Modern Soil Microbiology, Third Edition

Jan Dirk van Elsas, Jack T. Trevors, Alexandre Soares Rosado, Paolo Nannipieri, Jan Dirk van Elsas, Jack T. Trevors, Alexandre Soares Rosado, Paolo Nannipieri

• Éditeur: CRC Press
• Année: 2019
• ISBN:
  9780429602405
• Édition: 3
• Sujet: Technologie et ingénierie
• Sous-sujet: Agriculture

The living soil is crucial to photosynthesis, biogeochemical cycles, global food production, climate change, biodiversity, and plant and animal health. In the past decade, scientists have made significant advances in soil microbiology research. While the basic principles are now better understood, knowledge has been forthcoming on the best available technologies and methods applied to researching soil microorganisms, their diversity, interactions, biochemistry, survival, gene expression, and their roles in global climate change, plant disease suppression and growth stimulation, and biogeochemical cycles. This knowledge can be applied to better predict the transformation of pollutants in soil and the activities of microbes in the rhizosphere. It will also assist us in fostering crop production in an era with an increasing human population and intensification of agriculture.

Following the tradition of its predecessors, Modern Soil Microbiology, Third Edition, is an indispensable source that supports graduate/undergraduate teaching for soil and environmental microbiologists in academia, as well as in government and industrial laboratories. It is a comprehensive collection of chapters on various aspects of soil microbiology, useful for all professionals working with soils. Compiled by internationally renowned educators and research scholars, this textbook contains key tables, figures, and photographs, supported by thousands of references to illustrate the depth of knowledge in soil microbiology.

FEATURES

• Fully updated and expanded to include new key chapters on historical developments, future applications, and soil viruses and proteins
• Discusses molecular methods applied to soil microbiology, diverse soil microorganisms, and global climate change
• Emphasizes the role of terrestrial microorganisms and cycles involved in climate change
• Details the latest molecular methods applied to soil microbiology research
• User-friendly for students, and containing numerous tables, figures, and illustrations to better understand the current knowledge in soil microbiology

Section I

Fundamental Chapters

1 The Soil Environment^*

Jan Dirk van Elsas

University of Groningen

CONTENTS

• 1.1 Introduction
• 1.2 Scales and Gradients
  • 1.2.1 Introduction
  • 1.2.2 Spatial and Temporal Scales in Soil
• 1.3 The Soil Physicochemical Environment
  • 1.3.1 Water—The Essential Factor for Soil Life
    • 1.3.1.1 Definitions
  • 1.3.2 Soil as an Energy and Nutrient Source
  • 1.3.3 Soil Temperature
  • 1.3.4 Soil Light
  • 1.3.5 Soil Atmosphere and Redox Potential
  • 1.3.6 Soil pH
• 1.4 Concluding Remarks
• References

1.1 Introduction

Soil is a structured environment that “holds” a wealth of organisms with diverse activities and functions. Among these organisms, microorganisms have a central place, as they play major roles in key soil processes. However, a key problem in any discussion about soil as a microbiological habitat is our conceptual visualization of soil. The most commonly used unit of reference is 1 g. This unit has been an optimum mass from which biodiversity indices indicative of habitat richness are gained. One gram of soil consists of inorganic and organic fractions. The inorganic particles of soil are classified into three major groups according to their size: sand, silt, and clay. The proportions of these in any soil determine the soil texture. The number of particles in 1 g of soil can range from 90 (pure coarse sand) to 90 billion (pure clay), and the proportions of sand, silt, and clay in the soil sample determine the soil textural class. Assuming spherical shapes, the surface area of soil particles can range from 11 to 8 million cm² g⁻¹, illustrating the high degree of physical heterogeneity present in any given soil sample. Although the concept of an “average” soil is not entirely meaningful, we will consider a hypothetical soil aggregate (Figure 1.1) as the basic unit of the soil habitat. Many biogeochemical processes occur at scales more or less relevant to this unit, including processes such as gas diffusion and water movement, which create a mosaic of microsites and gradients (Paul and Clark 1996). Most, if not all, aggregates constitute potential habitats that allow the survival of one or more species of soil microorganisms. In our “hypothetical” habitat, a gram of soil and the arrangement of the soil particles (soil structure; see Table 1.1) are vital to the microbes present. About half the volume of an aggregate will be void spaces (pores) connected by tortuous pathways presenting a range of pore neck sizes. It is the relationship between the interconnecting pathways, channels, and pores in soil that provides the microhabitat space (niche, used here as the term to describe habitable space in soil) for the soil microbiota. The physical niches themselves will mainly be soil pore walls, although water in channels may contain, and transport, significant numbers of freely motile bacteria (Figure 1.2).

FIGURE 1.1 Schematic of a section through a 2 mm-diameter soil aggregate microsite yielding habitats for bacteria based on physiological requirements. The arrows show the main directions of diffusion for key processes. The increasing darkness of the soil particles indicates the increasing number of sites available for anaerobic bacterial function.

Soil water passes more rapidly through wider pores by means of gravity mass flow and diffusion (see below for a separate consideration of these topics) than through narrow pores. The physical niches in the wider pores are also mainly pore walls to which bacteria adhere.

1.2 Scales and Gradients

1.2.1 Introduction

The microbial habitat in soil is, essentially, a porous medium that varies both spatially and temporally. The structural form of this porous medium is the product of many different processes. Biological, physicochemical, and mechanical processes act together to aggregate, compact, crack, and fragment the soil, resulting in a soil structure consisting of solids and pores. The soil pores form a tripartite group—transmission pores being the main conduits for water and nutrient flow, storage pores that are empty under the influence of matric potential, and residual pores (with pore neck diameters less than 0.3 μm) that remain water-filled. In most soils, the transmission pores form the majority of pore space in the soil microbial habitat.

TABLE 1.1
Approximate Dimensions (μm) of Soil Particles and Biota and Comparison of Water-Filled Pores and Water Films

Historically, it has proven to be impossible to produce an overarching descriptor of soil habitats that fits all soil types (not to be confused with soil classification). It would be useful to have such a descriptor, as it may help us in understanding the observable conservation of microbial genes responsible for the processes carried out in soils, such as denitrification and carbon, nitrogen, and phosphorus mineralization.

Now entering a bit of theory: fractals (objects with fractional dimensions which possess self-similarity, composed of several parts, each of which is a small-scale copy of the whole) have been applied successfully to describe spatiotemporal, hierarchical, and complex systems. These fractal systems can be generated using scaling laws and iterative algorithms. To be classified as a fractal system, patterns must be self-similar over a range of scales (i.e., its properties are reproduced at a number of different spatial and temporal scales). As a result, no matter how intricate a particular pattern might be, its statistical properties allow its description, independent of scale (Bird and Perrier 2003, Perrier and Bird 2002). Within a given soil texture (except for very clayey soils), a description of soil as a system of fractals appears to be robust. However, high clay content soils do not display fractal particle size distributions (Millan et al. 2003).

1.2.2 Spatial and Temporal Scales in Soil

Spatial and temporal scales in soil can be best understood by way of an example. Here, we use a root with its surrounding soil to illustrate some key spatiotemporal aspects (Figure 1.3). The soil habitat generally constitutes an aerobic, oligotrophic (nutrient-poor) environment, which is not conducive to high population densities and activities of microorganisms. In contrast, the rhizosphere (further discussed in Chapter 10) provides an environment in which elevated population sizes and activities of fast-growing (formerly called zymogenous) microorganisms are supported by plant-derived carbon substrates, in the form of exudates and cell lysates. This constitutes the soil–plant interface, a habitat that incites a wide spectrum of beneficial as well as detrimental associations with microorganisms.

FIGURE 1.2 Possible niche space available to bacteria (shown in black, adhering to soil particle (gray hatching) surfaces showing the relationship between soil matric potential and pore size available.

Water movement and diffusion of molecules are key features of the soil and rhizosphere habitats in which microbial populations transmit information from one to another, for example, via quorum sensing (Whiteley et al. 2017). Bacterial interactions that are important in the rhizosphere (e.g., production of antibiotics and chitinases, biofilm formation, stationary phase, and motility) (Cha et al. 1998, Elasri et al. 2001, Pierson et al. 1998) are often driven by quorum sensing. See Chapters 9 and 10 for more detailed information about these interactions. Key issues arise here, such as the connectivity of the soil pores, which determines to a great extent the local concentrations of quorum sensing molecules. These concentrations ultimately determine the outcome of the quorum sensing-dependent processes.

1.3 The Soil Physicochemical Environment

1.3.1 Water—The Essential Factor for Soil Life

“Understanding the movement of water in soil is understanding the most significant feature of the soil as a habitat for microbial life”. Where water moves, so do ions and nutrients. Water carries dissolved gases and heat, and also bacteria and their predators. It protects microhabitats from desiccation and opens other potential habitats while closing others. The fundamental relationships between physics and chemistry that modulate soil water and biological activity are presented in the schematic picture in Figure 1.4. When considering any interaction of soil water and biological activity, it must be stressed that the four central boxes (representing physical and chemical laws) cannot be discussed in isolation: they all contribute to the interaction.

FIGURE 1.3 Schematic illustration of the soil environment around plant roots in terms of diffusion of materials (substrate carbon and nutrients) and information (signal molecules). Scale: 1 mm

FIGURE 1.4 The range of water-influenced soil properties and processes which determine the microbial activity. Eh: redox potential. See Section 1.3.5.

1.3.1.1 Definitions

Soil water potential is the sum of the matric, osmotic, and pressure potentials; it is the key measure of the activity of water in the soil. These three component terms are briefly outlined in the following text. For a fuller consideration of these topics, see Smith and Mullins (2000) and Marshall and Holmes (1996).

Matric potential: Water molecules adsorb onto the surface of soil minerals through hydrogen bonding, as well as bonding cohesively with other water molecules. These adhesive and cohesive forces act together to hold soil water under tension against external forces such as gravity. Because of this, the soil water always has less potential energy than free water (reference water: at the same temperature, pressure, and location as the soil water) and can never carry a positive sign. Thus, matric potential is always negative or zero.

Osmotic potential: Soil water is not pure water but a solution containing varying amounts of osmotically active organic molecules and inorganic salts, which decrease the potential energy of soil water relative to a pure water reference. Thus, like matric potential, osmotic potential is always negative or zero.

Pressure potential: The pressure potential component comes from external forces (including gravity) exerted on soil water. In a flooded soil with a layer of standing water, the atmosphere as well as the surface water exerts a positive pressure on the soil water. In the absence of flooding, it is simply the pressure of the atmosphere alone, and this is the reference state. The additional pressure of ponded water creates a positive pressure.

Water is held dynamically in the soil by forces that act to reduce the potential energy relative to that of free water (at the same temperature, pressure, and location). The relationship of the water potential to microbial habitat can be visualized in a moisture release curve when drying soil is considered (Figure 1.5). Water will be drained gravitationally out of large pores first, followed by drainage from successively smaller pores. It should be emphasized here that it is the pore neck diameter that determines the rate of water movement, that is, a large water-filled pore with a small pore neck diameter will empty slower than a small pore with a large pore neck diameter. As soils rewet, it is...