21st Century Guidebook to Fungi, SECOND EDITION, by David Moore, Geoffrey D. Robson and Anthony P. J. Trinci

Table of Contents

1. Chapter 1: 21st century fungal communities
   1. What and where are fungi
   2. Soil, the essential terrestrial habitat
   3. How much soil is there and where is it
   4. The nature of soil and who made it
   5. Soil biota are extremely varied and numerous
   6. Microbial diversity in soil
   7. Microbial diversity in general
   8. Geomycology
   9. The origins of agriculture and our dependence on fungi
   10. Chapter 1 References and further reading
   11. Buy a PDF of Chapter 1
2. Chapter 2: Evolutionary origins

1.4 The nature of soil and who made it

Soil is that part of the Earth’s surface that is comprised of fragmented rock and humus. It is made up of solid, liquid, and gaseous phases (Needelman, 2013).

• The solid phase is mineral and organic matter and includes many living organisms.
• The liquid phase is the 'soil solution', from which plants and other organisms take up nutrients and water.
• The gaseous phase is the soil atmosphere, supplying oxygen to plant roots and other organisms for respiration.

The solid phase of soil is made up of minerals and organic matter. Minerals may be either primary or secondary. Primary minerals are those that cooled from a molten mass, and are chemically unchanged from the day they came into existence. Secondary minerals form by chemical modification, precipitation or recrystallisation of chemicals released by the weathering of parental rocks. Rocks are mixtures of minerals. Igneous rock forms from molten magma. If the magma cools slowly it forms a network of large crystals as in granite, if it cools rapidly it forms small crystals as in basalt. Sedimentary rocks are cemented accumulations of minerals: common sedimentary rocks include limestone, sandstone, quartzite, and shale. Metamorphic rocks, which arise when an existing rock is transformed by exposure to high temperatures and pressures, include slate (hardened shale) and marble (hardened limestone).

‘Weathering’ is the term applied to the processes that cause rocks and minerals to disintegrate into smaller parts. Loose or unconsolidated products of weathering are called soil. Soil minerals may be fragmented versions of primary minerals (e.g. sand is fragmented quartz rock) or may be secondary minerals, like clays, slowly formed through chemical interactions in the soil, then becoming further chemically modified with time. The elements most commonly found in soil minerals are silicon, oxygen and aluminium.

Physical and chemical processes contribute to weathering. The main physical weathering effect is the force exerted by the expansion of water as it freezes, so physical weathering is most pronounced in cold climates. In dry climates abrasion by materials suspended in the wind causes weathering (and a similar effect occurs in flowing water). Chemical weathering predominates in warm and/or moist climates, and chemical weathering is generally more important for soil formation than physical. Chemical processes include:

• oxidation and reduction (of great importance for iron-containing minerals),
• carbonation (dissolution of minerals in water made acidic by carbon dioxide),
• hydrolysis (when water splits into hydrogen and hydroxide, and one or both components participate directly in the chemical process), and
• hydration (when water is incorporated into the crystal structure of a mineral, changing mineral properties) (Miller & Gardiner, 2004).

Soils are highly dynamic environments; they change over time, and all the while their particles are moved: downward by the leaching effect of rainwater; laterally by wind, water and ice.

The most potent soil-forming factor is often considered to be the climate, mainly temperature and rainfall. Temperature affects the rates of chemical reactions, so that soils of warmer climates tend to mature more rapidly. However, living organisms (the soil biota) both affect, and are affected by, soil formation. First thoughts tend to be about the profound effects of vegetation on soil formation. For one thing, the extent of vegetation cover influences water runoff and erosion. Fairly obviously, also, the vegetation type and amount directly affect the type and amount of organic matter that accumulates on and in the soil. Grasslands and forests form different soils; there being more rapid nutrient cycling in grassland.

Organic matter deposited on the surface contributes to soil solids. It is moved downward physically through rainwater leaching, and influences soil chemistry, pH and nutrient supply as it goes. This organic matter is the food source for most micro-organisms in the soil, so the vegetation influences soil microbial populations by providing their nutrients. Old soils can lose their ability to produce vegetation fast enough to keep up with microbial decomposition. In healthy agricultural soils organic material is initially decomposed rapidly, but within about a year organic materials like crop residues ‘stabilise’; the remaining residues decay very slowly.  This slowly decomposing material is comprised of ‘humic substances’ (commonly called humus). Humic substances are natural non-living organic substances that occur in all aquatic and terrestrial environments, being found in sediments, peat, sewage, composts and other deposits. This soil organic matter represents the main carbon reservoir in the biosphere, estimated at a grand total of 1600 × 10¹⁵ g C (Grinhut, Hadar & Chen, 2007). The organic matter of soil is crucial to its agricultural value because it aids structure, nutrition and water relations; everything that contributes to soil tilth (tilth is an Old English word that describes the structure and quality of cultivated soil in the sense that good tilth = potentially good crop growth).

Decomposing organic matter provides nutrients to other soil organisms (including, but not exclusively crop plants). Stable organic matter does not do this, but it improves the ability of the soil to hold nutrients and water. An organic soil is dominated by organic matter, rather than minerals. Such soils are found in wetlands, especially cold wetlands, where the primary production of organic materials by the plants exceeds the rates of decomposition in the soil. Ultimately, this equation results in peat formation.

The spaces between soil particles form the pore space, which contains air and water. The water, called the soil solution, contains soluble salts, organic solutes, and some suspended colloids. The amount and behaviour of soil water is controlled to a great extent by pore size (influenced by proportions of coarse material (like sand) and fine minerals (such as clays). Small pores have a greater affinity for water and hold it very tightly. Larger pores allow water to escape easily, by drainage or into the atmosphere by evaporation. Soil ‘air’ has more CO₂ but less O₂ than the open atmosphere. This is because organisms in the soil consume O₂ and produce CO₂, creating corresponding concentration gradients between the soil and the atmosphere. Similarly, soil air always has a relative humidity near 100%. Respiration releases water vapour, which evaporates only slowly into the atmosphere above the soil.

So, soil is a dynamic matrix of organic and mineral constituents enclosing a network of voids and pores, which contain liquids and gases. It is also a living system. Soil organic matter includes living organisms ranging from bacteria, fungi, algae, protozoa, and multicellular animals from rotifers and microarthropods to worms and small mammals (Haynes, 2014); the soil biota is extremely important to soil processes, and although living macroorganisms are usually not considered part of the soil, they can have considerable effect on soil; remember Darwin’s experiments on earthworms, animals that excrete more bacteria into the soil than they consume (Darwin, 1881; available 2017 from Amazon reprinted in several facsimile editions and online as an ebook). This is true even if we leave aside human activities like ploughing, irrigating, mining, clearing, waste-disposing, excavating, levelling, building, draining, flooding, etc.

Updated August, 2019