THE DIVERSITY OF FUNGI FROM POTTING SOIL

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ABSTRACT

The study was carried out to determine THE DIVERSITY OF FUNGI FROM POTTING SOIL. Five samples were collected for the study from different sites. Potting soil from corn flower was collected from Okigwe road flower shop, potting soil from Tuggai was collected from Port Harcourt road flower shop, potting soil from Ghana papper was collected from Egbeada Housing Estate off  Orlu road flower shop, potting soil from Elephant foot was collected at Graceland Estate, off Ontisha road flower shop, sandy soil used as control was collected from Imo State University premises. All samples were collected in Owerri, capital of Imo State. The analysis carried out in the soil samples showed different diversity of fungi. Five species of fungi were isolated from all samples which are Rhizopus spp., Mucor spp., Penicillum spp., Aspergillus spp., and Fusarium spp. of these species present, Rhizopus spp., and Mucor spp. occurred more. The control sample (Sandy soil), yielded no growth on of fungi on yeast extract agar. Fungi plays both detrimental and good roles on soil.

 

 

 

 

 

 

 

CHAPTER ONE

  • INTRODUCTION/LITERATURE REVIEW

1.1 INTRODUCTION

Soil is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth. Soil is a natural body called the pedosphere which has four important functions: it is a medium for plant growth; it is a means of water storage, supply and purification; it is a modifier of Earth’s atmosphere; it is a habitat for organisms; all of which, in turn, modify the soil.

Soil is called the Skin of the Earth (Miller and Austin, 1953) and interfaces with lithosphere, hydrosphere, atmosphere, and biosphere. The term pedolith, used commonly to refer to the soil, literally translates ‘ground stone’. Soil consists of a solid phase of minerals (the soil matrix) and organic matter, as well as a porous phase that holds gases (the soil atmosphere) and water (the soil solution) (Voroney et al., 2015). Accordingly, soils are often treated as a three-state system of solids, liquids, and gases (McCarthy and David, 2006).

Soil is a product of the influence of the climate, relief (elevation, orientation, and slope of terrain), organisms, and its parent materials (original minerals) interacting over time. Soil continually undergoes development by way of numerous physical, chemical and biological processes, which include weathering with associated erosion. Given its complexity and strong internal connectedness soil has been considered as an ecosystem by soil ecologists (Ponge and Jean-Francois, 2015).

Most soils have a dry bulk density (density of soil taking into account voids when dry) between 1.1 and 1.6 g/cm3, while the soil particle density is much higher, in the range of 2.6 to 2.7 g/cm3. Little of the soil of planet Earth is older than the Pleistocene and none is older than the Cenozoic (Buol et al., 1973), although fossilized soils are preserved from as far back as the Archean.

Soil science has two basic branches of study: edaphology and pedology. Edaphology is concerned with the influence of soils on living things. Pedology is focused on the formation, description (morphology), and classification of soils in their natural environment. In engineering terms, soil is referred to as regolith, or loose rock material that lies above the ‘solid geology’. Soil is commonly referred to as “earth” or “dirt“; technically, the term “dirt” should be restricted to displaced soil.

Soil bacteria and fungi play pivotal roles in various biogeochemical cycles (BGC)(Wall and Virgins, 1999) and are responsible for the cycling of organic compounds. Soil microorganisms also influence above ground ecosystem by contributing to plant nutrition, plant health, soil structure, population. An estimated 1,500,000 species of fungi exist in the world (Giller, et al., 1997). But unlike bacteria, many fungi cannot be cultured by current standard laboratory methods. Although molecular methods have been used to study soil bacterial communities, very little research has been undertaken for soil fungi. All organisms in the biosphere depend on microbial activity (Pace, 1997).

The diversity of physical characteristics of soil associate with aggregation of small scales means that soil can contain a large diversity of microorganisms in close proximity, and the chemical composition of soil is also highly heterogeneous in both vertical and horizontal dimensions (Dighton, et al., 1997).

Potting soil, also known as potting mix or potting compost, is a medium in which to grow plants, herbs and vegetables in a pot or other durable container. The first recorded use of the term is from an 1861 issue of the American Agriculturis (Oxford English Dictionary). Some common ingredients used in potting soil are peat, composted bark, sand, perlite and recycled mushroom compost, although many others are used and the proportions vary hugely. Most commercially available brands have their pH fine-tuned with ground limestone; some contain small amounts of fertilizer and slow-release nutrients. Despite its name, little or no soil is used in potting soil because it is considered too heavy for growing houseplants (Brown, 2003).

Some plants require potting soil that is specific for their environment. For example, an African violet would grow better in potting soil containing extra peat moss, while a cactus requires sharp (i.e. plenty of) drainage, most commonly perlite or sand. But potting soil is not ideal for all contained gardening. Insectivorous plants, such as the Venus flytrap and the pitcher plant, prefer nutrient-poor soils common to bogs and fens, while water-based plants thrive in a heavier topsoil mix (The Christian Science Monitor).

1.2 AIM AND OBJECTIVES

Aim

The aim of the study is evaluate the diversity of fungi in potting soil with the following objectives.

  • To determine the fungal load on potting soil
  • To isolate fungi species associated with potting soil
  • To identify various fungal isolates
  • To compare the diversity of fungi in control and in potting soil

 

 

 

1.3 LITERATURE REVIEW

1.3.1 Overview of potting soil fungi

Although spores from potting soil fungi are microscopic, they grow into what’s known as hyphae, which are thin tubular threads. When these threads accumulate into a mass, it’s called a mycelium. Under the right conditions, hyphae can grow so quickly that it’s been estimated the amount of hyphae produced in only one day by just one soil fungus would be almost a mile long, according to the Wayne’s World website. While many soil fungi are beneficial, others are harmful, so it’s important to recognize the symptoms of a bad fungus to treat a problem.

1.3.2 Benefits of potting soil fungi

Potting Soil fungi perform important functions linked to water dynamics, disease suppression and nutrient cycling. They serve a fundamental role as decomposers in a soil’s food web. These fungi convert organic materials that are hard to digest into forms that are usable for organisms. Hyphae, the main form of vegetative growth, bind soil particles to create stable aggregates that help to increase water infiltration and the holding capacity of soil water.

1.3.3 Types of potting fungi

Soil fungi fall into three functional groups, depending on the way they get their energy. Decomposers convert dead organic matter into small molecules such as carbon dioxide. Mutualists develop beneficial relationships with plants by colonizing plant roots and helping plants get nutrients such as nitrogen and phosphorus from the soil. Pathogens or parasites are mostly considered detrimental and reduce plant production or can even cause the death of a plant. These soil fungi include Phyium, Verticillium and Rhizoctonia. Microorganisms are frequently present in soil, manure and decaying plant tissues (Alexander, 1997). Agriculture soil is a dynamic medium in which a large number of pathogenic and non-pathogenic fungal floras live in close association. Microbes in the soil are the key to carbon and nitrogen recycling. Microorganisms produce some useful compounds, which are beneficial to soil health, plant growth and play an important role in nutritional chains that are important part of the biological balance in the life in our plant (Paul and Clerk; 1966, Kummerer, 2004).

Some fungi are very harmful causing food spoilage and diseases to plants, animals and humans with different significant economic losses and produce mycotoxins in certain products (Manoch, 1998). There are about 75,000 species of soil fungi in the world (Finlay, 2007) but in Thailand, soil fungi, identified until 1998, numbered only 89 genera and 95 species (Manoch, 2004). Many studies of soil fungi in Thailand in the past emphasized species diversity in soil ample collected from various agricultural areas and forest types (Manoch, 1993, 1998: Kosol, 1999; Manoch etal., 2000; Dethoup et al., 2007). However, relatively few studies have made efforts to compare quantitatively the fungal diversity among different habitats.

On the other hand, some fungi play a vital role as major decomposers in the soil ecosystem. They also provide mankind with very useful pharmaceutical products such as antibiotics and other valuable substances including organic acids, enzymes, pigments and secondary metabolites used in food industry and fermentation. In addition, many soil fungi are biological control agents for plant pathogens and insect pests.

There have been also very few studies on the relationships of soil fungal diversity with environmental factors. Wongseenin, (1971) reported that the soil fungal population and diversity were higher in the dry evergreen forest than in the dry dipterocarp forest on the Sakaerat Environmental research station, Nakhon Ratchasima province. These higher numbers corresponded with the higher moisture content, organic matter content, mineral levels and acidity of soil in the former type than in the latter (current) one.

Wongvuti, Y. (1993) compared the number of microorganisms (fungi and bacteria) in disturbed natural forest and in undisturbed forest following selection cutting in Kanchanaburi province and found out that two years after the cutting, there was no difference in the numbers of microorganisms between the two sites, because there had not been enough time for disturbance to change the environments of the microorganisms.

However, three years after the cutting, the number of microorganisms in the disturbed site showed a decreasing trend, as the soil that had a higher PH and lower organic matter and mineral P than the undisturbed natural forest soil. Since forest soil microbial biomass is dominated by fungi (Houston et al. 1998), studying fungal diversity in relation to soil properties may provide useful information on soil fungal diversity management of the areas.

Mycorrhizae

Those fungi that are able to live symbiotically with living plants, creating a relationship that is beneficial to both, are known as Mycorrhizae (from myco meaning fungal and rhiza meaning root). Plant root hairs are invaded by the mycelia of the mycorrhiza, which lives partly in the soil and partly in the root, and may either cover the length of the root hair as a sheath or be concentrated around its tip. The mycorrhiza obtains the carbohydrates that it requires from the root, in return providing the plant with nutrients including nitrogen and moisture. Later the plant roots will also absorb the mycelium into its own tissues.

Beneficial mycorrhizal associations are to be found in many of our edible and flowering crops. Shewell Cooper suggests that these include at least 80% of the brassica and solanum families (including tomatoes and potatoes), as well as the majority of tree species, especially in forest and woodlands. Here the mycorrhizae create a fine underground mesh that extends greatly beyond the limits of the tree’s roots, greatly increasing their feeding range and actually causing neighbouring trees to become physically interconnected. The benefits of mycorrhizal relations to their plant partners are not limited to nutrients, but can be essential for plant reproduction: In situations where little light is able to reach the forest floor, such as the North American pine forests, a young seedling cannot obtain sufficient light to photosynthesise for itself and will not grow properly in a sterile soil. But, if the ground is underlain by a mycorrhizal mat, then the developing seedling will throw down roots that can link with the fungal threads and through them obtain the nutrients it needs, often indirectly obtained from its parents or neighbouring trees.

David Attenborough points out the plant, fungi, animal relationship that creates a “Three way harmonious trio” to be found in forest ecosystems, wherein the plant/fungi symbiosis is enhanced by animals such as the wild boar, deer, mice, or flying squirrel, which feed upon the fungi’s fruiting bodies, including truffles, and cause their further spread (Private Life Of Plants, 1995). A greater understanding of the complex relationships that pervade natural systems is one of the major justifications of the organic gardener, in refraining from the use of artificial chemicals and the damage these might cause.

Recent research has shown that arbuscular mycorrhizal fungi produce glomalin, a protein that binds soil particles and stores both carbon and nitrogen. These glomalin-related soil proteins are an important part of soil organic matter (Comis and Don, 2002).

1.3.5 Symptoms of Common potting Soil Fungi

Fusarium wilt and Verticillium wilt are two of the most common soil fungi that infect grass, plants and trees. A main symptom of Fusarium wilt is a brown discoloration on a plant’s vascular system. When the bark of a main stem (slightly above the soil line) is cut and then peeled back, this brown discoloration of the plant’s vascular tissue can be clearly seen. Verticillium wilt, which afflicts many types of vegetable plants, can be detected by leaves that are discolored and limp. These signs can be seen on either individual branches or on an entire plant.

 

1.3.5 Physical Properties of Soil

The physical properties of soils, in order of decreasing importance, are texture, structure, density, porosity, consistency, temperature, colour and resistivity. Soil texture is determined by the relative proportion of the three kinds of soil mineral particles, called soil separates: sand, silt, and clay. At the next larger scale, soil structures called peds are created from the soil separates when iron oxides, carbonates, clay, silica and humus, coat particles and cause them to adhere into larger, relatively stable secondary structures. Soil density, particularly bulk density, is a measure of soil compaction. Soil porosity consists of the void part of the soil volume and is occupied by gases or water. Soil consistency is the ability of soil to stick together. Soil temperature and colour are self-defining. Resistivity refers to the resistance to conduction of electric currents and affects the rate of corrosion of metal and concrete structures. These properties may vary through the depth of a soil profile. Most of these properties determine the aeration of the soil and the ability of water to infiltrate and to be held within the soil.

1.3.6 Soil Structure

The clumping of the soil textural components of sand, silt and clay causes aggregates to form and the further association of those aggregates into larger units creates soil structures called peds (a contraction of the word pedolith). The adhesion of the soil textural components by organic substances, iron oxides, carbonates, clays, and silica, and the breakage of those aggregates from expansion-contraction, caused by freezing-thawing and wetting-drying cycles, shape soil into distinct geometric forms. The peds evolve into units which have various shapes, sizes and degrees of development (Soil Survey Division Staff, 1993). A soil clod, however, is not a ped but rather a mass of soil that results from mechanical disturbance of the soil. Soil structure affects aeration, water movement, and conduction of heat, plant root growth and resistance to erosion. Water, in turn, has its strongest effect on soil structure due to its solution and precipitation of minerals and its effect on plant growth.

Soil structure often gives clues to its texture, organic matter content, biological activity, past soil evolution, human use, and the chemical and mineralogical conditions under which the soil formed. While texture is defined by the mineral component of a soil and is an innate property of the soil that does not change with agricultural activities, soil structure can be improved or destroyed by the choice and timing of farming practices. At a smaller scale, plant roots extend into voids and remove water causing the open spaces to increase, thereby decreasing aggregate size. At the same time, roots, fungal hyphae, and earthworms create microscopic tunnels that break up peds.

At an even smaller scale, soil aggregation continues as bacteria and fungi exude sticky polysaccharides which bind soil into smaller peds. The addition of the raw organic matter that bacteria and fungi feed upon encourages the formation of this desirable soil structure (Soil Structure, 2012).

At the lowest scale, the soil chemistry affects the aggregation or dispersal of soil particles. The clay particles contain polyvalent cations which give the faces of clay layers localized negative charges. At the same time, the edges of the clay plates have a slight positive charge, thereby allowing the edges to adhere to the negative charges on the faces of other clay particles or to flocculate (form clumps). On the other hand, when monovalent ions, such as sodium, invade and displace the polyvalent cations, they weaken the positive charges on the edges, while the negative surface charges are relatively strengthened. This leaves negative charge on the clay faces that repel other clay, causing the particles to push apart, and by doing,the flocculation of clay particles into larger, open assemblages. As a result, the clay disperses and settles into voids between peds, causing those to close. In this way the open structure of the soil is destroyed and the soil is made impenetrable to air and water. Such sodic soil tends to form columnar structures near the surface (Soil structure, 2012).

1.3.7 Soil Nutrients

Sixteen elements or nutrients are essential for plant growth and reproduction. They are carbon C, hydrogen H, oxygen O, nitrogen N, phosphorus P, potassium K, sulfur S, calcium Ca, magnesium Mg, iron Fe, boron B, manganese Mn, copper Cu, zinc Zn, molybdenum Mo, and chlorine Cl. Nutrients required for plants to complete their life cycle are considered essential nutrients. Nutrients that enhance the growth of plants but are not necessary to complete the plant’s life cycle are considered non-essential. With the exception of carbon, hydrogen and oxygen, which are supplied by carbon dioxide and water, the nutrients derive originally from the mineral component of the soil.

Plant uptake of nutrients can only proceed when they are present in a plant-available form. In most situations, nutrients are absorbed in an ionic form from (or together with) soil water. Although minerals are the origin of most nutrients, and the bulk of most nutrient elements in the soil is held in crystalline form within primary and secondary minerals, they weather too slowly to support rapid plant growth. For example, The application of finely ground minerals, feldspar and apatite, to soil seldom provides the necessary amounts of potassium and phosphorus at a rate sufficient for good plant growth, as most of the nutrients remain bound in the crystals of those minerals (Soil Structure, 2012).

The nutrients adsorbed onto the surfaces of clay colloids and soil organic matter provide a more accessible reservoir of many plant nutrients (e.g. K, Ca, Mg, P, Zn). As plants absorb the nutrients from the soil water, the soluble pool is replenished from the surface-bound pool. The decomposition of soil organic matter by microorganisms is another mechanism whereby the soluble pool of nutrients is replenished – this is important for the supply of plant-available N, S, P, and B from soil (Soil Structure, 2012).

Gram for gram, the capacity of humus to hold nutrients and water is far greater than that of clay minerals. All in all, small amounts of humus may remarkably increase the soil’s capacity to promote plant growth.

Nitrogen is the most critical element obtained by plants from the soil and nitrogen deficiency often limits plant growth. Plants can use the nitrogen as either the ammonium cation (NH4+) or the anion nitrate (NO3). Usually, most of the nitrogen in soil is bound within organic compounds that make up the soil organic matter, and must be mineralized to the ammonium or nitrate form before it can be taken up by most plants. The total nitrogen content depends largely on the soil organic matter content, which in turn depends on the climate, vegetation, topography, age and soil management. Soil nitrogen typically decreases by 0.2 to 0.3% for every temperature increase by 10 °C. Usually, grassland soils contain more soil nitrogen than forest soils. Cultivation decreases soil nitrogen by exposing soil organic matter to decomposition by microorganisms, and soils under no-tillage maintain more soil nitrogen than tilled soils (Soil Structure, 2012).

Some micro-organisms are able to metabolise organic matter and release ammonium in a process called mineralisation. Others take free ammonium and oxidise it to nitrate. Nitrogen-fixing bacteria are capable of metabolising N2 into the form of ammonia in a process called nitrogen fixation. Both ammonium and nitrate can be immobilized by their incorporation into the microbes’ living cells, where it is temporarily sequestered in the form of amino acids and protein. Nitrate may also be lost from the soil when bacteria metabolise it to the gases N2 and N2O. The loss of gaseous forms of nitrogen to the atmosphere due to microbial action is called denitrification. Nitrogen may also be leached from the soil if it is in the form of nitrate or lost to the atmosphere as ammonia due to a chemical reaction of ammonium with alkaline soil by way of a process called volatilisation. Ammonium may also be sequestered in clay by fixation. A small amount of nitrogen is added to soil by rainfall (Soil Structure, 2012).

Micronutrients

The micronutrients essential for plant life, in their order of importance, include iron, manganese,  zinc, copper, boron, chlorine and molybdenum. The term refers to plants’ needs, not to their abundance in soil. They are required in very small amounts but are essential to plant health in that most are required parts of some enzyme system which speeds up plants’ metabolisms. They are generally available in the mineral component of the soil, but the heavy application of phosphates can cause a deficiency in zinc and iron by the formation of insoluble zinc and iron phosphates. Iron deficiency may also result from excessive amounts of heavy metals or calcium minerals (lime) in the soil. Excess amounts of soluble boron, molybdenum and chloride are toxic.

Non-Essential Nutrients

Nutrients which enhance the health but whose deficiency does not stop the life cycle of plants include: cobalt, strontium, vanadium, silicon and nickel. As their importance are evaluated they may be added to the list of essential plant nutrients.

Soil Organic Matter

Soil organic matter is made up of organic compounds and includes plant, animal and microbial material, both living and dead. A typical soil has a biomass composition of 70% microorganisms, 22% macrofauna, and 8% roots. The living component of an acre of soil may include 900 lb of earthworms, 2400 lb of fungi, 1500 lb of bacteria, 133 lb of protozoa and 890 lb of arthropods and algae.

A small part of the organic matter consists of the living cells such as bacteria, molds, and actinomycetes that work to break down the dead organic matter. Were it not for the action of these micro-organisms, the entire carbon dioxide part of the atmosphere would be sequestered as organic matter in the soil.

Most living things in soils, including plants, insects, bacteria, and fungi, are dependent on organic matter for nutrients and/or energy. Soils have organic compounds in varying degrees of decomposition which rate is dependent on the temperature, soil moisture, and aeration. Bacteria and fungi feed on the raw organic matter, which are fed upon by amoebas, which in turn are fed upon by nematodes and arthropods. Organic matter holds soils open, allowing the infiltration of air and water, and may hold as much as twice its weight in water. Many soils, including desert and rocky-gravel soils, have little or no organic matter. Soils that are all organic matter, such as peat (histosols), are infertile.[181] In its earliest stage of decomposition, the original organic material is often called raw organic matter. The final stage of decomposition is called humus.

In grassland, much of the organic matter added to the soil is from the deep, fibrous, grass root systems. By contrast, tree leaves falling on the forest floor are the principal source of soil organic matter in the forest. Another difference is the frequent occurrence in the grasslands of fires that destroy large amounts of aboveground material but stimulate even greater contributions from roots. Also, the much greater acidity under any forests inhibits the action of certain soil organisms that otherwise would mix much of the surface litter into the mineral soil. As a result, the soils under grasslands generally develop a thicker A horizon with a deeper distribution of organic matter than in comparable soils under forests, which characteristically store most of their organic matter in the forest floor (O horizon) and thin A horizon (Soil Structure, 2012).

Humus

Humus refers to organic matter that has been decomposed by soil flora and fauna to the point where it is resistant to further breakdown. Humus usually constitutes only five percent of the soil or less by volume, but it is an essential source of nutrients and adds important textural qualities crucial to soil health and plant growth. Humus also hold bits of undecomposed organic matter which feed arthropods and worms which further improve the soil. The end product, humus, is soluble in water and forms a weak acid that can attack silicate minerals.[182] Humus is a colloid with a high cation and anion exchange capacity that on a dry weight basis is many times greater than that of clay colloids. It also acts as a buffer, like clay, against changes in pH and soil moisture.

Humic acids and fulvic acids, which begin as raw organic matter, are important constituents of humus. After the death of plants and animals, microbes begin to feed on the residues, resulting finally in the formation of humus. With decomposition, there is a reduction of water-soluble constituents, cellulose and hemicellulose, and nutrients such as nitrogen, phosphorus, and sulfur. As the residues break down, only stable molecules made of aromatic carbon rings, oxygen and hydrogen remain in the form of humin, lignin and lignin complexes collectively called humus. While the structure of humus has few nutrients, it is able to attract and hold cation and anion nutrients by weak bonds that can be released into the soil solution in response to changes in soil pH (Pimentel, D., 1995).

Lignin is resistant to breakdown and accumulates within the soil. It also reacts with amino acids, which further increases its resistance to decomposition, including enzymatic decomposition by microbes. Fats and waxes from plant matter have some resistance to decomposition and persist in soils for a while. Clay soils often have higher organic contents that persist longer than soils without clay as the organic molecules adhere to and are stabilised by the clay. Proteins normally decompose readily, but when bound to clay particles, they become more resistant to decomposition. Clay particles also absorb the enzymes exuded by microbes which would normally break down proteins. The addition of organic matter to clay soils can render that organic matter and any added nutrients inaccessible to plants and microbes for many years. High soil tannin (polyphenol) content can cause nitrogen to be sequestered in proteins or cause nitrogen immobilization (Vertaik, et al., 2006).

Humus formation is a process dependent on the amount of plant material added each year and the type of base soil. Both are affected by climate and the type of organisms present. Soils with humus can vary in nitrogen content but typically have 3 to 6 percent nitrogen. Raw organic matter, as a reserve of nitrogen and phosphorus, is a vital component affecting soil fertility (Pimentel, 1995). Humus also absorbs water, and expands and shrinks between dry and wet states, increasing soil porosity. Humus is less stable than the soil’s mineral constituents, as it is reduced by microbial decomposition, and over times its concentration diminshes without the addition of new organic matter. However, humus may persist over centuries if not millennia.