-sounding mechanism, bacteria thrive everywhere! Bacteria cannot digest lignin, found in wood, but fungi can.

There are fascinating details of bacterial lifecycles, types of bacteria and fungi. Fungi cannot make their own food from carbon as plants do. They rely on other organisms in the soil or on the surface as their food. Soil is home for about 70,000 species of fungi. As bacteria do, fungi excrete enzymes that break down large organic molecules. The smaller molecules can then be absorbed and transferred several feet along the hyphae.

Oyster mushrooms
Photo Ezra Freeman

Fungi can reproduce asexually (by fragmenting) and sexually (via spores, when conditions are not right for fragmentation). Mycorrhizal fungi are symbiotic with their host plants. They can increase tolerance for diseases, drought and chilling in their associated plants, as well as increase yields.  The plant supplies the fungi with sugars from photosynthesis and the fungi supply other nutrients to the plant. If the soils are nutrient-rich, the plant needs less from the fungi, and transfers less sugars to them.

Yeasts also play an important role in the biosphere, including decomposition of organic matter, cycling of nutrients, and supplying plants with growth-stimulating compounds. Yeasts are a type of fungus, with complex single cells. Most convert carbohydrates into alcohol and CO2. This is the process of fermentation. Yeast lifecycle includes asexual reproduction (budding) as well as sporulation, a form of sexual reproduction, which happens when the environment becomes inhospitable. Spores can become dormant and survive until conditions improve.

Powdery mildew is a yeast fungus that grows on leaves. Research is being done into antagonistic yeast species to combat powdery mildew, which requires particular yeast for particular plants. Simply using bakers’ yeast does not work. Adding compost can sometimes help plants outgrow infections.

South Anna Butternut winter squash, a Moschata bred by Edmund Frost to resist Downy mildew
Photo Southern Exposure Seed Exchange

Some fungi can attack living prey using sticky goo, poison filaments or entangling snare strands. Some yeasts contain pieces of viral RNA that produce toxins and bad beer. The interactions between bacteria, nematodes and protozoa in the soil are responsible for making many plant nutrients available. The soil environments, including the soil type and pore size, influence the amount and type of protozoa and nematodes found there, which in turn affects the number and type of bacteria. The result affects the type of plants that thrive.

Nematodes are tiny worms, up to 2 mm long, living in the top 6″ (15 cm) of the soil and moving in films of water, eating bacteria, fungi, protozoa and smaller nematodes. They are multicellular, but have only simple bodies without circulatory or respiratory systems. Some species are beneficial to plants, some parasitic, some carry viruses.

Protozoa are single-celled organisms (remember the amoeba from biology classes?), that eat mostly bacteria, and also algae, fungi, some pathogenic nematodes, and smaller protozoa. Grazing of root growth by some protozoa, and production of plant hormones by amoebae lead to an increase of root exudates, and then to an increase of bacterial populations, to the benefit of the protozoa who eat them.

Some protozoa can photosynthesize. Some live inside other organisms, large and small. Some cause human diseases, such as malaria and giardia. Nematodes, arthropods and larger protozoa eat protozoa and keep their numbers in balance. In inhospitable conditions they enter a durable cyst stage. The weight of protozoa produced each year in healthy soil is about the same as that produced by earthworms. Let’s value their contribution to nutrient cycling as much as we value that of earthworms!

Viruses are extremely small and are not composed of cells, but usually small pieces of DNA wrapped in a layer of protein. Most scientists do not consider them living or dead. They don’t grow or reproduce or move on their own, and they cannot make proteins or produce energy. They use their hosts to provide these functions. Some are beneficial, many cause diseases, some have not been studied enough for us to know. Most are short-lived, although tobacco mosaic virus can survive for decades. There are no cures for viral diseases. Prevention and limitation of spread by control of the vector is required. Bleach does not kill viruses. Vinegar is of limited effectiveness. Rubbing alcohol is the best choice for disinfecting pruners.

Most viruses infect bacteria, not plants or people. These viruses are called microphages, or just phages. Bacteria defend themselves against viruses by chopping up their genetic material. This is the process humans learned from when developing CRISPR technology. There are also bacteriophages that control plant-pathogenic bacteria. Their action is specific to particular bacteria. This is an area of active research.

Robert Pavlis, author of the “Science for Gardeners” series. Photo from his website

After covering these major types of microbe, the author takes us on an exploration of other types, including archaea, actinomycetes, cyanobacteria, and algae.

It is a mistake to think of various types of microbes living in isolation. Most live in diverse microbial communities, and also in combination with plants. “Microbiome” is the word used to describe a microbe community in a specific location, such as on a leaf, or among a tree’s roots. Microbes from neighboring communities may be in competition, or may be complementary. Microbes hoard carbon and nitrogen by deterring others with toxins and repellents.

Microbes signal to each other not as communication, but in the sense of exuding compounds that cause particular actions by other microbes, such as moving closer or further away. Potential foods exude compounds that cause microbes to produce digestive enzymes. When the sign (scent, flavor) of a predator is received by a microbe, it produces an enzyme that makes a toxic substance and secretes it into the adjacent water. The toxin makes the microbe dangerous to its predators, repelling them. The author is attentive to avoiding giving the impression that microbes are conscious and “choosing” to send “messages”, when in fact the situation is one of chance and chemical reactions.

Lichens are symbiotic relationships between three microorganisms: a fungus, a green alga or a cyanobacterium, and a yeast. The participation of the yeast is a relatively new discovery. The fungus can survive without its lichen partners, but benefits from the community. It absorbs water from the air and provides shade, benefiting the light-sensitive alga. The alga or cyanobacterium photosynthesizes, supplying sugars. The yeast helps deter predator microbes. Lichens do not harm the plants they grow on. Their presence indicates clean air.

The above-ground parts of plants are also home to a multitude of microbes, but so far they have been less studied than those in the soil. Microbes grow and reproduce on and in the plant, are washed and blown from one plant to another. Microbes can exit and enter leaves via the stomata. Immunity receptors on the leaves can detect arrival of pathogens and trigger the closure of individual stomata.

Hydroponic plants carry very few microbes, perhaps to the detriment of the health of diners. We are mistaken if we think pesticides (natural or synthetic) can kill only “bad bugs”. All bugs are interconnected and usually interdependent. Avoid sprays, as everything that kills something visible is also killing microbes we can’t see.

The rhizosphere, a thin layer of water, soil and air coating the roots, is crucial to plant health. There is a great photo showing the roots of a plant removed from the ground, coated with a layer of soil and microbes, called a rhizosheath. Look for this sign of a healthy soil as you work with your plants. There is good information about roots, root tips, the rhizosphere, the mycorhizosphere, rhiozophagy and more rhizowords.

We know that tillage reduces soil aggregation and water-holding capacity, cuts roots and fungal hyphae, and causes some microbe populations to die back, making it easier for pathogens to take hold. Crop rotation and inclusion of cover crops usually increase microbial diversity, benefiting the next crop, sometimes a little, sometimes a lot. Long cycles allow pathogens to decrease, although some soil-borne pathogens can persist for a long time. If you only have a small backyard garden, the distance you can move your crops is small, as are the benefits.

Most plant diseases are preventable with the right microbes present and active. Early-stage diseases are dealt with by the plant and its support team of beneficial and neutral microbes. Most plants fight off bacterial pathogens thanks to microbial competition, although some plants have some immunity. Often we don’t see the disease a plant has, unless it takes over. Disease spores are all around us. It’s fine to compost most diseased plants! Not those with virus diseases, or very contagious diseases like verticillium wilt.

Diseased squash, mid-June.
Photo Pam Dawling

Pavlis includes information on what to do when you suspect a plant disease: Identify the problem, research reliable sources, decide if action is required, and find a solution that really works. Most often that won’t be one recommended on social media by people using kitchen products. There is a four-page descriptive list of 20 plant diseases and possible controls and management strategies, followed by discussion of household remedies such as milk or baking soda for powdery mildew (yes, if . . .), chamomile tea or cinnamon against damping off disease (yes, not sure why), neem oil against some fungal diseases but not others, and insect vectors of viral diseases (yes, if you get the agricultural kind with active azadirachtin).

The next chapter is about using microbes to grow better plants. Soils from different plant communities have different Fungal:Bacterial ratios. This ratio can be modified by adding organic matter with a high C:N ratio to improve conditions for fungi. It is hard to accurately measure F:B ratios and different methods give different answers. It is a mistake to think higher F:B ratios are always better, or that certain plants require a fixed ratio throughout their growth. There is little if any scientific research. We don’t know if trees need to grow in a high F:B ratio soil, only that forest soils do have a high F:B ratio. Possibly plants modify their own soil environment and don’t usually benefit from us making changes.

Adding the appropriate rhizobium bacterial inoculants to legumes has long been proven to work, increasing nitrogen-fixation 30%-70%. The bacteria remain in the soil for 4-40 years, and the inoculant does not need to be replied annually. Avoid adding too much nitrogen fertilizer, or the inoculated bacteria will give up. Before flowering, 60% of a legume’s fixed nitrogen is in the leaves and stems, with 40% in the roots. After mature seed forms, 80% is in the seed, 11% in the roots, and 9% in the leaves and stems.

The author cautions us to beware terms like “beneficial microbes”, which is just a marketing ploy selling non-pathogenic microbes said to increase the population in the soil. These usually include molasses or another form of sugar, which causes an initial microbe population explosion. When the nutrient is all gone, microbes die and feed each other, and population returns to its previous level.

“Effective microorganisms” is a label for a combination of up to 80 different microbes the seller thinks will improve the decomposition of organic matter. Microbes populate soils quickly by themselves, until the many species are in balance and the soil is carrying its maximum capacity. Adding more is just a waste of money and time. Slower-decomposing organic matter provides a better, longer-term benefit, increasing your soil’s capacity to host more microbes.

Bottled bioinoculants, biostimulants, biofertilizers and probiotics are usually selected microbes, mostly fungi and bacteria. Many do not contain live microbes. The Oregon Dept of Agriculture tested 51 products for bacteria and found only 9 functional. Of 14 products tested for Trichoderma fungus, none were worthwhile. Of 17 containing mycorrhizal fungi, only 3 met the label description. DNA testing showed that some products had never contained the beneficial organism. There’s lots of snake oil out there!

Compost teas are DIY inoculants, popular either as a hopefully concentrated form of nutrients or a more populous source of (hopefully good, not pathogenic) microbes. Making tea cannot increase the amount of nutrients beyond that available in the original compost. It can reduce some soil-borne diseases, if the soil, climate and microbes are exactly what is needed. Rather hit-and-miss, for gardeners and farmers. Compost tea can contain more microbes than the original compost, but they can be good, bad or even deadly, including E.coli and Salmonella. Incidentally, the deadly ones are more likely if you add molasses to your brew, Pavlis claims.

Pickled garlic scapes, okra and beets.
Photo Bridget Aleshire

If all this talk of microbes on and in your food is creeping you out, relax! Wash your hands, wash your vegetables, enjoy your food. Forget soap, bleach and baking soda. A 1:1 mix of household vinegar and water can be used for a 10-minute vegetable soak, if you get sick easily. Otherwise, plain water is adequate. Remember you too are full of microbes, and your well-being depends on some of them.

You can read more of Robert Pavlis’s work on his Facebook page, website and YouTube channel: