Soil as a Habitat PDF

Chapter 1 The soil as a habitat Introduction In this chapter we will briefly revisit the soil architecure or soil structure, as the physical living environment of soil organisms, and the main abiotic factors that rule soil biological activity. More detail on all these aspe...

Chapter 1 The soil as a habitat Introduction In this chapter we will briefly revisit the soil architecure or soil structure, as the physical living environment of soil organisms, and the main abiotic factors that rule soil biological activity. More detail on all these aspects can be found in textbooks on general soil science. Soil is a central component of the earth’s critical zone and deserves special status due to its role in regulating the earth’s environment, thus affecting the sustainability of life on the planet. The soil environment is the most complex habitat on earth. This complexity governs soil biodiversity, as soil is estimated to contain one third of all living organisms and regulates the activity of the organisms responsible for ecosystem functioning and evolution. Soils (pedosphere) develop at the interface where organisms (biosphere) interact with rocks and minerals (lithosphere), water (hydrosphere), and air (atmosphere), with climate regulating the intensity of these interactions. In terrestrial ecosystems, the soil affects energy, water and nutrient storage and exchange, and ecosystem productivity. Scientists study soil because of the fundamental need to understand the dynamics of geochemical–biochemical–biophysical interactions at the earth’s surface, especially in light of recent and ongoing changes in global climate and the impact of human activity. Geochemical fluxes between the hydrosphere, atmosphere, and lithosphere take place over the time span of hundreds to millions of years. Within the pedosphere, biologically induced fluxes between the lithosphere, atmosphere, and biosphere take place over a much shorter time frame, seconds to years, which complicates the study of soils. The soil habitat is defined as the totality of living organisms inhabiting soil, including plants, animals, and microorganisms, and their abiotic environment. The exact nature of the habitat in which the community of organisms lives is determined by a complex interplay of geology, climate, and plant vegetation. The interactions of rock and parent material with temperature, rainfall, elevation, latitude, exposure to sun and wind, and numerous other factors, over broad geographical regions, environmental conditions, and plant communities, have evolved into the current terrestrial biomes with their associated soils. Because soils provide such a tremendous range of habitats, they support an enormous biomass, with an estimated 2.6 1029 for prokaryotic cells alone, and harbor much of the earth’s genetic diversity. A single gram of soil contains kilometers of fungal hyphae, more than 10 9 bacterial and archael cells and organisms belonging to tens of thousands of different species. Zones of good aeration may be only millimeters away from areas that are poorly aerated. Areas near the soil surface may be enriched with decaying organic matter and other accessible nutrients, whereas the subsoil may be nutrient poor. The variance of temperature and water content of surface soils is much greater than that of subsoils. The soil solution in 3 some pores may be acidic, yet in others more basic, or may vary in salinity depending on soil mineralogy, location within the landscape, and biological activity. The microenvironment of the surfaces of soil particles, where nutrients are concentrated, is very different from that of the soil solution. Equally, the rhizosphere is a totally different environment than the bulk soil (solution) from a chemical and nutrient point of view, and is a real biological hotspot in soil. In this chapter we briefly revisit the properties of the soil – its structure/architecture, its mineral components, the abiotic variables that define the soil environment, but from the biological point of view rather than from the pedologic one. When reading this course, try to imagine that you are a (microscopically small) soil dweller, exploring the enormous and complex 3-D soil environment, it may help you in understanding concepts and processes, and the interactions between organisms. Given the extremely small body sizes of the bacteria the soil environment is a massive space where there can be an insurmountable distance between different individuals or groups of bacteria, the enzymes they produce, and the substrate on which they depend, even at the soil aggregate level of the order of magnitude of millimeters. For these microorganisms, the soil can be regarded as a desert, with vast distances to be covered before reaching an oasis with nutrients and organic matter. In those oases, life is plentiful, while most of the other parts of soil may be practically devoid of life. 1. Soil structure/soil architecture Depending on the size of the organism and the level of magnification, the soil is the room, the house, the city, or the world of soil organisms. A good insight into the soil architecture - i.e. the organisation of primary mineral particles, and particulate organic matter, into (small) aggregates, and the organisation of small aggregates into larger aggregates - is therefore crucial to understand the behaviour and ecology of soil organisms. Soil structure will be discussed in detail in the Soil science course and can be reviewed there, so here we briefly revisit those aspects that determine the habitable space for organisms. 1.1. Soil particle size fractions The mineral soil particles are distributed over 4 broad size fractions, namely coarse fragments (> 2000 µm), sand (2000 – 50 µm), silt (50 – 2 µm) and clay (< 2 µm). The individual size fractions cover between 1 to almost 2 orders of magnitude and are thus a remarkably coarse subdvision. The reason for this coarse subdivision is that the “large particles”, traditionally the coarse fraction, the sand and the silt fractions, are seen as relatively inert, and to only contribute to shaping soil structure and soil physical properties, whereas chemical reactions take place at the colloidal surfaces i.e. at the clay surfaces. But organisms also interact directly with soil constituents. E.g. Li et al. (2016) 1 investigated the direct interaction between single fungal hyphae (of Talaromyces flavus) and primary minerals, 1 Z. Li, L. Liu, J. Chen, H.H. Teng. 2016. Cellular dissolution at hypha- and spore-mineral interfaces revealing unrecognized mechanisms and scales of fungal weathering. Geology, 44(4), pp. 319-322. 4 to see what would happen if the fungus was attached directly to minerals (Fe containing lizardite), mimicking real-world bioweathering conditions (Fig. 1.1). The fungi first unleashed acid on the mineral surface, dissolving surface minerals, and then siderophores to extract the iron, both in large concentrations. Previous studies that mixed minerals and fungi in a solution registered only weak levels of acid and siderophores, leading researchers to believe that fungi like T. flavus had limited impact on bioweathering. Results from their inspection showed (1) significant pH reduction in the vicinity of cells upon mineral surface attachment, (2) exclusive Fe loss from the mineral at the cell-mineral interfaces, and (3) destruction of the mineral crystal structure below the area colonized by hyphae but not that by spores. Compared to the results from bulk experiments and at the mineral-water interface, these observations indicate that (1) only attached cells release siderophores and (2) biomechanical forces of hyphal growth are indispensable for fungal weathering and strong enough to breach the mineral lattice. Estimated mineral mass loss at the interface suggests that cellular dissolution can ultimately account for ∼40%–50% of the overall bio-weathering, significantly larger than the previous estimate of ∼1% contribution. Fig. 1.1. Fungal hyphae (of Talaromyces flavus) attaching to and attacking/dissolving primary minerals (Fe containing serpentine mineral) 1.2. Soil aggregates as habitats for microbiota The shape and arrangement of soil mineral and organic particles are such that pores of various shapes and sizes are created during the aggregate formation process. In a well-aggregated soil, up to 60% of the total soil volume will be comprised of pores that are either air- or water- filled depending on the moisture conditions. These pores may be open and connected to adjoining pores or closed and isolated from the surrounding soil. It are these pores that make up the living environment of soil organisms. 5 Soil pores may be subdivided into four categories (but many other subdivisions may be thought of): micropores ranging in size from less than 0.2 to 10 μm and found inside microaggregates; pores of between 10 and 100 μm, located between microaggregates but within macroaggregates; pores between macroaggregates; and macropores created by roots and earthworms or by abiotic processes such as cracking or the shrinking and swelling of certain clay minerals when exposed to drying–wetting cycles. The size distribution and degree of continuity of soil pores depend to a large degree on soil texture. In clay soils, nearly 50% of the pores, which are often poorly interconnected, are less than 0.2 μm in size. Pores of 6–30 μm are most abundant in sandy soils and less than 20% are smaller than 0.2 μm. Less than 10% of pores in all soil types are greater than 150 μm. Because soil does not contain discrete objects with obvious boundaries that could be called individual pores, the precise delineation of a pore unavoidably requires artificial, subjectively established distinctions. This contrasts with soil particles, which are easily defined, being discrete material objects with obvious boundaries. The arbitrary criterion required to partition pore space into individual pores is often not explicitly stated when pores or their sizes are discussed. Because of this inherent arbitrariness, some scientists argue that the concepts of pore and pore size should be avoided. Much valuable theory of the behavior of the soil-water- air system, however, has been built on these concepts, defined using widely, if not universally, accepted criteria. A particularly useful conceptualization takes the pore space as a collection of channels through which fluid can flow. The effective width of such a channel varies along its length. Pore bodies are the relatively wide portions and pore openings are the relatively narrow portions that separate the pore bodies. Other anatomical metaphors are sometimes used, the wide part of a pore being the “belly” or “waist”, and the constrictive part being the “neck” or “throat”. In a medium dominated by textural pore space, like a sand, pore bodies are the intergranular spaces of dimensions typically slightly less than those of the adjacent particles. At another extreme, a wormhole, if it is essentially uniform in diameter along its length, might be considered a single pore. The boundaries of such a pore are of three types: (1) interface with solid, (2) constriction— a plane through the locally narrowest portion of pore space, or (3) interface with another pore (e.g. a crack or wormhole) or a hydraulically distinct region of space (e.g. the land surface). Pores of different shapes, sizes, and degree of continuity provide a mosaic of microbial habitats with very different physical, chemical, and biological characteristics, resulting in an uneven distribution of soil organisms. Since soil organisms themselves vary in size, structural heterogeneity determines where a particular organism can reside, the degree to which its movement is restricted, and its interactions with other organisms. In this regard, it is the diameter of pore necks, or pore openings, rather than the enlarged section of pores that determines the location of soil organisms. Every aggregate is a microcosm containing a highly variable microbial community of hundreds to thousands of different species of bacteria, actinomycetes, fungi, protozoa, and algae. The numbers and types of organisms vary from aggregate to aggregate and even between pores within a given aggregate. Mycelial fungi, unlike the other microbial groups, do not require a water film for growth and movement, and can therefore extend their hyphae across air-filled macropores, connecting aggregates and binding them together. Bacteria and protozoa, 6 however, require water for motility and are thus largely restricted from movement between aggregates, since there is typically a discontinuous water film in the pore network, except when the soil becomes saturated following a precipitation or irrigation event. Soil bacteria, which typically average 0.5–2.0 μm in size, can occupy both large and small pores; however, more than 80% of bacteria are thought to reside preferentially in small pores. The maximum diameter of pores most frequently colonized by bacteria is estimated to range from 2.5 to 9 μm for fine- and coarse-textured soils, respectively. There is a positive correlation between bacterial biomass and pores with a mean diameter of 1.2 μm. Few bacteria have been observed to reside in pores less than 0.8 μm in diameter, which means that 20–50% of the total soil pore volume, depending on soil texture and the pore-size distribution, cannot be accessed and utilized by the microbial community. Electron microscopy has revealed that bacteria often occur as isolated cells or small colonies (less than 10 cells) associated with decaying organic matter; however, larger colonies of several hundred cells have been observed on the surface of aggregates isolated from a clayey pasture soil and in soils under native vegetation (Figure 1.2a). Bacterial cells are often embedded in mucilage, a sticky substance of bacterial origin to which clay particles attach. Clay encapsulation and residence in small pores may provide bacteria with protection against desiccation, predation, bacteriophage attack, digestion during travel through an earthworm gut, and the deleterious effects of introduced gases such as ethylene bromide, a soil fumigant. Fungi, protozoa, and algae are mainly found in pores larger than 5 μm. Fungi are commonly observed on aggregate surfaces (Fig. 1.2c) and typically do not enter small microaggregates (less than 30 μm). Like bacteria, fungal hyphae are often sheathed in extracellular mucilage, which not only serves as protection against predation and desiccation, but also is a gluing agent in the soil aggregation process (Fig. 1.2b). Mycelial fungi develop extensive hyphal networks and, as they grow through the soil and over aggregate surfaces, they bind soil particles and microaggregates (53–250 μm) together, thereby playing an important role in the formation and stabilization of macroaggregates (greater than 250 μm). 7 Figure 1.2. Scanning electron micrographs of (a) a colony of bacteria adhered to particle surfaces; (b) fungal hyphae encrusted with clay particles; (c) a microaggregate between 53 and 250 μm in size; and (d) particulate organic matter and soil particles bound together by roots, fungal hyphae, and microbial exudates into a macroaggregate (>250 μm). The relative abundance and distribution of bacteria and fungi vary across aggregate size classes within a given soil and between soils differing in clay content. Macroaggregates have been observed to contain higher total microbial biomass and higher fungal biomass in particular than microaggregates. Aggregates isolated from sandy soils tend to have a more even distribution of microorganisms than those from clayey soils. That is, bacterial cells and fungal hyphae occur on both the surfaces and inside aggregates from sandy soils, while microbes are largely concentrated on the surface of aggregates in clayey soils, with few microbes being present inside. This is probably due to the differential pore-size distribution of soils with different textures and especially the preponderance of pores less than 0.2 μm in diameter in clay soils. The heterogeneous nature of the soil-pore network plays a fundamental role in determining microbial abundance, activity, and community composition by affecting the relative proportion of air- versus water-filled pores, which in turn regulates water and nutrient availability, gas diffusion, and biotic interactions such as competition and predation. Microbial activity, measured as respiratory output (i.e., CO 2 evolution), is maximized when approximately 60% 8 of the total soil-pore space is water-filled. As soil moisture declines below this level, pores become poorly interconnected, water circulation becomes restricted, and dissolved nutrients which are carried by the soil solution become less available for microbial utilization. Soil drying leads to a reduction of microbial biomass, particularly in the larger pores, where organisms are subjected to more frequent alterations between desiccation and wetting. At the other extreme, when most or all of the pores are filled with water, O2 becomes limiting, since diffusion rates are significantly greater in air than through water. Gas diffusion into micropores is particularly slow, since small pores often retain water even under dry conditions. Restricted O2 diffusion into micropores combined with biological O2 consumption during the decomposition of organic matter can lead to the rapid development and persistence of anaerobic conditions. Thus survival of bacteria residing in small pores depends on their ability to carry out anaerobic respiration (e.g., denitrification), replacing O2 with an alternative electron acceptor (e.g. nitrate, ferric (Fe3+) iron). More than 85% of the potential denitrifying activity of whole soil has been attributed to the microaggregate fraction, where most micropores are located. 1.3. Soil structure and microorganism interactions Ecologic interactions between soil organisms, such as competition and predation, regulate the flow of nutrients in ecosystems, as we will see in more detail in further chapters. For example, the release of plant-available nutrients such as nitrogen is stimulated when bacterial cells are consumed by protozoa. It is estimated that as much as 30% of the inorganic nitrogen released into the soil solution from decomposing organic matter is due to protozoan predation of bacteria; and more nitrogen is taken up by plants in soils containing protozoa compared with those without protozoa. The release of carbon from soils as CO 2 is also often enhanced in the presence of protozoa. Soil heterogeneity indirectly influences nutrient-cycling dynamics by restricting organism movement and thereby modifying the interactions between organisms. For example, small pores influence trophic relationships and nutrient mineralization by providing refuges and protection for smaller organisms, particularly bacteria, against attack from larger predators (e.g., protozoa) that are typically unable to enter smaller pores. The location of bacteria within the pore network is a key factor in their survival and activity. Bacterial populations are consistently high in small pores, but highly variable in large pores, where they are vulnerable to being consumed. This may explain, in part, why introduced bacteria (e.g., Rhizobium and biocontrol organisms) often exhibit poor survival relative to indigenous bacteria. When they are introduced in such a way as to be transported by water movement into small, protected pores, their ability to persist is enhanced. This example stresses the importance of integrating structural aspects into soil microbiological studies. Protozoa can consume 2000–12 000 bacteria per protozoan cell division and, since bacteria often occur as individual cells or small colonies, predation is greatest under conditions in which protozoa can readily move between and access a large number of pores. Thus predation rates are high if protozoan numbers are high and they are present in a large number of pores; whereas predation is low if protozoa are restricted to a few large pores. Under typical soil- 9 moisture conditions, protozoan movement is restricted, since they require a continuous water film for migration between pores. Only at high soil-moisture contents (more than 60% of water filled pore space) are protozoa free to move from pore to pore and perhaps from aggregate to aggregate. This may explain, in part, why nutrient release is stimulated following a rain or irrigation event. 1.4. Soil as a spatially continuous medium Much of what is known about the relationships between soil structure, microorganisms, and microbial-mediated processes is based on studies where soil has been broken down into aggregates of different sizes. The isolated size fractions represent those aggregates that are resistant to the method of disruption employed and as such are arbitrary structures. Intact soil is a continuum of soil particles, pore spaces, organic materials, and organisms rather than a collection of discrete aggregates. Traditional aggregate-isolation techniques remove aggregates and their associated microbial communities from their spatial context and fail to capture the heterogeneity and connectivity of the pore network within which soil organisms live. Methods which combine soil thin-sectioning or better 3-D techniques such as X-ray (micro) CT with image analysis, geostatistical tools, and mathematical models are now available to describe and quantify the spatial distribution of microbial cells in relation to soil particles and pore spaces. Such nondestructive approaches should provide a more complete understanding of soil microbial communities and the ecosystem processes they mediate. 1.5. "Self organisation" in the soil A key distinction between older geological features, such as sandstone or granite, and younger soil systems is that the latter exhibit pore structures that are defined not only by the chemical nature of the material (as in geological materials) but by life itself and thus experience significant biophysical and biochemical changes over relatively short spatial and temporal scales. This distinction appears to dominate all fertile soils and is possibly a key diagnostic for the health of soil ecosystems because it represents an important functional bridge between the physics and biology of soil (Young and Crawford, 2004). Soils are highly dynamic and there are continuous changes in soil structure/soil architecture as a result of the complex interactions between chemical, physical and biological processes. The structural organisation of soils is not determined in the first place by external factors, but is regulated and continuously changed by internal processes mainly driven by the soil organisms, which is thus called self- organisation. The example of Young and Crawford (2004) goes as follows: substrate arrives at a location in soil, and the potential microbial respiration rate increases, leading to local depletion of O2. But increased microbial activity changes the local structure, creating a more open aggregated state. This leads to enhanced rates of O2 supply. As substrate is used up, activity declines and the structure collapses to a more closed state again. The open and closed states may represent optimal configurations for O2 supply in a high potential activity regime (open) and protection from desiccation and predation in a low potential activity regime (closed). 10 2. The abiotic soil environment Soil temperature and moisture are the critical factors affected by climate regulating soil biological activity. This control is affected by changes in the underlying rates of enzyme- catalyzed reactions and sizes of the substrate organic and inorganic pools. Where water is nonlimiting, biological activity may depend primarily on temperature. Standard Arrhenius theory can be used to predict these temperature effects. However, as soils dry, moisture is a greater determining factor of biological processes than is temperature. Likely these two environmental influences do not affect microbial activity in linear fashion, but display complex, nonlinear interactions that reflect the individual responses of the various microorganisms and their associated enzyme systems. 2.1. Temperature Temperature is the single most important environmental factor affecting microbial activity and microbially mediated processes in soil. The relationship between temperature and specific biologically mediated processes is complicated as individual species differ in their optimal temperature response, different microbial communities are active as temperatures change, and microorganisms are able to adapt by altering their physiology and cellular mechanisms, membrane fluidity and permeability, and structural flexibility of enzymes and proteins. The relative sensitivity of soil microbial activity to temperature can be expressed as a Q10 function, which is the proportional change in activity associated with a 10°C temperature change: where k2 and k1 are the rate constants for a microbial process under study at temperatures differing by 10°C. It is generally accepted that a Q10 of ~2 can be used to describe the temperature sensitivity of soil biochemical processes, such as soil respiration, over the mesophilic temperature range (20-45°C); that is, microbial activity at 30°C is twofold higher than it is at 20°C. At temperatures beyond 45°C, the microbial community composition shifts from mesophilic to thermophilic, and microorganisms adapt by increasing concentrations of saturated fatty acids in their cytoplasmic membrane and by production of heatstable proteins. Microorganisms that have an upper growth temperature limit of ≤ 20°C, commonly referred to as psychrophiles, are capable of growth at low temperatures by adjusting upward both the osmotic concentration of their cytoplasmic constituents to permit cell interiors to remain unfrozen and the proportion of unsaturated fatty acids in their cytoplasmic membrane. A common adaptive feature of psychrophiles to low temperatures is that their enzymes have much lower activation energies and much higher (up to 10-fold) specific activities than do those of mesophiles, resulting in a reaction rate, k(cat), that is largely independent of temperature. Soils in Alpine and boreal/arctic environments contain a great diversity of cold- adapted microorganisms, able to thrive even at subzero temperatures and to survive repeated freeze/thaw events. A bacterium isolated from a permafrost soil in northern Canada can grow at -15°C and remain metabolically active at temperatures down to -25°C. So our general 11 assumption that microbial activity is zero at temperatures ≤ 0°C clearly is a simplification. But at such low temperatures, microbial activity for sure will be very small. Given the strong temperature dependence of microorganisms and microbially driven processes, the process of global warming, the effect of which is several times larger at the high latitudes, has already affected and will continue to affect microbial communities and microbial processes in these environments, with dramatic positive feedback mechanisms. 2.2. Soil water Soil water affects the moisture available to organisms as well as soil aeration status, the nature and amount of soluble materials, the osmotic pressure, and the pH of the soil solution. Water acts physically as an agent of transport by mass flow and as a medium through which reactants diffuse to and from sites of reaction. Chemically, water acts as a solvent and as a reactant in important chemical and biological reactions. Soil microorganisms (microflora, protozoa, nematodes, rotifers) essentially depend on water for movement and food, and live in water filled pores or in water films surrounding primary soil particles or aggregates. Drying of soils to an extent that makes these water films disappear thus leads to their inactivation. The optimum water content for aerobic microbial activity in soil is slightly below field capacity. At water contents exceeding field capacity, there is no limit on diffusion of substrates and nutrients towards microbial enzymes, but the diffusion of O2 starts to limit the aerobic microbial activity. As the soil dries and water potential decreases, water films on soil particles become thinner and more disconnected, restricting substrate and nutrient diffusion, and increasing the concentration of salts in the soil solution. Although many plants grown for agricultural purposes wilt permanently when the soil water potential reaches -1500 kPa, rates of soil microbial activity are less affected as the relative humidity within the soil remains high. Protozoa are active at water potentials near field capacity in water films > 5 μm thick, whereas microorganisms can be active at lower water potentials, due to their size and association with the surfaces of soil particles. Fungi are generally considered to be more tolerant of lower soil water potentials than are bacteria, presumably because soil bacteria are relatively immobile and rely more on diffusion processes for nutrition. Fungi can explore much larger soil volumes through their extensive network of hyphae. Given these above considerations, the influence of water content on soil microbial activity can best be described in a differentiated manner, namely by percentage of water filled pore space (%WFPS) at the high water content range (starting from field capacity), and by the water potential (expressed in kPa or m water) at the low water content (starting below field capacity). In theory, the maximum diameter (D, in m) of the water filled pores in a soil can be derived from the water potential (ΔP, in Pa) at a given moment, using the Young Laplace equation (assuming complete wetting of the pore wall by water): D = 4γ/ΔP with γ the surface tension of water (γ = 0.0728 J/m2 at 20 °C), or more practically 12 D (m) = 3.10-5/h with h the water tension expressed in m water height, e.g. at 1 m water tension: D ≈ 30 µm. However, this relation is only very approximate, given that soil pores are all but perfectly cylindrical, and that this diameter corresponds more to an ‘equivalent’ pore neck size. The cellular, equivalent-capillary conceptualization of pores as described in §1.2 is especially relevant to hydraulic behavior, as has been recognized at least since the early 1930s. The initial application was to Haines jumps, illustrated in Figure ***, a basic phenomenon of capillary hysteresis. The pore openings, which control the matric pressure P at which pores empty, are smaller than the pore bodies, which control the P at which pores fill. As the medium dries and P decreases, water retreats gradually as the air-water interface becomes more curved. At the narrowest part of the pore opening, this interface can no longer increase curvature by gradual amounts, so it retreats suddenly to narrower channels elsewhere. An analogous phenomenon occurs during wetting, when the decreasing interface curvature cannot be supported by the radius of the pore at its maximum width. The volume that empties and fills in this way is essentially an individual pore. Not all pore space is subject to Haines jumps—water remains in crevices and in films (not seen in Figure 3) coating solid surfaces. Fig. 1.3. Dynamics of a "Haines jump". 13 2.3. Soil air/aerobic and anaerobic soil - redox potential The soil air is composed of gases not different from those in the bulk atmosphere, but with very different distribution. Typically soil air contains much higher concentrations of CO 2 as a result of heterotrophic activity (respiration by plant roots and microflora and fauna) and limited gas diffusion rates. Concentrations of O 2 in soil pores can also rapidly change as a result of this heterotrophic activity in combination with very slow O 2 diffusion in water. At water contents higher than field capacity (and certainly above 60% WFPS) O2 diffusion into soil becomes increasingly limited and microbial activity can lead to a rapid depletion of the available O2, effectively leading to anaerobic conditions and to a rapid shift to anaerobic microbial metabolism (denitrification, Mn and Fe reduction, methanogenesis, …). The aeration of a soil, or the degree of anaerobicity, is expressed by the soil redox potential (E h), which can be effectively measured using redox probes. 2.4. Soil reaction - 2.5. Soil salinity For these abiotic factors we refer to the Soil science course. 2.6. Toxic compounds The soil environment and notably the chemical composition of the soil (solution) may be abruptly and strongly altered by antropogenic activities, with addition of xenobiotics that may very negatively affect soil life and hence soil functioning. Organic xenobiotics will be degraded eventually by the soil microorganisms but this may take long periods of time, depending on the nature of the pollutant. For more detail on this aspect we refer to the course on Soil pollution and soil remediation. 3. The soil ecosystem engineers Larger soil organisms are able to physically modify the soil matrix to (re)create their habitat, as will be discussed in more detail in the chapter on soil fauna. 4. Human alterations to the soil architecture Soil organisms slowly build-up their own living environment by interactions with organic matter inputs, chemical reactions and physical processes, the self-organisation of a soil. However, the soil habitat that is built up over time may be damaged or destroyed again in a matter of seconds as a consequence of human interventions, usually linked with agricultural soil management. In recent decades problems of soil compaction have increased enormously, as 14 a consequence of unadapted cultural practices and harvesting with increasingly heavy machinery. Intensive soil tillage e.g. is known to lead to soil compaction (plough pan) and to a destruction of soil macroaggregates over the long term, very negatively affecting soil life (notably earthworms, large arthropods, nematodes and fungal hyphae). Likewise, harvest in unfavorable conditions (wet soil) with heavy machinery and heavy wheel loads leads to soil compaction, reducing mainly the macroporosity and leading to the formation of anaerobicity in soils, which in turn may promote gaseous N losses and reduce biologically mediated nutrient transformations such as N mineralization. 15