Fungi
Over 100,000 different kinds of fungi are known, and some authorities suggest a million more are out there waiting to be discovered. Say the word, however, and most gardeners immediately think of the familure white toadstools, bracket and coral fungi, and puffballs that appear in the lawn or on the bark of trees (or they know soil fungi from the diseases they cause). But except for the white threads and the spore-producing mushrooms, soil fungi are as invisible as bacteria, requiring a microscope of several hundred powers to be seen. Even the visible congregations of mycelia are usually hidden in the organic matter they are in the process of decaying.
Fungi, too, are underappreciated by gardeners, and yet they play a key role in the soil food web and are an important tool for those who garden using soil food web principles. It wasn't too long ago that they were considered plants without chlorophyll and unable to photosynthesize, and build their cell walls from chitin instead of cellulose, among other unique characteristics, they are now placed in their own kingdom in the domain Eukarya.
Fungi, like higher plants and animals, are eukaryotes: organisms that have cells with distinct, enclosed nuclei. Each cell can have more than one nucleus. Fungi usually grow from spores into thread-like structures called hyphae (singular, septum). The walls connecting hyphae growing in close enough proximity form visible threads, or mycelia (singular, mycelium), which you may have seen in decomposing leaf litter. Fungi reproduce in many different ways, not just by spores, but never by seeds, as the most advanced plants commonly do.
A fungal hypha is considerably larger than a bacterium, the average length being 2 to 15 micrometers with a diameter of 0.2 to 3.5 micrometers---still so thin that it takes hundreds of thousands of individual hyphal strands to form a network thick enough for the human eye to see. A teaspoon of good garden soil may contain several yards of fungal hyphae, invisible to the naked eye, millions upon millions merge together to produce something as obvious as a king bolete or an intricate Amanita muscaria in all their fruiting glory. These and other mushrooms are simply the fruiting bodies of fungi. Consider the energy and nutrients required to produce them.
One major advantage fungi have over bacteria, and perhaps the reason they were misclassified for so long as plants, is the ability of fungal hyphae to grow in length. Unlike bacterial cells, whose world is a very finite one, fungal hyphae can travel over space measured in feet or meters, distances that for a bacterium are truly epic. And unlike bacteria, fungi do not need a film of water in order to spread through the soil. Fungal hyphae are thus able to bridge gaps and go short distances, which allows them to locate new food sources and transport nutrients from one location to another, relatively far away from its origin.
The ability to transport nutrients is another key difference between fungi and bacteria. Fungal hyphae contain cytoplasm, a liquid circulated throughout the septa in their cells. When a hyphal tip invades a nematode, for example, it drains its hapless victim of its nutrients and distributes them in the hyphal cytoplasm and from there though the main body of fungus. Nutrients are thus transferred from the tip of the fungal hypha to a wholly new location that can be several yards away (think conveyor belt). Once inside the fungus, the nutrients are immobilized and will not be lost from the soil.
Fungi produce special structures---for example, mushrooms above ground or truffles below---to disperse spores. Since fungi grow in all sorts of environments, they have devised some elaborate methods to achieve spore dispersal, including attractive scents, triggers, springs, and jet propulsion systems. To ensure survival, fungal spores can develop tough membranes that allow them to go dormant for years if the conditions are not right for immediate germination.
As with bacteria, fungi occur universally; some species even exist in the frozen region of Antarctica. Airborne dispersal of spores helps explain why visitors from, say, Alaska, will recognize species of fungi growing in far-off Australia. While dormant spores can be found around the world, they need the right conditions to germinate and grow. Thus, fungal spores may be found continents away from their source, but they may not be functional because the conditions for growth are not right.
Fungal growth and decay
While some fungi prefer the "softer," easier-to-digest sugars characteristic of the foods that feed bacteria, most go for tougher-to-digest foods (mainly because bacteria are better and faster at grabbing and taking up simple sugars). Fungi, however, win in the competition for more complex foods: they produce phenol oxidase, a strong enzyme that dissolves even lignin, the woody compound that binds and protects cellulose. Another characteristic of fungi is their ability to penetrate hard surfaces. Fungi have perfected apical growth--- that is, growth at their hyphal tip. Apical or tip growth is an incredibly complex process, and engineering job akin to building a tunnel under a river and requiring great coordination of events. Even before electron microscopes, scientists identified a dark spot, the Spitzenkorper, in the tip of actively growing hyphae; when hyphal growth stopped, the Spitzenkorper disappeared. It seems this mysterious region has something to do with controlling or perhaps directing apical growth.
During apical growth, new cells are constantly being pushed into the tip and along the sidewalls, elongating the hyphal tube. Materials for the growth of fungal hyphae are supplied to the advancing tip by the cytoplasm, which transports vesicles loaded with all necessary "construction" supplies. Of course, it is important to keep extraneous material from flowing into the hypha as well as out while this growth is happening. All the while, powerful enzymes capable of dissolving all but the most recalcitrant carbon compounds are released as the new cells are put into place. Think about it: these enzymes are powerful enough to convert lignin, cellulose, and other tough organic matter into simple sugars and amino acids, yet they do not decay the chitin cell walls of the fungi.
Fungi can grow up to 40 micrometers a minute. Discount for the moment the speed, which is incredibly fast for such tiny organisms, and compare the distance covered to the movement of a typical soil bacterium, which may travel only 6 micrometers in its entire life.
As with the death of any organism in the soil, the death of fungi means the nutrients contained within them become available to other members of the soil food web. But when fungi die, their hyphae leave a subway system of microscopic tunnels, up to 10 micrometers in diameter, through which air and water can flow. These "tubes" are also important safety zones for bacteria trying to elude protozoa: protozoa are considerably bigger than the tunnels.
Fungi are the primary decay agents in the soil food web. The enzymes they release allow fungi to penetrate not only the lignin and cellulose in plants (dead or alive) but also the hard, chitin shells of insects, the bones of animals, and ---as many gardeners have learned---even the protein of strong toenails and fingernails. Bacteria can hold their own, but they require simpler-to-digest foods, often the by-products of fungal decay, and often only after such food has been broken or opened up by fungi and others. Compared to fungi, bacteria are in the Minor Leagues of decaying ability.
Fungal feeding
The acidic digestive substances produced by fungi and leaked out of their hyphal tips are similar to those utilized by humans; fungi don't require a stomach as a vessel in which to digest food, however, Like bacteria, fungi lack mouthparts; instead, fungal decay breaks up organic materials into compounds the fungus can then ingest through its cell walls via diffusion (osmosis) and active transport. Nutrients taken in by fungi are usually immobilized, just as they are when ingested by bacteria, and later released like bacteria, then, fungi should be viewed as living containers of fertilizer.
Excess acids, enzymes, and wastes are left behind as the fungus continues to grow and as a consequence, the digestion of organics continues even through the fungus has moved on, opening up organic material for bacterial decay and making nutrients available to plants and others in the soil community. Hyphal growth gives a fungus the ability to move relatively long distances to food sources instead of waiting for its food to come close (through it can clearly do this, too, as the nematode-trapping fungus proves). Fungi can, for example, extend up into the leaf litter on the surface of the soil, decay leaves, and then bring the nutrients back down into the root zone---a huge advantage over bacteria, the other primary nutrient recycler in the soil food web.
Soil fungi are usually branched and quite capable of gathering organic compounds from different sources simultaneously. Once the nutrient material is inside the cellular membrane, it is transported back through the network of fungal hyphae that often ends at the root of a plant, where some fungi trade for exudates. Thus the same fungus can extend hyphae downward and outward, absorbing several crucial nutrients---phosphorus, copper, zinc, iron, nitrogen---as well as water. In the case of phosphorus, for example, the propensity of fungi to gather and transport it over distances is truly remarkable. This mineral is almost always chemically locked up in soil: even when it is applied as fertilizer, phosphorus becomes unavailable to plants within seconds. Not only do fungi seek out this necessary plant nutrient, but they have the ability to free it from its chemical and physical bonds. Then they transport their quarry back to plant roots, where the phosphorus is absorbed and utilized.
Don't forget that in those instances where a fungus brings food back to a plant root tip, it was attracted to that plant by the plant's exudates. Fungi are good, but the plant is in control.
Fungi and plant-available nitrogen
Some fungi trade nutrients for exudates, but most often nutrients are released as waste after they are consumed by fungi or when the fungi die and are decayed. Much of what is released is nitrogen. A key tenet of gardening with the soil food web is that plants can take up nitrogen in two forms, either as ammonium ions (NH4+) or as nitrate ions (NO3-). The nitrogen released by fungi is in ammonimum form (NH4+). If nitrifying bacteria are present, this is converted in two steps to nitrate (NO3-).
The enzymes produced by fungi are decidedly acidic and lower the pH. Remember that bacterial slime raises soil pH; nitrogen-fixing bacteria generally require a pH above 7. As soils become dominated by fungi, the populations of nitrogen-fixing bacteria require to convert ammonium into nitrates diminish because the pH is lowered by the acids the fungi produce. More ammonium therefore remains as plant-available ammonium instead of being converted to nitrates. This has an important implication to gardening with the soil food web: fungally dominated soils tend to have nitrogen in ammonium form. This is great if you are a plant that prefers ammonium to nitrate, but not so good if you prefer to have your ammonium converted to nitrates.
Fungal adaptations
Fungi have developed all sorts of clever strategies to make it through life---our nematode-strangling fungus proves it. The fungus that developed this very artful and useful adaptation is Artrobotrys dactyloides. The ring that trapped the nematode is actually just a hyphal branch, twisted back on itself. These branches each consist of only three cells, which when touched, produce a signal to let water in; the cells then swell to three times their size and the unsuspecting victim is killed in a tenth of a second. Pretty amazing---a sophisticated trapping mechanism developed from an inverted branch using only three cells. Once again, nanotechnology can only hope to duplicate such as complicated process. Not only does the fungus figure out a way to kill nematodes, which are all blind, but it attracts them to its trap in the first instance. In this case, the fungus releases a chemical that attracts the worm.
Within a matter of only a few minutes after trapping, the tip of a fungal hypha enters the nematode's body, secretes its powerful enzymes, and starts absorbing nutrients. As this is exactly what the nematode has for the fungus. These nutrients, of course, are then locked up inside the fungus until the fungus is eaten by one of its predators or it trades them for exudates. Then the nutrients are mineralized and again are available to plants.
The fungus Pleurotus ostreatus, the common oyster mushroom you can buy at the supermarket, uses another clever technique to trap food. It emits toxic drops from the tips of its hyphae; an unsuspecting nematode (our perennial fungal fall guy), out and about, looking for food, touches a drop with its mouth and within minutes is immobilized. A few hours later, and the fungus is inside the nematode, already digesting it.
This is not a bad way to ensure a meal: attract your food and either trap it or stun it and then consume it. Other mechanisms have evolved as well. Some fungi use adhesives to stick to nematodes. Other soil fungi trap protozoa and even springtails, much larger microarthropods that are big enough to see with the naked eye. Once attached, the fungi digest their prey and again lock up or immobilize plant nutrients.
What drives soil fungi in the direction of particular nutrients is still an open question. It is known that some send out filaments as if they were scouts looking for nutrients. If you have ever seen a well-trained bird dog look for a downed bird, you get the idea. The dog circles until its nose finds the bird. Some fungi clearly possess tactile-or contact-sensing capabilities that allow then to orient in a certain direction so they can invade their prey or other food source. Others demonstrate the ability to track specific chemicals they know to be in the vicinity of specific prey.
For the gardener it is sufficient to know that fungi can find nutrients. When a source is found, fungal strands head over to the area and literally settle in, digesting the material, often combining one nutrient source material with another and transporting nutrients back to the base of the fungus. All the while, other strands "scout" for more food to attack. Nutrients are held inside cell walls, preventing them from leaching away.
Fungi and symbiosis
Soil fungi also form two extremely important mutual relationships with plants. The first is the association of certain fungi with green algae, which results in the formation of lichens. In this symbiotic relationship, the fungus gets food from the alga, which utilizes its photosynthetic powers while the fungal strands make up the thallus, or body, of the lichen, in which the pair lives. Chemicals secreted by the fungus break down the rock and wood upon which the lichens grow. This creates minerals and nutrients for soil, soil microbes, and plants.
The second are mycorrhizae (from the Greek for "fungus-root"), symbiotic associations between plant roots and fungi. In return for exudates from plant roots, mycorrhizal fungi seek out water and nutrients and then bring them back to the plant. The plant becomes dependent on the fungi, and the fungi, in turn, cannot live without the plant's exudates. It is a wonderful world, indeed.
Mycorrhizae have been known since 1885, when German scientist Albert Benhard Frank compared pines grown in sterilized soil to those grown in sterilized soil inoculated with forest fungi. The seedlings in the inoculated soil grew faster and much larger than those in the sterilized soil. Yet it was only in the 1990s that the terms mycorrhiza (the symbiotic root-fungus relationship; plural, mycorrhizae) and mycorrhizal (its associated adjective) started to creep into the agricultural industry's lexicon, much less the home gardener's.
We're the first to admit that we were blindsided by the subject---and one of us had written a popular garden column every week for 30 years and never once mentioned them out of sheer ignorance, a state shared with most gardeners. We now know the extent of our ignorance: at least 90% of all plants form mycorrhizae, and the percentage is probably 95% and even higher. What is worse, we learned that these relationships began some 450 million years ago, with terrestrial plant evolution: plants started growing on the earth's surface only after fungi entered into relationships with aquatic plants. Without mycorrhizal fungi, plants do not obtain the quantities of kinds of nutrients needed to perform at their best; we must alter our gardening practices so as not to kill these crucial beneficial fungi.
Perhaps gardeners lack appreciation for fungi because all soil fungi are very fragile. Too much compaction of soil and fungal tubes are crushed and fungi killed. Clearly fungicides but also pesticides, inorganic fertilizer, and physical alteration of the soil (rototilling, double digging) destroy fungal hyphae. Chemicals do so by sucking the cytoplasm out of the fungal body. Rototilling simply breaks up the hyphae. The fruiting bodies of mycorrhizal fungi even decrease when fungi are exposed to air pollution, particularly that containing nitrogenous substances.
Mycorrhizal fungi are of two kinds. The first, ectomycorrhizal fungi, grow close to the surface of roots and can form webs around them. Ectomycorrhizal fungi associate with hardwoods and conifers. The second are endomycorrhizal fungi. These actually penetrate and grow inside roots and well as extend outward into the soil. Endomycorrhizal fungi are preferred by most vegetables, annuals, grasses, shrubs, perennials, and softwood trees.
Both types of mycorrhizal fungi can extend the reach as well as the surface area of plant roots; the effective surface area of a tree's roots, for example, can be increased a fantastic 700 to 1000 times by the association. Mycorrhizal fungi get carbohydrates they need from the host plant's exudates and use that energy to extend out into the soil, pumping moisture and mining nutrients from places the plant roots alone could not access. These fungi are not lone miners, either. They form intricate webs and sometimes carry water and nutrients to the roots of different plants, not only the one from which they started. It is strange to think of mycorrhizal fungus in association with one plant helping others at the same time, but this occurs.
Finding and bringing back the phosphorus that is so critical to plants seems to be a major function of many mycorrhizal fungi; the acids produced by mycorrhizal fungi can unlock, retrieve, and transport chemically locked-up phosphorus back to the host plant. Mycorrhizal fungi also free up copper, calcium, magnesium, zinc, and iron for plant use. As always, any nutrient compounds not delivered to the plant roots are locked up in the fungi and are released when the fungi die and are decayed.
Pathogenic and parasitic fungi
Beneficial fungi compete for nutrients and form protective webs and nets, often in conjunction with bacteria, around roots (and even on leaf surfaces, as leaves produce exudates that attract bacteria and fungi as well); this prevents some of their pathogenic and parasitic fungal cousins from invading the plant. The list of fungal pathogens impacting agricultural and horticultural crops is long; the topic fills many books and is beyond the scope of this one. Smut fungi, for example, impact the flowers of cereal grains. Rust fungi cause diseases on wheat, oats, rye, fruits, and pines. More common garden problems are downy mildew (Plasmopara spp., Sclerophthora spp.), root rots (Phytophthora spp.), and white rusts (Albugo spp.).
Be there a gardener who has not encountered botrytis or powdery mildew, a catch-all name for a group of fungi that infects different plants with the same results, an unsightly gray or white powdery fungal growth that covers leaves, stems, and flowers? Most powdery mildew fungi produce airborne spores that do not require free water to germinate. Given temperatures between 60 and 80F (15 and 27C) and high humidity, these spores germinate and infect their host in your yard. How about grusarium wilt on tomatoes, the first thing to suspect when a tomato's leaves start to yellow from the bottom of the plant up? It is caused by Fusarium oxysporum f.sp. lycopersici, a soil-borne fungus that can survive for a decade or more in dormant stages. It enters the plant through roots and invades its water distribution network. Further testament to the power of fungi is Armillaria mellea (oak root fungus), which causes sudden oak death--a tiny fungus taking down towering oaks. The fungal activity decays a tree's lignin and cellulose to such an extent that the tree dies.
Pathogenic and parasitic fungi make use of various entry points into plants, including stomata (the opening on leaf surfaces that allow plants to breathe) and wounds. And, of course, with all this talk of enzymes decaying tough-to-digest lignin, it shouldn't surprise any gardener that some fungi can dissolve the cuticle and cell walls of the plant it is attacking. If you think this is difficult, think about the fungi that penetrate bathroom tile, and know that some fungi can penetrate granite in search of food.
This entire book could be filled with descriptions of fungi that get their nutrition at the expense of living plants. This is not our purpose---only that you realize that soil is loaded with fungi, and concept most gardeners readily grasp because of direct experience.
Functional overlap with bacteria
It should be obvious by now that in a healthy soil food web, fungi and bacteria shoulder much the same work and share many of the same functions. Like bacteria, some fungi produce vitamins and antibiotics that kill pathogens in the soil as well as in the human body. Remember penicillin, the most famous fungus-turned-antibiotic of all? In 1928, when English bacteriologist Alexander Fleming returned to his lab after his vacation, he found a fungus had contaminated a petri dish full of Staphylococcus bacteria. It ruined his experiment, but no bacteria were found growing near the fungus, and the world of medicine has never been the same.
Fungi, like bacteria, play crucial roles in the soil food web as decomposers, nutrient cycles, soil structure builders, and beneficial symbionts, preventing as well as causing diseases. As well, their ability to impact soil pH makes them an important tool for gardening with the soil food web.
carbon compounds, the former found in plant wall cells and latter in fungal cell walls and in arthropod shells. These are not normal foods of other bacteria. Actinomycetesare also adapted to live in a wider range of pH than other bacteria, from acidic to alkaline.
Hey trichome fiend does ph matter if i am cloning in rockwool and I use compost tea to clone? 
NP
