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31: Soil and Plant Nutrition - Biology

31: Soil and Plant Nutrition - Biology


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31: Soil and Plant Nutrition

The Chemical Composition of Plants

Since plants require nutrients in the form of elements such as carbon and potassium, it is important to understand the chemical composition of plants. The majority of volume in a plant cell is water it typically comprises 80 to 90 percent of the plant’s total weight. Soil is the water source for land plants, and can be an abundant source of water, even if it appears dry. Plant roots absorb water from the soil through root hairs and transport it up to the leaves through the xylem. As water vapor is lost from the leaves, the process of transpiration and the polarity of water molecules (which enables them to form hydrogen bonds) draws more water from the roots up through the plant to the leaves ([Figure 1]). Plants need water to support cell structure, for metabolic functions, to carry nutrients, and for photosynthesis.

Figure 1: Water is absorbed through the root hairs and moves up the xylem to the leaves.

Plant cells need essential substances, collectively called nutrients, to sustain life. Plant nutrients may be composed of either organic or inorganic compounds. An organic compound is a chemical compound that contains carbon, such as carbon dioxide obtained from the atmosphere. Carbon that was obtained from atmospheric CO2 composes the majority of the dry mass within most plants. An inorganic compound does not contain carbon and is not part of, or produced by, a living organism. Inorganic substances, which form the majority of the soil solution, are commonly called minerals: those required by plants include nitrogen (N) and potassium (K) for structure and regulation.


Chapter Summary

Plants can absorb inorganic nutrients and water through their root system, and carbon dioxide from the environment. The combination of organic compounds, along with water, carbon dioxide, and sunlight, produce the energy that allows plants to grow. Inorganic compounds form the majority of the soil solution. Plants access water though the soil. Water is absorbed by the plant root, transports nutrients throughout the plant, and maintains the structure of the plant. Essential elements are indispensable elements for plant growth. They are divided into macronutrients and micronutrients. The macronutrients plants require are carbon, nitrogen, hydrogen, oxygen, phosphorus, potassium, calcium, magnesium, and sulfur. Important micronutrients include iron, manganese, boron, molybdenum, copper, zinc, chlorine, nickel, cobalt, silicon and sodium.

31.2 The Soil

Plants obtain mineral nutrients from the soil. Soil is the outer loose layer that covers the surface of Earth. Soil quality depends on the chemical composition of the soil, the topography, the presence of living organisms, the climate, and time. Agricultural practice and history may also modify the characteristics and fertility of soil. Soil consists of four major components: 1) inorganic mineral matter, 2) organic matter, 3) water and air, and 4) living matter. The organic material of soil is made of humus, which improves soil structure and provides water and minerals. Soil inorganic material consists of rock slowly broken down into smaller particles that vary in size, such as sand, silt, and loam.

Soil formation results from a combination of biological, physical, and chemical processes. Soil is not homogenous because its formation results in the production of layers called a soil profile. Factors that affect soil formation include: parent material, climate, topography, biological factors, and time. Soils are classified based on their horizons, soil particle size, and proportions. Most soils have four distinct horizons: O, A, B, and C.

31.3 Nutritional Adaptations of Plants

Atmospheric nitrogen is the largest pool of available nitrogen in terrestrial ecosystems. However, plants cannot use this nitrogen because they do not have the necessary enzymes. Biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen to ammonia. The most important source of BNF is the symbiotic interaction between soil bacteria and legumes. The bacteria form nodules on the legume’s roots in which nitrogen fixation takes place. Fungi form symbiotic associations (mycorrhizae) with plants, becoming integrated into the physical structure of the root. Through mycorrhization, the plant obtains minerals from the soil and the fungus obtains photosynthate from the plant root. Ectomycorrhizae form an extensive dense sheath around the root, while endomycorrhizae are embedded within the root tissue. Some plants—parasites, saprophytes, symbionts, epiphytes, and insectivores—have evolved adaptations to obtain their organic or mineral nutrition from various sources.


31.3 Nutritional Adaptations of Plants

By the end of this section, you will be able to do the following:

  • Understand the nutritional adaptations of plants
  • Describe mycorrhizae
  • Explain nitrogen fixation

Plants obtain food in two different ways. Autotrophic plants can make their own food from inorganic raw materials, such as carbon dioxide and water, through photosynthesis in the presence of sunlight. Green plants are included in this group. Some plants, however, are heterotrophic: they are totally parasitic and lacking in chlorophyll. These plants, referred to as holo-parasitic plants, are unable to synthesize organic carbon and draw all of their nutrients from the host plant.

Plants may also enlist the help of microbial partners in nutrient acquisition. Particular species of bacteria and fungi have evolved along with certain plants to create a mutualistic symbiotic relationship with roots. This improves the nutrition of both the plant and the microbe. The formation of nodules in legume plants and mycorrhization can be considered among the nutritional adaptations of plants. However, these are not the only type of adaptations that we may find many plants have other adaptations that allow them to thrive under specific conditions.

Link to Learning

This video reviews basic concepts about photosynthesis. In the left panel, click each tab to select a topic for review.

Nitrogen Fixation: Root and Bacteria Interactions

Nitrogen is an important macronutrient because it is part of nucleic acids and proteins. Atmospheric nitrogen, which is the diatomic molecule N2, or dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. However, plants cannot take advantage of this nitrogen because they do not have the necessary enzymes to convert it into biologically useful forms. However, nitrogen can be “fixed,” which means that it can be converted to ammonia (NH3) through biological, physical, or chemical processes. As you have learned, biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen (N2) into ammonia (NH3), exclusively carried out by prokaryotes such as soil bacteria or cyanobacteria. Biological processes contribute 65 percent of the nitrogen used in agriculture. The following equation represents the process:

The most important source of BNF is the symbiotic interaction between soil bacteria and legume plants, including many crops important to humans (Figure 31.10). The NH3 resulting from fixation can be transported into plant tissue and incorporated into amino acids, which are then made into plant proteins. Some legume seeds, such as soybeans and peanuts, contain high levels of protein, and serve among the most important agricultural sources of protein in the world.

Visual Connection

Farmers often rotate corn (a cereal crop) and soy beans (a legume), planting a field with each crop in alternate seasons. What advantage might this crop rotation confer?

Soil bacteria, collectively called rhizobia , symbiotically interact with legume roots to form specialized structures called nodules , in which nitrogen fixation takes place. This process entails the reduction of atmospheric nitrogen to ammonia, by means of the enzyme nitrogenase . Therefore, using rhizobia is a natural and environmentally friendly way to fertilize plants, as opposed to chemical fertilization that uses a nonrenewable resource, such as natural gas. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen from the atmosphere. The process simultaneously contributes to soil fertility because the plant root system leaves behind some of the biologically available nitrogen. As in any symbiosis, both organisms benefit from the interaction: the plant obtains ammonia, and bacteria obtain carbon compounds generated through photosynthesis, as well as a protected niche in which to grow (Figure 31.11).

Mycorrhizae: The Symbiotic Relationship between Fungi and Roots

A nutrient depletion zone can develop when there is rapid soil solution uptake, low nutrient concentration, low diffusion rate, or low soil moisture. These conditions are very common therefore, most plants rely on fungi to facilitate the uptake of minerals from the soil. Fungi form symbiotic associations called mycorrhizae with plant roots, in which the fungi actually are integrated into the physical structure of the root. The fungi colonize the living root tissue during active plant growth.

Through mycorrhization, the plant obtains mainly phosphate and other minerals, such as zinc and copper, from the soil. The fungus obtains nutrients, such as sugars, from the plant root (Figure 31.12). Mycorrhizae help increase the surface area of the plant root system because hyphae, which are narrow, can spread beyond the nutrient depletion zone. Hyphae can grow into small soil pores that allow access to phosphorus that would otherwise be unavailable to the plant. The beneficial effect on the plant is best observed in poor soils. The benefit to fungi is that they can obtain up to 20 percent of the total carbon accessed by plants. Mycorrhizae functions as a physical barrier to pathogens. It also provides an induction of generalized host defense mechanisms, and sometimes involves production of antibiotic compounds by the fungi.

There are two types of mycorrhizae: ectomycorrhizae and endomycorrhizae. Ectomycorrhizae form an extensive dense sheath around the roots, called a mantle. Hyphae from the fungi extend from the mantle into the soil, which increases the surface area for water and mineral absorption. This type of mycorrhizae is found in forest trees, especially conifers, birches, and oaks. Endomycorrhizae, also called arbuscular mycorrhizae, do not form a dense sheath over the root. Instead, the fungal mycelium is embedded within the root tissue. Endomycorrhizae are found in the roots of more than 80 percent of terrestrial plants.

Nutrients from Other Sources

Some plants cannot produce their own food and must obtain their nutrition from outside sources. This may occur with plants that are parasitic or saprophytic. Some plants are mutualistic symbionts, epiphytes, or insectivorous.

Plant Parasites

A parasitic plant depends on its host for survival. Some parasitic plants have no leaves. An example of this is the dodder (Figure 31.13), which has a weak, cylindrical stem that coils around the host and forms suckers. From these suckers, cells invade the host stem and grow to connect with the vascular bundles of the host. The parasitic plant obtains water and nutrients through these connections. The plant is a total parasite (a holoparasite) because it is completely dependent on its host. Other parasitic plants (hemiparasites) are fully photosynthetic and only use the host for water and minerals. There are about 4,100 species of parasitic plants.

Saprophytes

A saprophyte is a plant that does not have chlorophyll and gets its food from dead matter, similar to bacteria and fungi (note that fungi are often called saprophytes, which is incorrect, because fungi are not plants). Plants like these use enzymes to convert organic food materials into simpler forms from which they can absorb nutrients (Figure 31.14). Most saprophytes do not directly digest dead matter: instead, they parasitize fungi that digest dead matter, or are mycorrhizal, ultimately obtaining photosynthate from a fungus that derived photosynthate from its host. Saprophytic plants are uncommon only a few species are described.

Symbionts

A symbiont is a plant in a symbiotic relationship, with special adaptations such as mycorrhizae or nodule formation. Fungi also form symbiotic associations with cyanobacteria and green algae (called lichens). Lichens can sometimes be seen as colorful growths on the surface of rocks and trees (Figure 31.15). The algal partner (phycobiont) makes food autotrophically, some of which it shares with the fungus the fungal partner (mycobiont) absorbs water and minerals from the environment, which are made available to the green alga. If one partner was separated from the other, they would both die.

Epiphytes

An epiphyte is a plant that grows on other plants, but is not dependent upon the other plant for nutrition (Figure 31.16). Epiphytes have two types of roots: clinging aerial roots, which absorb nutrients from humus that accumulates in the crevices of trees and aerial roots, which absorb moisture from the atmosphere.

Insectivorous Plants

An insectivorous plant has specialized leaves to attract and digest insects. The Venus flytrap is popularly known for its insectivorous mode of nutrition, and has leaves that work as traps (Figure 31.17). The minerals it obtains from prey compensate for those lacking in the boggy (low pH) soil of its native North Carolina coastal plains. There are three sensitive hairs in the center of each half of each leaf. The edges of each leaf are covered with long spines. Nectar secreted by the plant attracts flies to the leaf. When a fly touches the sensory hairs, the leaf immediately closes. Next, fluids and enzymes break down the prey and minerals are absorbed by the leaf. Since this plant is popular in the horticultural trade, it is threatened in its original habitat.


Review Questions

For an element to be regarded as essential, all of the following criteria must be met, except:

  1. No other element can perform the function.
  2. The element is directly involved in plant nutrition.
  3. The element is inorganic.
  4. The plant cannot complete its lifecycle without the element.

The nutrient that is part of carbohydrates, proteins, and nucleic acids, and that forms biomolecules, is ________.

Most ________ are necessary for enzyme function.

What is the main water source for land plants?

Which factors affect soil quality?

  1. chemical composition
  2. history of the soil
  3. presence of living organisms and topography
  4. all of the above

Soil particles that are 0.1 to 2 mm in diameter are called ________.

A soil consists of layers called ________ that taken together are called a ________.

  1. soil profiles : horizon
  2. horizons : soil profile
  3. horizons : humus
  4. humus : soil profile

What is the term used to describe the solid rock that lies beneath the soil?

Which process produces an inorganic compound that plants can easily use?

Through mycorrhization, a plant obtains important nutrients such as ________.

  1. phosphorus, zinc, and copper
  2. phosphorus, zinc, and calcium
  3. nickel, calcium, and zinc
  4. all of the above

What term describes a plant that requires nutrition from a living host plant?

What is the term for the symbiotic association between fungi and cyanobacteria?

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    Calcium in Soil Structure and Plant Nutrition

    Calcium plays a critical role in crop yield and quality. To understand the function and role in agronomy, it should be understood from a plant point of view, and from a soil point of view. It is critical that plant calcium nutrition be addressed early and adequately. It is equally critical that soil calcium is constant and consistent throughout the growing season to maintain soil structure.

    Calcium is important in soil structure. Calcium in soils comes in many forms. Calcium is present in most soils as insoluble calcium carbonate (CaCO3-). When high levels of phosphoric acid are utilized in agricultural cropping systems, most of the phosphorous is tied up with ionic calcium to form insoluble calcium phosphate (CaPO4). Only ionic calcium (Ca++) is able to affect soil function and structure. To maintain soil structure, soils must maintain adequate levels of ionic calcium.


    The divalent positive charge of ionic calcium (Ca++) interacts with the negatively charged soil colloid to create soil flocculation. Calcium and organic matter have the strongest effect on soil flocculation. Soil structure is influenced in the micropore spaces of the soil where air and water exchange are taking place on a capillary scale. Since much of the calcium is in the form of insoluble calcium carbonate or calcium phosphate, it is important to manage soil biology and soil chemistry so that these insoluble calcium compounds may be broken to yield ionic calcium. Soil biology and soil humic matter are critical to improving soil ionic calcium content.

    Plants can only absorb the ionic form of Calcium (Ca++). As mentioned in the soil section, maintaining ionic calcium is very important in maintaining or improving soil structure. Equally important is the availability of calcium for plant nutrition, yield, and quality.

    Calcium plays several critical roles in plant nutrition, namely cell wall structure and stabilization, membrane structure and function, root growth and development, and plant cell signaling.

    Cell wall Structure and Stabilization

    The majority of plant calcium is found in the plant cell walls, mainly in the outer portion of the plant cell wall (middle lamella). Pectin is a structural carbohydrate in plants. Plants higher in calcium will form calcium pectate. Calcium pectate is the main form of pectin in plant cell walls. The amount of calcium and calcium pectate in cell walls directly affects the form and function of the plant cell wall. Plants high in calcium pectate will have improved cell wall structure and will be less susceptible to invasive disease and insects.


    Membrane Stabilization and Function

    Plant cell membranes act as barriers to the movement of molecules. In plants, active solute transport will improve overall plant quality and reduce pest and pathogen presence. Calcium acts in plant membranes to improve active solute transport thru the membrane by bridging phosphate and carboxylate compounds and binding them to the membrane surface. This calcium function stabilizes the cell membrane and reduces leakage and/or passive movement of cell solutes. Reducing leakage and passive movement of cell solutes will reduce invasive pests and pathogens.

    Root growth

    In the absence of soil solution calcium, root growth will cease. Calcium is critical for root cap formation and strength, and thus for root growth and development. Directly behind the root cap is the zone of highly active cell division, promoting root growth. As calcium is critical in cell structure and membrane stability, he soil solution concentration of calcium will determine root growth and structure.

    Plant Cell Signaling

    Plant cells have the ability to communicate abiotic or biotic pressure and communicate via calcium binding proteins within plant cells. As environmental stresses change, calcium will bind to proteins based on what the environmental stress is. This in turn will dictate physiological and metabolic changes in the plant to respond to the stress event, allowing the plant to adapt and thus reducing the negative influences of stress.


    How to influence calcium nutrition.

    To study calcium agronomically is to study both soil and plant. You cannot have adequate soil ionic calcium for improved soil structure without plant influence (soil biology and organic matter). Conversely you cannot have adequate plant calcium nutrition without proper soil structure. One acts on the other. It is critically that from an agronomic perspective, action is taken to improve soil biology to maintain adequate soil structure and plant available calcium.

    At Redox, we provide calcium in a microencapsulated form. As water is added, the microencapsulation is influenced, and ionic calcium is released into the environment Microencapsulation is important in that it prevents calcium tie-up and allows calcium to be transported via water movement to soil micropores. It is in these micropores that calcium is influential in improving soil structure.

    Microencapsulation is also important in calcium plant nutrition. As the plant absorbs water, it also absorbs the minerals in the water. Microencapsulated calcium is able to be absorbed into plant roots via water transpiration. Once inside the plant, the microencapsulation is broken down, and ionic calcium is delivered to the plant for utilization in metabolic processes.

    The importance of the microencapsulation process cannot be overstated. During early season growth, it is not possible for the soil solution to provide the demands of high yielding crops.


    31.1 Nutritional Requirements of Plants

    By the end of this section, you will be able to do the following:

    • Describe how plants obtain nutrients
    • List the elements and compounds required for proper plant nutrition
    • Describe an essential nutrient

    Plants are unique organisms that can absorb nutrients and water through their root system, as well as carbon dioxide from the atmosphere. Soil quality and climate are the major determinants of plant distribution and growth. The combination of soil nutrients, water, and carbon dioxide, along with sunlight, allows plants to grow.

    The Chemical Composition of Plants

    Since plants require nutrients in the form of elements such as carbon and potassium, it is important to understand the chemical composition of plants. The majority of volume in a plant cell is water it typically comprises 80 to 90 percent of the plant’s total weight. Soil is the water source for land plants, and can be an abundant source of water, even if it appears dry. Plant roots absorb water from the soil through root hairs and transport it up to the leaves through the xylem. As water vapor is lost from the leaves, the process of transpiration and the polarity of water molecules (which enables them to form hydrogen bonds) draws more water from the roots up through the plant to the leaves (Figure 31.2). Plants need water to support cell structure, for metabolic functions, to carry nutrients, and for photosynthesis.

    Plant cells need essential substances, collectively called nutrients, to sustain life. Plant nutrients may be composed of either organic or inorganic compounds. An organic compound is a chemical compound that contains carbon, such as carbon dioxide obtained from the atmosphere. Carbon that was obtained from atmospheric CO2 composes the majority of the dry mass within most plants. An inorganic compound does not contain carbon and is not part of, or produced by, a living organism. Inorganic substances, which form the majority of the soil solution, are commonly called minerals: those required by plants include nitrogen (N) and potassium (K) for structure and regulation.

    Essential Nutrients

    Plants require only light, water, and about 20 elements to support all their biochemical needs: these 20 elements are called essential nutrients (Table 31.1). For an element to be regarded as essential , three criteria are required: 1) a plant cannot complete its life cycle without the element 2) no other element can perform the function of the element and 3) the element is directly involved in plant nutrition.

    Macronutrients Micronutrients
    Carbon (C) Iron (Fe)
    Hydrogen (H) Manganese (Mn)
    Oxygen (O) Boron (B)
    Nitrogen (N) Molybdenum (Mo)
    Phosphorus (P) Copper (Cu)
    Potassium (K) Zinc (Zn)
    Calcium (Ca) Chlorine (Cl)
    Magnesium (Mg) Nickel (Ni)
    Sulfur (S) Cobalt (Co)
    Sodium (Na)
    Silicon (Si)

    Macronutrients and Micronutrients

    The essential elements can be divided into two groups: macronutrients and micronutrients. Nutrients that plants require in larger amounts are called macronutrients . About half of the essential elements are considered macronutrients: carbon, hydrogen, oxygen, nitrogen, phosphorus, potassium, calcium, magnesium and sulfur. The first of these macronutrients, carbon (C), is required to form carbohydrates, proteins, nucleic acids, and many other compounds it is therefore present in all macromolecules. On average, the dry weight (excluding water) of a cell is 50 percent carbon. As shown in Figure 31.3, carbon is a key part of plant biomolecules.

    The next most abundant element in plant cells is nitrogen (N) it is part of proteins and nucleic acids. Nitrogen is also used in the synthesis of some vitamins. Hydrogen and oxygen are macronutrients that are part of many organic compounds, and also form water. Oxygen is necessary for cellular respiration plants use oxygen to store energy in the form of ATP. Phosphorus (P), another macromolecule, is necessary to synthesize nucleic acids and phospholipids. As part of ATP, phosphorus enables food energy to be converted into chemical energy through oxidative phosphorylation. Likewise, light energy is converted into chemical energy during photophosphorylation in photosynthesis, and into chemical energy to be extracted during respiration. Sulfur is part of certain amino acids, such as cysteine and methionine, and is present in several coenzymes. Sulfur also plays a role in photosynthesis as part of the electron transport chain, where hydrogen gradients play a key role in the conversion of light energy into ATP. Potassium (K) is important because of its role in regulating stomatal opening and closing. As the openings for gas exchange, stomata help maintain a healthy water balance a potassium ion pump supports this process.

    Magnesium (Mg) and calcium (Ca) are also important macronutrients. The role of calcium is twofold: to regulate nutrient transport, and to support many enzyme functions. Magnesium is important to the photosynthetic process. These minerals, along with the micronutrients, which are described below, also contribute to the plant’s ionic balance.

    In addition to macronutrients, organisms require various elements in small amounts. These micronutrients , or trace elements, are present in very small quantities. They include boron (B), chlorine (Cl), manganese (Mn), iron (Fe), zinc (Zn), copper (Cu), molybdenum (Mo), nickel (Ni), silicon (Si), and sodium (Na).

    Deficiencies in any of these nutrients—particularly the macronutrients—can adversely affect plant growth (Figure 31.4). Depending on the specific nutrient, a lack can cause stunted growth, slow growth, or chlorosis (yellowing of the leaves). Extreme deficiencies may result in leaves showing signs of cell death.

    Link to Learning

    Visit this website to participate in an interactive experiment on plant nutrient deficiencies. You can adjust the amounts of N, P, K, Ca, Mg, and Fe that plants receive . . . and see what happens.

    Everyday Connection

    Hydroponics

    Hydroponics is a method of growing plants in a water-nutrient solution instead of soil. Since its advent, hydroponics has developed into a growing process that researchers often use. Scientists who are interested in studying plant nutrient deficiencies can use hydroponics to study the effects of different nutrient combinations under strictly controlled conditions. Hydroponics has also developed as a way to grow flowers, vegetables, and other crops in greenhouse environments. You might find hydroponically grown produce at your local grocery store. Today, many lettuces and tomatoes in your market have been hydroponically grown.

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      Rhizobia and legumes: mutualistic relationship between bacteria and roots

      Nitrogen is an important macronutrient because it is part of nucleic acids and proteins. Atmospheric nitrogen, which is the diatomic molecule N2, or dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. However, plants cannot take advantage of this nitrogen because they do not have the necessary enzymes to convert it into biologically useful forms. However, nitrogen can be “fixed”which means that it can be converted to ammonia (NH3) through biological, physical, or chemical processes. Biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen (N2) into ammonia (NH3), exclusively carried out by prokaryotes such as soil bacteria or cyanobacteria. Biological processes contribute 65 percent of the nitrogen used in agriculture.

      The most important source of BNF is the symbiotic and mutualistic interaction between soil bacteria and legume plants, including many crops important to humans. The NH3 resulting from fixation can be transported into plant tissue and incorporated into amino acids, which are then made into plant proteins. Some legume seeds, such as soybeans and peanuts, contain high levels of protein, and serve among the most important agricultural sources of protein in the world.

      Specific soil bacteria called rhizobiacan symbiotically interact with legume roots to form specialized structures called nodules , in which nitrogen fixation takes place. This process entails the reduction of atmospheric nitrogen to ammonia, by means of the enzyme nitrogenase . Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen from the atmosphere. The process simultaneously contributes to soil fertility because the plant root system leaves behind some of the biologically available nitrogen. As in any symbiotic mutualism , both organisms benefit from the interaction: the plant obtains ammonia, and bacteria obtain carbon compounds generated through photosynthesis, as well as a protected niche in which to grow. Importantly, the nitrogenase enzyme is inactivated in the presence of oxygen, and thus the root nodules help maintain a low concentration of oxygen to “protect” the nitrogenase within the rhizobia from oxygen poisoning.

      Soybean roots contain (a) nitrogen-fixing nodules. Cells within the nodules are infected with Bradyrhyzobium japonicum, a rhizobia or “root-loving” bacterium. The bacteria are encased in (b) vesicles inside the cell, as can be seen in this transmission electron micrograph. (credit a: modification of work by USDA credit b: modification of work by Louisa Howard, Dartmouth Electron Microscope Facility scale-bar data from Matt Russell)


      Using Sequence Data to Predict Microbial Effects on Plant N, P, and S Nutrition

      Mechanisms of Microbial Nutrient Provision to Plants

      As described above, plants give large amount of carbon away to the rhizosphere that nourishes soil microorganisms. So what do plants get back? In natural soils the vast majority of N, P, and S atoms are organically bound, while in the atmosphere the vast majority of N is contained in the N2 molecule. Due to the different metabolic capacities of plants and microbes, these nutrient sources are minimally bioavailable to plants, but can be metabolized by various soil microbes. This means that nitrogen fixing and nutrient mineralization processes carried out by soil microbes are crucial for plant nutrition in natural ecosystems, because these reactions metabolize recalcitrant forms of N, P, and S to liberate these elements for plant nutrition (Rovira, 1965 van der Heijden et al., 2008). It must be briefly stated that this established paradigm has been somewhat questioned in recent years, as several studies have demonstrated direct plant uptake of various organic-N forms (Nasholm et al., 1998 Paungfoo-Lonhienne et al., 2008). However, it is still generally accepted that microbes are better competitors for these nutrients due to the low diffusivity of organic-N molecules in soil, and the results of isotope labeling studies generally support the concept that most organic-N is first assimilated by microbial taxa, then subsequently assimilated by plants upon microbial turnover (Richardson et al., 2009 Kuzyakov and Xu, 2013).

      Over several decades, the soil microbiology literature has accumulated a list of microbial metabolic processes that are linked to plant N, P, and S nutrition (summarized in Table ​ Table1 1 ). Commercially, the symbiotic association between legumes and bacteria is routinely exploited when field crops are inoculated with nitrogen-fixing rhizobia strains (Bashan et al., 2014). But, how can this phenomenon be refined and optimized for widespread use in more sustainable agricultural systems—not only for nitrogen fixation in legumes, but also for N, P, and S nutrition in non-leguminous crops? Given that different bacterial strains exhibit differing metabolic capabilities (Brader et al., 2014 Timm et al., 2015), coupled with the huge amount of genomic sequence data from soil microbes that has recently been generated (Bai et al., 2015 Muller et al., 2016), one possibility is to pinpoint the genes that encode metabolic pathways for agriculturally beneficial N, P, and S metabolism, and to boost the microbes that contain these specific genes in agricultural soils. This section will briefly outline what are the key known bacterial genes for boosting plant N, P, and S nutrition, and what strategies exist for promoting the abundance of these genes in agricultural soils.

      Table 1

      Key microbial metabolic processes related to plant nutrition.

      ElementBiochemicalMicrobialSoil enzymologyCulture-independentCulture-dependent
      processgenesliteratureliteratureliterature
      NitrogenNitrogen fixationnifD, nifH, nifK Reganold et al., 2010 Xue et al., 2013Bremer et al., 1990
      Protein depolymerizationapr, npr, subMader et al., 2002Rasche et al., 2014Kohler et al., 2007
      Urea catabolismureA, ureB, ureCDick et al., 1988 Bowles et al., 2014Reganold et al., 2010 Fierer et al., 2012, Xue et al., 2013Kohler et al., 2007
      PhosphorousPhosphate ester cleavagephoA, phoD, phoX, ACPase, glpQ, ushA, appA, phyA, phyBMader et al., 2002 Garcia-Ruiz et al., 2008Fraser et al., 2015Kohler et al., 2007
      Phosphonate breakdownphnJ, phnX Bergkemper et al., 2016
      SulfurSulfate ester cleavageaslA, asfAGarcia-Ruiz et al., 2008Schmalenberger et al., 2008Schmalenberger et al., 2008
      Sulfonate breakdownssuD Kertesz and Mirleau, 2004

      Cultivation-Independent or Cultivation-Dependent Approaches

      The major difficulty in investigating soil microbial communities is that only a small fraction of the inhabiting taxa can be cultivated in the laboratory, where experimenters can undertake detailed and controlled analyses (Pham and Kim, 2012). Therefore, the literature investigating root-associated microbes can be roughly divided into either cultivation-independent or cultivation-dependent studies. Generally, most cultivation-independent approaches extract root-associated microbes in situ, and then analyze the properties of this community. In contrast, cultivation-dependent approaches generally inoculate soil or root-associated microbes onto laboratory growth medium, before analyzing distinct strains that have been cultivated in the laboratory. For cultivation-independent approaches, techniques typically used to analyze soil microbiota often include: (1) 16S sequencing and PLFA measurements to infer taxonomic breakdown (2) metagenomic, metatranscriptomic, or metaproteomic analyses to infer functional capacity of microbial communities and (3) enzyme assays, respiratory measurements, or substrate utilization assays to measure functional activity of microbial communities. In cultivation-dependent approaches, the analytical possibilities are multitude—once root-associated organisms have been cultivated in a laboratory setting, they can be analyzed with any available technique. In the literature, there are many studies that use both cultivation-dependent and cultivation-independent techniques to draw links between microbial properties and plant nutrition (Kertesz and Mirleau, 2004 Richardson et al., 2009). But, can these acquired data inform the rational selection of microbes that will improve plant N, P, and S nutrition?

      Microbial Taxa and Metabolic Pathways in Cultivation-Independent Literature Linked to Plant–Microbe Nutrient Transfers

      Several studies have used cultivation-independent approaches to investigate microbial community structure/function across soils exposed to different fertilization regimes (Allison et al., 2007 Williams and Hedlund, 2013 Bowles et al., 2014). Typically, these studies compare soil microbiota from highly fertilized soils against those from unfertilized or poorly fertilized soils, in situations where the low-fertilization regimes have encouraged mutualistic nutrient transfers between plants and microbes. From analyses of microbial taxonomy, it has been shown that the abundance of certain bacterial taxa is related to amount of applied fertilizer, with the copiotrophic phylum Actinobacteria being positively correlated with N fertilization, whereas the oligotrophic phylum Acidobacteria is negatively correlated (Ramirez et al., 2010, 2012). However, the results of a meta-analysis suggest that it is difficult to generalize a consistent response of microbial taxon abundance to N fertilization, because local environment and management play a dominant role in shaping microbial community structure (Geisseler and Scow, 2014). The work of Hartmann et al. (2015) examines bacterial 16S and fungal ITS2 sequences in a long-term field experiment comparing organic with conventional farming systems, showing correlations between taxon abundance and fertilization regime, with the bacterial Firmicutes phylum and several fungal taxa being more abundant on soils fertilized with manure.

      The last 15 years has seen an exPLOSion in the number of rhizospheric microbiome sequencing studies, offering new taxonomical insights into the microbial communities associated with plants (Bulgarelli et al., 2013). However, the utility of taxonomic analyses for predicting microbial community function can be questioned, because in the bacterial literature it is becoming increasingly apparent that taxonomic groupings derived from 16S homology are imperfect predictors of a bacterial strain’s functionality (Beiko, 2015). Recent studies have sequenced the whole genomes of several closely related strains, and have discovered that although these strains are categorized as closely related due to the presence of a homologous core genome, in fact there can be considerable divergence in the accessory genome, meaning that the encoded functional capacities will also be significantly different. By sequencing the bacterial 16S gene, researchers infer the phylogeny of a strain’s core genome, but it can be argued that this gives little information about metabolic traits, because many of the key genes involved in N, P, and S metabolism are accessory genes, which are not taxonomically conserved due to the high prevalence of horizontal gene transfer between bacteria (Kumar et al., 2015 Young, 2016). Therefore, metagenomics studies that profile the abundance of all gene sequences (not just 16S) should have more power to unravel links between microbial genetics and plant nutrition, although it should be remembered that only a small proportion of the soil DNA pool is actively expressed. From metagenomic studies that compare the effects of different fertilizer inputs, it seems apparent that certain genes are more abundant in soils with lower fertilizer inputs, such as urea metabolism (Fierer et al., 2012) and unclassified metabolic genes (Leff et al., 2015). These genes are thus positioned as potential targets for improving the microbial provision of plant-bioavailable N, P, and S. However, the sheer complexity of the soil microbiome makes it difficult to draw mechanistic links between specific genes and ecosystem processes, which is one of the reasons why many researchers are adopting SynCom experiments that attempt to re-construct a simplified rhizosphere microbiome in a controlled setting (Busby et al., 2017).

      In the soil biology literature, enzyme assays have established a set of enzymes linked to high-functioning soil microbiota, such as protease, urease, various phosphatases, and sulfatase (Garcia-Ruiz et al., 2008 Bowles et al., 2014). Therefore, the bacterial strains that possess the genes encoding these proteins are candidates for boosting nutrient transfers to plants. However, one challenge involves managing the stoichiometric availability of different nutrients to promote the activity of these enzymes. In the priming literature, it is generally accepted that soil microbiota are usually limited by the amount of labile C. Supply of labile carbon (e.g., root exudates) can relieve this limitation, such that N, P, or S then becomes the limiting nutrient, and microbes then express enzymes that can depolymerize recalcitrant forms of these nutrients. So, even if the soil microbiota contains strains with genes encoding the aforementioned enzymes linked to soil health, soil conditions must be optimized for these microbial proteins to be expressed and active (Paterson, 2003). Another method to measure metabolic capacity of soils involves community level physiological profiling assays, which measures substrate degradation affinity across different fertilization regimes, although usually these assays are designed with an emphasis on degradation of C-sources rather than sources of N, P, and S. This technique has been applied to soil receiving different fertilization practices, and it has been shown that the capacity to degrade a diverse range of substrates is correlated to other aspects of soil health, such as organic carbon content and disease suppression (Perez-Piqueres et al., 2006 Nair and Ngouajio, 2012 Dumontet et al., 2017). Perhaps future studies could modify this approach to develop assays that measure the capacity of soil microbes to degrade various sources of N, P, and S. However, the mechanistic insight derived from these assays is sometimes questioned, because they measure the capacity of soil microbiota to grow on specific nutrients under laboratory conditions. This setup may therefore select for a small number of fast-growing taxa and not correlate with the in situ activity of these substrate degradation pathways (Ros et al., 2008 Rutgers et al., 2016).

      Microbial Genes in Cultivation-Dependent Literature Linked to Soil Fertility

      It can be posited that soils with high rates of microbial N, P, and S cycling should harbor microbes with specialized genes encoding these traits, and therefore that microbial strains isolated from these soils should possess useful metabolic attributes for boosting plant nutrition. Interestingly, Rhizobia strains isolated from N-fertilized soils exhibited a lower capacity to promote plant growth compared to strains isolated from adjacent unfertilized plots (Weese et al., 2015), indicating that the management history of the isolation site impacts the degree of mutualism in the resulting isolate. In the P literature, a similar phenomenon has been observed, with phosphate mineralization being more common in isolates from soils where bioavailable-P was less abundant (Hu et al., 2009 Mander et al., 2012). For sulfur, one example is from soils from the Rothamsted Broadbalk experiment, where different S-fertilization practices had led to fields that exhibit high versus low sulfatase activity. Bacterial strains were isolated from these contrasting soils, and functional assays such as enzyme measurements and growth on minimal media revealed that the strains isolated from low-SO4 2- soils contained several mechanisms for depolymerizing organic-S (Schmalenberger et al., 2008). Together, these results imply that research programs seeking 𠇎lite” microbial strains that can maximally boost plant nutrition could begin with inocula from sites that favor plant–soil feedbacks, such as unfertilized soils or organic farms (Xia et al., 2015 Melo et al., 2016).

      Microbial Strains That Promote Plant Growth by Enhancing N, P, and S Nutrition

      To truly be useful in an agricultural setting, it must be proven that candidate growth-promoting strains can be re-inoculated onto plants, successfully colonize the rhizospheric niche, and then mediate nutrient mobilization that benefits plant growth. This can be tested through plant–microbe interaction assays, where candidate strains are tested for their ability to promote plant growth and nutrient acquisition (Ahemad and Kibret, 2014). Once again, this research field is most mature for the case of nitrogen-fixing Rhizobia, where decades of research have endeavored to define the optimal inoculation practice, searching for the right combination of plant genotypes and rhizobia strains to suit specific climates and soils (Lindstrom et al., 2010). Regarding the taxonomy of nitrogen-fixing symbioses, it should be mentioned that nitrogenase genes are present in diverse bacterial taxa (Gyaneshwar et al., 2011), and that non-leguminous plants have been documented to host N2-fixing bacterial strains (Santi et al., 2013), perhaps implying that other plant–microbe combinations (not just legumes and Rhizobia) could be similarly optimized to promote nitrogen fixation (Mus et al., 2016). There are also reports of plant growth promotion via microbial mobilization of other nitrogen sources, shown by higher yield in plants inoculated with bacterial strains (Shaharoona et al., 2008 Adesemoye et al., 2009), although for one of these experimental setups, it seems that the source of this N was directly from the ammonium sulfate fertilizer rather than from organically bound soil N (Adesemoye et al., 2010). It has been shown that unsterilized grass seeds can better access protein-N compared to sterilized seeds, but the specific strains that provide this service were not elucidated (White et al., 2015). The ability of the fungi Glomus intraradices to transfer organic nitrogen to plants has also been shown (Thirkell et al., 2016), suggesting that future experiments could focus on documenting other fungal strains with this capacity and characterizing the relevant genes and mechanisms. For phosphorous, the literature contains a large number of reports of both fungal and bacterial strains with the capacity to solubilize inorganic P, and also many reports of strains that can mineralize organic P (Plassard et al., 2011 Ahemad and Kibret, 2014). Many of these P-mobilizing strains are also characterized as growth promoting microbes, but microbial promotion of plant growth can operate through a wide variety of mechanisms, and sometimes it is not conclusive that P-mobilization is responsible for the plant growth promotion elicited by these strains (Richardson and Simpson, 2011). For sulfur, studies of a plant growth-promoting Pseudomonas strain have used genetic knockout of the sulfonate monooxygenase enzyme to show that organic-S mineralization accounts for some fraction of the growth-promoting phenotype (Kertesz and Mirleau, 2004).

      The research field is beginning to build large collections of genomically sequenced bacterial isolates that can be re-assembled into SynComs (Bai et al., 2015). Xia et al. (2015) isolated endophytic bacterial strains from plants grown under organic management, and showed that over half of these strains can boost tomato growth in a greenhouse experiment. This high proportion of growth-promoting isolates shows that the capacity to promote plant growth is widespread amongst plant-associated bacteria, but to gain a mechanistic understanding into how these growth-promoting effects are manifested, it will be necessary to conduct detailed investigations into the genetics, biochemistry and physiology of these growth-promoting strains. Furthermore, microbial community experiments should also consider how the interaction between different strains affects plant growth promotion. Such knowledge will enable the rational selection of growth-promoting strains and communities, driven by defined genetic and biochemical mechanisms.


      The Role of Soil pH in Plant Nutrition and Soil Remediation

      In the natural environment, soil pH has an enormous influence on soil biogeochemical processes. Soil pH is, therefore, described as the “master soil variable” that influences myriads of soil biological, chemical, and physical properties and processes that affect plant growth and biomass yield. This paper discusses how soil pH affects processes that are interlinked with the biological, geological, and chemical aspects of the soil environment as well as how these processes, through anthropogenic interventions, induce changes in soil pH. Unlike traditional discussions on the various causes of soil pH, particularly soil acidification, this paper focuses on relationships and effects as far as soil biogeochemistry is concerned. Firstly, the effects of soil pH on substance availability, mobility, and soil biological processes are discussed followed by the biogenic regulation of soil pH. It is concluded that soil pH can broadly be applied in two broad areas, i.e., nutrient cycling and plant nutrition and soil remediation (bioremediation and physicochemical remediation).

      1. Introduction

      To many, soil pH is only essential for the chemistry and fertility of soils. However, the recognition of soil functions beyond plant nutrient supply and the role soil as a medium of plant growth required the study of the soil and its properties in light of broader ecosystem functions through a multidisciplinary approach. This allows scientists to view processes from landscape to regional and global levels. One process that denotes the multidisciplinary approach to soil science is soil biogeochemistry, which studies biogeochemical processes. The ecosystem functions of soil, to some extent, have a strong relationship with soil biogeochemical processes, which are linkages between biological, chemical, and geological processes [1]. The soil is the critical element of life support systems because it delivers several ecosystem goods and services such as carbon storage, water regulation, soil fertility, and food production, which have effects on human well-being [2–4]. These ecosystem goods and services are broadly categorized as supporting, provisioning, regulating, and cultural services [5]. According to the Millennium Ecosystem Assessment [5], the provisioning and regulating functions are said to have the greatest impact on the components of human well-being in terms of safety, the basic material for a good life, health, and good social relations.

      In the natural environment, the pH of the soil has an enormous influence on soil biogeochemical processes. Soil pH is, therefore, described as the “master soil variable” that influences myriads of soil biological, chemical, and physical properties and processes that affect plant growth and biomass yield [6, 7]. Soil pH is compared to the temperature of a patient during medical diagnoses because it readily gives a hint of the soil condition and the expected direction of many soil processes (lecture statement, Emeritus Prof. Eric Van Ranst, Ghent University). For instance, soil pH is controlled by the leaching of basic cations such as Ca, Mg, K, and Na far beyond their release from weathered minerals, leaving H + and Al 3+ ions to dominant exchangeable cations the dissolution of CO2 in soil water producing carbonic acid, which dissociates and releases H + ions humic residues from the humification of soil organic matter, which produces high-density carboxyl and phenolic groups that dissociate to release H + ions nitrification of

      produces H + ions removal of N in plant and animal products and inputs from acid rain and N uptake by plants [8]. On the other hand, pH controls the biology of the soil as well as biological processes. Consequently, there is a bidirectional relationship between soil pH and biogeochemical processes in terrestrial ecosystems, particularly in the soil. In this sense, the soil pH influences many biogeochemical processes, whereas some biogeochemical processes, in turn, influence soil pH, to some extent, as summarised in Figure 1.

      For many decades, intensive research has revealed that soil pH influences many biogeochemical processes. Recent advances in research have made intriguing revelations about the important role of soil pH in many soil processes. This important soil property controls the interaction of xenobiotics within the three phases of soil as well as their fate, translocation, and transformation. Soil pH, therefore, determines the fate of substances in the soil environment. This has implications for nutrient recycling and availability for crop production, distribution of harmful substances in the environment, and their removal or translocation. This functional role of soil pH in soil biogeochemistry has been exploited for the remediation of contaminated soils and the control of pollutant translocation and transformation in the environment. Unfortunately, in many studies, soil pH is often measured casually as a norm without careful consideration for its role in soil. This paper seeks to explore the importance of pH as an indicator of soil biogeochemical processes in environmental research by discussing the biogeochemical processes that are influenced by soil pH, the biogeochemical processes that also control soil pH, and the relevance of the relationship for future research, planning, and development.

      2. Biogeochemical Processes Influenced by Soil pH

      2.1. Substance Translocation

      Simultaneously, in accordance with biochemical changes, physicochemical processes, including dissolution, precipitation, adsorption, dilution, volatilization, and others, influence leachate quality [9].

      2.1.1. Trace Element Mobility

      Soil pH controls the solubility, mobility, and bioavailability of trace elements, which determine their translocation in plants [10]. This is largely dependent on the partition of the elements between solid and liquid soil phases through precipitation-dissolution reactions [10, 11] as a result of pH-dependent charges in mineral and organic soil fractions. For instance, negative charges dominate in high pH whereas positive charges prevail in low pH values [12]. Additionally, the quantity of dissolved organic carbon, which also influences the availability of trace elements, is controlled by soil pH. At low pH, trace elements are usually soluble due to high desorption and low adsorption. At intermediate pH, the trend of trace element adsorption increases from almost no adsorption to almost complete adsorption within a narrow pH range called the pH-adsorption edge [13]. From this point onwards, the elements are completely adsorbed [13]. For instance, Bradl [13] found that at pH 5.3, the adsorption of Cd, Cu, and Zn onto a sediment composite consisting of Al-, Fe-, and Si-oxides was 60%, 62%, and 53%, respectively. In contrast, he found that 50% of Cd and Zn sorbed onto humic acids between pH 4.8–4.9 [13]. The fate of readily available trace elements depends on both the properties of their ionic species formed in the soil solution and that of the chemical system of soil apart from soil pH itself [14]. Research has established that with increasing soil pH, the solubility of most trace elements will decrease, leading to low concentrations in soil solution [14]. Any increase or decrease in soil pH produces distinct effects on metal solubility. This may probably depend on the ionic species of the metals and the direction of pH change. Rengel [15] observed that the solubility of divalent metals decreases a hundred-fold while trivalent ones experience a decrease of up to a thousand-fold. In contrast, Förster [10] found that a decrease in soil pH by one unit resulted in a ten-fold increase in metal solubility. In an experiment, he observed that at pH 7, only about 1 mg Zn·L −1 of the 1200 mg·kg −1 total Zn content was present in soil solution. At pH 6, the concentration reached 100 mg Zn·L −1 while at pH 5, 40 mg Zn·L −1 was present. Aside from adsorption, trace element concentrations at high soil pH may also be caused by precipitation with carbonates, chlorides, hydroxides, phosphate, and sulphates [11, 16]. Apatite and lime applied to soils produced the highest effect on pH and simultaneously decreased the concentrations of available, leachable, and bioaccessible Cu and Cd [16].

      2.1.2. Mobility of Soil Organic Fractions

      Soil organic matter exists in different fractions ranging from simple molecules such as amino acids, monomeric sugars, etc. to polymeric molecules such as cellulose, protein, lignin, etc. These occur together with undecomposed and partly decomposed plant and microbial residues [17]. The solubility and mobility of the fractions differ during and after decomposition and could lead to the leaching of dissolved organic carbon and nitrogen in some soils. Dissolved organic carbon is defined as the size of organic carbon that passes through a 0.45 mm diameter filter [18]. Soil pH increases the solubility of soil organic matter by increasing the dissociation of acid functional groups [19] and reduces the bonds between the organic constituents and clays [20]. Thus, the content of dissolved organic matter increases with soil pH and consequently mineralizable C and N [20]. This explains the strong effects of alkaline soil pH conditions on the leaching of dissolved organic carbon and dissolved organic nitrogen observed in many soils containing substantial amounts of organic matter [19, 21]. The same observation has been made on the dissolved organic carbon concentration in peatland soils [22]. The pH-dependence of dissolved organic carbon concentration gets more pronounced beyond pH 6 [23].

      Within the pH condition in a specific soil system, the solubility of organic matter is strongly influenced by the type of base and is particularly greater in the presence of monovalent cations than with multivalent ones [23]. According to Andersson and Nilsson [24] and Andersson et al. [19], soil pH controls the solubility of organic matter in two major ways: (i) its influence on the charge density of the humic compounds, and (ii) either the stimulation or repression of microbial activity. The former is found to be more pronounced than the latter [19].

      2.2. Soil Biological Processes
      2.2.1. Microbial Ecophysiological Indicators

      Ecophysiology is an interlinkage between cell-physiological functioning under the influence of environmental factors [25]. It is estimated using the metabolic quotient (qCO2) as an index [25] to show the efficiency of organic substrate utilization by soil microbes in specific conditions [26]. A decrease in microbial community respiration makes C available for more biomass production, which yields higher biomass per unit [27]. The metabolic quotient is, therefore, described as a cell-physiological entity that reflects changes in environmental conditions [25]. This implies that any change in environmental conditions towards the adverse state will be indicated by the index [25]. This is controlled by soil pH [28]. Soil pH as a driving force for microbial ecophysical indices stems from its influence on the microbial community together with the maintenance demands of the community [28] and was among the predictors of the metabolic quotient [29, 30]. The metabolic quotient was found to be two-and-a-half times higher in low pH soils compared to neutral pH soils [28]. This has been associated with the divergence of the internal cell pH (usually kept around 6.0) from the surrounding pH conditions, which increases the maintenance requirements and reduces total microbial biomass produced [25].

      It is observed from the literature that soil pH conditions required for microbial activity range from 5.5–8.8 [26, 31, 32]. Thus, soil respiration often increases with soil pH to an optimum level [26]. This also correlates with microbial biomass C and N contents, which are often higher above pH 7 [26]. In low pH conditions, fungal respiration is usually higher than bacterial respiration and the vice versa [25] because fungi are more adapted to acidic soil conditions than bacteria.

      2.2.2. Soil Enzyme Activities

      Extracellular enzymes are produced by soil microorganisms for the biogeochemical cycling of nutrients [33]. Soil pH is essential for the proper functioning of enzyme activity in the soil [34, 35], and may indirectly regulate enzymes through its effect on the microbes that produce them [36]. However, there are myriad of enzymes in biological systems which assist in the transformation of various substances. Besides, enzymes are of different origins and with differing degrees of stabilization on solid surfaces. Thus, the pH at which they reach their optimum activity (pH optima) is likely to differ [33]. It is striking that enzymes that act on the same substrates could vary considerably in their pH optima. This is evident in phosphorus enzymes, which have both acid and alkaline windows of functioning in the range of pH 3–5.5 and pH 8.5–11.5 [33]. In a study on the optimum pH for specific enzyme activity in soils from seven moist tropical forests in Central Panama, Turner [33] classified enzymes into three groups depending on their pH optima as found in the soils. These were: (a) enzymes with acidic optima that appeared consistent among soils, (b) enzymes with acidic pH optima that varied among the soils, and (c) enzymes with optima in both acid and alkaline soil pH. Stursova and Walker [37] found that organophosphorus hydrolase has optimal activity at higher pH. For instance, glycosidases have an optimal pH range between 4 and 6 compared to proteolytic and oxidative enzymes whose optima was between 7 and 9 [35, 36, 38]. Shifts in microbial community composition could potentially influence enzyme production if different microbial groups require lower nutrient concentrations to construct biomass, or have enzymes which differ in affinity for nutrients [39].

      2.2.3. Biodegradation

      Soil microorganisms are described as ecosystem engineers involved in the transformation of substances in the soil. One of such transformations is biodegradation, a process through which microbes remediate contaminated soils by transforming toxic substances and xenobiotics into least or more toxic forms. Biodegradation is the chemical dissolution of organic and inorganic pollutants by microorganisms or biological agents [34, 40]. Like many soil biological processes, soil pH influences biodegradation through its effect on microbial activity, microbial community and diversity, enzymes that aid in the degradation processes as well as the properties of the substances to be degraded. Soil pH was the most important soil property in the degradation of atrazine [41]. Generally, alkaline or slightly acid soil pH enhances biodegradation, while acidic environments pose limitations to biodegradation [34, 37, 42]. Usually, pH values between 6.5 and 8.0 are considered optimum for oil degradation [43]. Within this range, specific enzymes function within a particular pH spectrum. For instance, the pesticide fenamiphos degraded in two United Kingdom soils with high pH (>7.7) and two Australian soils with pH ranging from pH 6.7 to 6.8. The biodegradation process rather slowed down in three acidic United Kingdom soils (pH 4.7 to 6.7) in 90 days after inoculation [42]. Xu [44] found some strains of bacteria isolated from petroleum-contaminated soil in northern China being able to degrade over 70% of petroleum at pH 7 and 9. In a degradation experiment involving polycyclic aromatic hydrocarbons (PAHs), half of the PAHs degraded at pH 7.5 within seven days representing the highest amount degraded [34]. This was associated with the highest bacterial populations [34]. Furthermore, Houot et al. [41] found increased degradation of atrazine in French and Canadian soils, which occurred with increased soil pH. They observed maximum soil respiration in atrazine-contaminated soils at soil pH values higher than 6.5 compared to those with soil pH value less than 6.0 where metabolites rather accumulated.

      2.2.4. Mineralization of Organic Matter

      Organic matter mineralization is often expressed as carbon (C), nitrogen (N), phosphorus (P), and sulphur (S) mineralization through microbial action. Soil pH controls mineralization in soils because of its direct effect on the microbial population and their activities. This also has implications for the functions of extracellular enzymes that aid in the microbial transformation of organic substrates. Additionally, at a higher soil pH, the mineralizable fractions of C and N increase because the bond between organic constituents and clays is broken [20]. In a study on the mineralization of C and N in different upland soils of the subtropics treated with different organic materials, Khalil et al. [45] found that soil pH and C/N ratio were responsible for 61% of the decomposition rate, with corresponding increases in CO2 effluxes, net N mineralization, and net nitrification in alkaline than in acid soils. Similar results had earlier on been obtained by Curtin et al. [20].

      2.2.5. Nitrification and Denitrification

      Nitrification and denitrification are important nitrogen transformation processes of environmental concern. Like many of the biogeochemical processes, the processes, to a large extent, are controlled by soil pH. Nitrification involves the microbial conversion of ammonium to nitrate. It generally increases with increasing soil pH but reaches an optimum pH [45–47]. In a four-year study, Kyveryga et al. [47] observed that soil pH range of 6 to 8 strongly influenced the nitrification rates of fertilizer N. Generally, the nitrification rate decreases at lower soil pH values. In some soils, nitrification and nitrification potential substantially decrease or are negligible below a pH value of 4.2. However, nitrification may still occur even below pH 4.14, suggesting that ammonia-oxidizing and nitrifier communities might remain active at low soil pH [48].

      Denitrification is the microbiological process in which oxidized N species such as nitrate ( ) and nitrite (

      ) are reduced to gaseous nitric oxide (NO), nitrous oxide (N2O), and molecular nitrogen (N2) under limited oxygen conditions [49]. Soil pH affects denitrification rate, potential denitrification, and the ratio between the two main products of denitrification (N2O and N2). The ratio has an inverse relation with soil pH [49]. At pH values below 7, N2O was the main denitrification product whereas N2 prevailed at pH values above 8 [49]. Sun et al. [50] discovered that soil pH was the best predictor of denitrification rate where the ratio of N2/N2O increased exponentially with an increase in soil pH. This is because low pH prevents the assembly of functional nitrous oxide reductase, the enzyme reducing N2O to N2 in denitrification [15, 20] and this mostly depends on the natural soil pH [49]. However, the soil pH at which the highest activity of nitrous oxide reductase occurred was around pH 7.3. This occurred in soils amended with potassium hydroxide (KOH) [51]. This suggests the inhibition of denitrification at high pH, particularly up to pH 9 [50]. Furthermore, maximum denitrification of between 68% and 85% occurred in a sandy and a loamy soil with pH 5.2 and 5.9, respectively [52]. The optimum pH for long-term potential denitrification was between 6.6 and 8.3. Additionally, the short-term denitrifying enzyme activity depended on the natural soil pH [49]. The effect of soil pH on denitrification is partly due to pH controls over the denitrifying microbial populations. The population size of the resident nitrate-reducing bacterial population increased dramatically when the pH of the acid soil was increased [53].

      2.2.6. Ammonia Volatilization

      The volatilization of ammonia is a phenomenon that occurs naturally in all soils [54] and has been attributed to the dissociation of to NH3 and H + shown in equation (1) [55]

      The dissociation approaches equilibrium through the acidification of the medium. The rate of acidification depends on the initial and final concentrations of ammonium as well as on the buffering capacity of the medium [55]. When solution pH increases above 7, H + is consumed in the reaction. Thus, the dissociation of ammonium to ammonia in equation (1) will favour ammonia volatilization. In neutral and acid soils, containing fertilizers are less subject to NH3 loss than urea and urea-containing fertilizers [54]. However, the degree will also depend on the specific fertilizer and its effect on soil pH. In a study involving ammonia volatilization from an alkaline salt-affected soil cultivated with rice, Li et al. [56] found that ammonia volatilization increased rapidly with pH and peaked at pH 8.6. Ammonia volatilization is strongly correlated with pH and calcium carbonate, which suggested that the soil pH was a key factor in ammonia volatilization because calcium carbonate increases soil pH which in turn controls the concentration of ammonia and ammonium in soil solution [57].

      3. Biogenic Regulation of Soil pH

      Soil biological processes from living organisms and biochemical transformations of the remains of dead organisms induce changes in soil pH. This can either occur through the direct effect of biochemical processes occurring in the living organisms in the soil system, mostly through rhizosphere processes or through the direct and indirect effects of applied organic residues, whether in unburnt, burnt, or charred forms as well as their decomposition.

      3.1. Rhizosphere Processes

      The rhizosphere is the volume of soil in the neighbourhood of roots that is influenced by root and microbial activities [58–60] Hiltner 1904 cited by [60]. It is a longitudinal and radial gradient [61], ranging from 0 to 2.0 mm from the root mat [62, 63]. In this small soil volume, roots take up water and nutrients, undergo root elongation and expansion, release exudates, respire, and thus have higher microbial activity [59, 63]. Through some of these biological processes, plant roots have the ability to induce pH changes in the rhizosphere either by releasing protons (H + ) or hydroxyl ions (OH − ) to maintain ion balance [58, 64], depending on the nutritional status of the plants [65]. Therefore, rhizosphere pH could increase or decrease depending on the prevailing process and types of ions released.

      Plant root-induced soil pH change in the rhizosphere is controlled by specific processes and factors such as (i) ion uptake coupled with the release of inorganic ions that maintain electroneutrality, (ii) the excretion of organic acid anions, (iii) root exudation and respiration, (iv) redox-coupled processes, (v) microbial production of acids after the assimilation of released root carbon, and (vi) plant genotype [58, 59]. Surprisingly, roots have a greater tendency to raise the pH of the rhizosphere rather than lower it [65, 66]. The dominant mechanism responsible for pH changes in the rhizosphere is plant uptake of nutrients in the form of cations and anions [58, 59, 65], primarily due to plant uptake of the two major forms of inorganic nitrogen ( and ), which is usually taken up in large quantities [59]. Nitrogen is taken up by plants in three major forms: ammonium ( ), nitrate ( ), and molecular nitrogen (N2) [59], although amino acids can also be taken up [58]. The uptake of each of the three forms of nitrogen accompanies the release of corresponding ions to maintain electroneutrality in the rhizosphere. When nitrate dominates in soil or when its uptake dominates, plants must release bicarbonate (

      ) or hydroxyl ions (OH − ) to maintain electrical neutrality across the soil-root interface resulting in rhizosphere pH increase [58, 59, 64]. In contrast, protons are released by plants in response to uptake, causing a decrease in rhizosphere pH [58, 62]. It has been revealed that 15, 6, and 0%, respectively, of the N from the total N present in the soil is required to decrease rhizosphere pH decrease by 1.2 units, maintain it, or increase it by 0.4 pH unit [62].

      The extent of effects of the processes and factors controlling rhizosphere pH change depends on plant species and growth stages [65]. For instance, in a study on rhizosphere acidification interactions, Faget et al. [67] found differences between rhizosphere acidification in maize (Zea mays L.) and beans (Phaseolus vulgaris L.). Maize initially acidified the rhizosphere and gradually alkalized it over time while beans showed opposite effects. They found an interaction effect of the two plant species on the rhizosphere pH change whereby the degree of acidification or alkalization was weaker when roots grew within the same neighbourhood than when the roots were not growing near each other. However, the rhizosphere pH changes with time as a result of variable uptake of nitrogen ions, plant species, and their growth stages of the plants [67]. This was revealed in an experiment on apple trees (Malus pumila Miller), buckwheat (Fagopyrum esculentum Moench), corn (Zea mays L.), cowpeas (Vigna unguiculata (L) Walp.), kaffir lime (Citrus hystrix DC.), lettuce (Lactuca sativa L.), pine trees (Pinus sp. L.), and wheat (Triticum aestivum L.), where Metzger [66] found maximum concentrations of in the rhizosphere during the blooming and fruiting stages (Figure 2), which was 10–29% higher compared to the bulk soil. The concentrations of in the rhizosphere of the plants was in the order, lettuce = buckwheat > pine > apple > kaffir > cowpeas > corn > wheat. These values were much lower than those obtained in the rhizosphere of soybean (Glycine max (L.) Merr.) [64]. Furthermore, Turpault et al. [59] found that 93% of NO3-N was taken up by a Douglas fir (Pseudotsuga menziesii (Mirb.) Franco) stands during April–September compared to 83% uptake during the October-March period. This likely increased rhizosphere pH and implies that during periods of low nitrate uptake, soil pH may decrease due to buffering or due to a response to the uptake of .

      3.2. Raw and Combusted Organic Materials

      When unburnt organic materials or raw plant residues are applied to the soil, the pH increases to a peak and decrease afterwards. For instance, Forján et al. [68] found initial increases in soil pH when they applied a mixture of sludge from a bleach plant, urban solid waste and mine wastes, and a mixture of sludge from a purification plant, wood chips, and remnants from agri-food industries to the soil. Furthermore, the addition of young Kikuyu (Pennisetum clandestinum L.) shoots also increased soil pH by up to one pH unit [69]. The major causes of this pH change is due to the (i) release of excess residue alkalinity attributed to the basic cations such as Ca, K, Mg, and Na [70] (ii) decarboxylation of organic anions that occurs during C mineralisation, causing the consumption of protons and release of OH − [71, 72] (iii) ammonification of the residue N (iv) nitrification of mineralised residue N and (v) association/dissociation of organic compounds [70]. These processes are determined by the quantity applied and the prevailing soil and environmental conditions [70]. According to Xu et al. [70] direct chemical reactions and oxidation of the organic anions during residue decomposition are the main mechanisms involved in organic anion-induced soil pH increase. Additionally, organic anions and other negatively charged chemical functional groups present in organic matter can undergo association reactions with H + ions [71, 73].

      The increase in soil pH after residue application also depends on the type of residue (either from monocots or dicots), which is related to the amount of alkalinity present, residue quality (C/N ratio), the rate of residue application and decomposition, the initial pH, and buffering capacity of the soil [70, 71]. Different residues have different chemical and biochemical compositions, which determine the processes responsible for soil pH change. This was detected in an incubation experiment involving three soils and five different residue types where soil pH increased according to lucerne > chickpea > medic > high-N wheat > low-N wheat [70]. Furthermore, in a 59-day laboratory incubation [71] and field experiments [74], it was found that the magnitude of soil pH increase following residue amendment was in the order chickpea > canola > wheat [71, 74]. They observed that 40–62% of soluble alkalinity in canola and chickpea residues were responsible for the pH increases. It is obvious from these, and many other studies [69], that the residues of dicots, particularly legumes, have high alkalinity and produce larger effects on soil pH change than monocots. The pH increase after residue addition often reaches a peak and declines thereafter as a result of nitrification. Residues with low carbon-nitrogen (C/N) ratios are often associated with sharp pH decline after a certain period and the extent varies with soil type and soil buffering capacity [70, 71, 74], whereas those with high C/N ratios produce smaller pH increase, or none at all [70].

      The initial pH and buffering capacity of soils receiving plant residues have a profound role in the extent of pH change after application. For instance, three soil types of different initial soil pH, namely, Wodjil sandy loam with pH(CaCl2) 3.87, Bodallin sandy loam soil with pH 4.54, and Lancelin sandy soil with pH 5.06, were incubated with residues of chickpea, lucerne, medic, high-N wheat, and low-N wheat. Thereafter, the pH increased by about 3.3 units with lucerne in the Wodjil soil (3.87), 1.6 with chickpea, 1.5 with medic, and 0.5 with high-N wheat, and no increase with low-N wheat. The pH increased and peaked at 42 days of incubation for Bodallin and Wodjil sandy loams followed by a decline whereas, in the Lancelin sandy soil, the pH peaked at day 14 before declining [70]. In another incubation study [71], a Podzol with an initial pH of 4.5 and a Cambisol with an initial pH of 6.2 were amended with residues of canola, chickpea, and wheat. For all the residues, the pH increase in the moderately acidic Cambisol was up to sixfold larger than in the more acidic Podzol. This peaked at 14 days after application and declined afterwards. However, in a field study on the same soils [74], the application of chickpea residue increased soil pH by 1.3 units in both soils and reached a maximum at 3 months, whereas canola residue increased pH by 0.82 and 1.02 units in the Podzol and Cambisol, respectively, and reached a maximum pH at 9 months.

      Similar to unburnt organic materials, burnt or charred plant residues contain a larger amount of alkalinity due to the volatilization of organic constituents under thermal conditions leading to the concentration of alkaline constituents. The actual alkalinity depends on the type of biomass involved, their origin, and burnt temperature. Burnt and charred forms of organic materials include biochar and ash. Biochar is a solid consistent product pyrolysis, while ash is a loose powdery material obtained by combustion. The pH of biochar produced at 500–600°C was 6.4–9.3 and showed a strong relationship with the total alkalinity (i.e., organic and inorganic alkalinities) [75]. The inorganic alkalinity increased with increasing pyrolysis temperature and with increasing divalent cation contents [75] because the organic constituents volatilize during pyrolysis. This alkalinity of biochar neutralizes acidity and increases soil pH depending on the amount of alkalinity and soil buffering capacity [76]. Biomass ash contains substantial alkalinity, which is often expressed as percent calcium carbonate equivalence (% CCE). It ranges from 17–95% [77, 78]. Similarly to biochar, the combustion temperature has effects on the alkalinity of biomass aside the biomass type and source. Recently, Neina et al. (submitted) found that ash from charcoal had higher CCE, pH, and K contents than firewood ash. Depending on the alkalify and buffering capacity of the soil receiving the biomass ash, soil pH increase can be high or low. For instance, in two Ghanaian Acrisols, biomass ash applied at 2.5 g·kg −1 soil increased soil pH by about 1 unit after 12 weeks of laboratory incubation [79]. This pH change is mostly short-lived due to other biogeochemical processes.

      4. Conclusions

      The content of this paper highlights the role of soil pH as a master soil variable that has a bidirectional relationship with soil biogeochemical processes. Although not all biogeochemical processes were discussed in this paper, those discussed have substantial influences on soil health, nutrient availability, pollution, and potential hazards of pollutants as well as their fate in the food chain. The mobility of unwholesome substances through the hydrological cycle cannot be overlooked here because of the intimate relationship between soil and water. Thus, an understanding of this can form a basis and a guide to decisions and choices of soil management, remediation, rehabilitation, and the maintenance of soil quality. The observed soil pH-biogeochemistry relationships provide insight for future applications for increased yields for specific crops through nutrient recycling and availability, which enhances crop growth. The transient rhizosphere soil pH could also be used to enhance the availability of certain nutrients in certain soil conditions [80]. More importantly, soil pH could be useful for soil pollution control through the distribution and removal of harmful substances from systems. For instance, the mineralization and degradation processes such as those of C and N mineralisation and the degradation of pesticide occur between pH 6.5 and 8, while the maximum degradation of petroleum and PAHs occur between pH 7 and 9. These, as well as pH maxima for various microbial enzymes, could be utilized in many soil remediation strategies, particularly in bioremediation. Ultimately, soil pH can broadly be applied in two broad areas, i.e., nutrient cycling and plant nutrition and soil remediation (bioremediation and physicochemical remediation).

      Conflicts of Interest

      The author declares that there are no conflicts of interest regarding the publication of this article.

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