**4. The soil system**

It is easier to recognize physical boundaries in terrestrial ecosystems as the environment changes at slower velocities than the very dynamic aquatic environment. Soil is a heterogenic environment, the opposite to the aquatic ones. It is an environment that cannot be seen through and be dived in. Soil matrix is composed of a very complex mixture of mineral particles, organic matter and living organisms. This mixture is organized in aggregates that may facilitate or resist water and air passing through it but, most importantly, these aggregates proportionate spaces where all living beings can move through soil.

At a microscale, soil aggregates divide the open spaces in two types, the fast water passing by (the space between aggregates) and the slow motion of water in the space inside the aggregate, and consequently of slow-moving air too, as air and water move through the same spaces). These are the soil's physical boundaries, and this is the environment where roots move and look for hotspots of nutrients, as well as places where microbial symbionts may be found (normally inside soil aggregates). Water reaching soil aggregates dissolved salts and polar molecules that may contain nutrients that will be taken by roots, mycorrhiza, or bacteria. This is a complementary start of plants primary productivity, because plants have to take water from soil together with other nutrients to produce a wide range of molecules, from non-protein forming amino acids to scents and pheromones, as result of what is known as the "secondary metabolism." Plant primary productivity comprises both photosynthesis-respiration (primary metabolism) and secondary metabolism, irrespective of being vascular or nonvascular.

Soil productivity is dependent on the nutrient exchange velocity rather than the gross amount of bioavailable nutrients. Nutrients used and released very fast means energy is being captured, transformed, and degraded very fast, implying the activities of all participating organisms are taking place so fast that production

#### *Food Webs DOI: http://dx.doi.org/10.5772/intechopen.97252*

of biomass at all levels is gaining momentum and its control may come only from consumption (top-down) no matter that nutrients exist in limited quantity. This feature also explains why the smaller organisms can sustain productivity of the biggest ones. In other words, aerial part of plants are very important for primary productivity because it is the place were light, inorganic carbon, and water are used to produce organic molecules that are at the base of primary productivity (Sun's energy fixation in organic molecules).

Without diminishing photosynthesis' importance, most of terrestrial plants gather a "productivity teamwork" inside and around their roots, involving mycorrhizal fungi and mutualistic bacteria, a functional place known as the rhizosphere. Almost 80% of the known terrestrial plants need the association with a mycorrhiza, to appropriately complete their life cycle, but all plants need mutualistic bacteria to grow. Microbial partners are indeed an important part of primary productivity, as they actively participate in the acquisition, modification, and metabolization of many organic molecules containing the elements we call "Nutrients." For example, it has largely been demonstrated that mycorrhiza translocate phosphorus to plants. At present, very few people challenge this. However, what form of phosphorus is translocated from mycorrhiza to plant? Surely, it is not the phosphorous as molecule, but organic molecule where P is forming part of the structure. Plants can take up P from inorganic molecules in general or from phosphoric acid. Why do they need mycorrhiza to supply P? It is still an open question, but the degree of specificity of the plant-mycorrhiza association allows to conjecture that plant and mycorrhiza share metabolites containing nutrients (not just P) for metabolic complementation, and the same could be true for mutualistic bacteria. This would explain why one species of mycorrhizal fungi is mutualistic to several plant species but functions as pathogenic or parasite to other ones.

Contrary to what happens in waters, soil fungi and bacteria are scattered through soil and physically constrained to available surfaces. If they keep growing unchecked, bacteria may become effective nutrient competitors to plants, as nutrients forming bacterial biomass are non-available to plants. Mycorrhiza may move farther away from the root than bacteria and can establish a mutualistic relationship with other roots (whether they are from the same plant or from a different species, it does not matter) to avoid becoming competitors. Absence of bacterivores is a needed condition for bacteria to become a plant competitor in the rhizosphere [83, 84]. Bacterivores ciliates, flagellates, and amoebae release nutrients trapped in bacterial biomass, stimulating both plant and bacterial growth. In the first case, nutrient release allows roots to take them in and bacteria microcolonies may grow again in the root surfaces, already cleaned out, and obtain nutrients from predators' wastes [84].

Soil's physical constrains allow growth of bacteria and fungi in differentiated places. Sometimes bacteria also grow on the surface of hypha, helping fungi to mimic bacteria and somehow escape from fungal predators. It has been possible to observe protists feeding predominantly on fungi and avoiding bacteria as much as possible (*Dermamoeba granifera*, *Cochliopodium* sp.). There are also protist species feeding on soil algae (*Colpoda* sp., *Polychaos* sp., *Thecamoeba* sp.) Consequently, it is possible to recognize the existence of several functional groups of soil protists: few species of phototrophs feeders, large quantity of bacterivores, fungal feeders, raptorial feeders (*Balamuthia mandrillaris*), and omnivores (*Acanthamoeba castellanii*, *A. polyphaga*, *A astronyxis*).

This differentiation of soil's physical spaces makes it easier to visualize the small productivity compartments around roots, absorbing hairs inside small soil aggregates, bigger compartments covering aggregates on the tip of the root and getting in contact through fungal hypha.

Motility of bigger protists are limited to litter and upper soil layer by the available spaces, restricting their abundance in the underneath layers. Testate amoeba, ciliates, and flagellates, around 100 μm, dominate in these 2 layers and actively participate nutrient recycling from litter, while smaller size ciliates like *Colpoda cucullus*, small flagellates and small naked amoebae distribute better in the underlying soil strata in and around soil aggregates.

Primary productivity in soil is restricted to the upper layers where cyanobacteria and eukaryote algae may survive and even form thin layers known as microbial soil crusts. Both phototrophic bacteria and algae may form stable mutualistic symbiosis with other organisms, like fungi, to develop thicker structures composing soil crusts showing lichens and mosses. Beneath and into soil crusts, ciliates, flagellates, and amoebae are among the most important microbial predators, active mainly during the time of water availability [85, 86]. However, the main photosynthetic carbon input is released by roots into soil layers [87]. Roots secrete amino acids and other complex organic molecules to attract symbiotic bacteria and mycorrhiza conforming the trio of soil productivity sustaining microbial food webs deep into soil [88, 89]. Consequently, protists' species diversity may be higher around roots and the dominance of ciliates may be restricted to the sizes of soil pores [86, 90–92]. Soil protists were recognized as purely bacterivorous because fungi feeding protists may transitorily feed also on bacteria. However more detailed studies have recognized species of soil protists feeding only on bacteria or fungi [93–95]. Among the main bacterivorous ciliates are Colpodida (*Breslaua vorax*, *Colpoda aspera*, *Colpoda inflata*, *Colpoda maupasi*, *Colpoda steinii*, *Cyrtolophosis elongata*, *Cyrtolophosis mucicola*, *Platyophrya vorax*, *Pseudocyrtolophosis terricola*, *Pseudoplatyophrya nana* [85, 96].

Fungi and bacteria normally use different kind of organic molecules, bacteria normally metabolize low molecular weight organic molecules while fungi normally metabolize complex organic polymers of high molecular wight [97]. This metabolic difference allows to conceptualize two pathways for nutrient cycling: the bacterial and the fungal paths. However, this concept is being challenged because of the abundance of protists feeding on both kind of microorganisms [98, 99]. All the early recognized fungi feeding ciliates and amoebae in soil ranges from 50 microns to above 150 μm [100]. However, there are also smaller ciliates and flagellates feeding on both spores and hypha [100]. The main groups of specialized fungal feeder ciliates are grouped in the family Grossglockneriidae [93]. This family of ciliates may account for mora than 2% of the protists sequences in the forest litter and grassland while may drop below 0.3% in peatland soil, probably due to the reduction of soil pore sizes [100]. Although, counting techniques based in MPN calculated around 200 cells/gram soil DW in previous studies [101]. Protists have a very limited capacity to disperse throughout the soil system by themselves. However, oligochaeta disperse them as cysts farther than a few centimeters, in the range of several meters both horizontally as well as vertically into the soil system.

Soil functioning is much more variable than the aquatic systems, as it is regularly subjected to dryness and several flooding events per year. For microbial ecologists, soil is a natural stressed environment, having enormous variations of water availability through seasons, especially in arid and semiarid environments. However, there is a comparable situation, although at lesser degree, in the tropical dry forests, temperate, and tundra regions. Even at the equator, the rainy forests may show an excess of soil in water, stressing microbial food webs.
