**2. Soil microbiota: key component of soil biodiversity and ecosystem**

Soil microorganisms present a great diversity, although more of them are not cultured at moment. They are acknowledged as a key component of soil biodiversity due to their involvement in numerous and significant interactions in terrestrial ecosystems. Such interactions control soil's physical, chemical, and biological processes. Components of soil microbiota directly mediate and influence the stability and cycling of relevant elements and climate change. Microorganisms activities are related to the regulation of soil C sequestration and mineralization, nutrient cycling (N, P, etc.), and not finally with ecosystem productivity once that they facilitate the nutrient resource for higher components of biota (e.g., plants) through fast turnover [13]. Soil

microbiota community components are also a relevant source of enzymes. They liaise soil potential for enzyme-mediated substrate catalysis [14, 15]. Microbiota components are indigenous to the environment and most of the time are capable to adapt to variable environmental conditions (temperature, redox potential, pH, moisture regime, and pressure) or to exist under oligotrophic conditions (low nutrients).

#### **2.1 Soil microbiota community structure**

Microbiota constituents could be grouped into three domain systems consisting *Archaea*, *Eukarya,* and *Bacteria*. *Bacteria* and *Archaea* are generally named as prokaryotes, while *Eukarya* as eukaryotes [16].

#### *2.1.1 Bacteria*

*Bacteria,* the most abundant microorganisms as a number of individuals (around 50 phyla) are free-living fewer complex organisms with great metabolic flexibility. Due to these features, they easily and promptly respond and adapt to changing environmental conditions. Bacteria can be grouped either by considering their cell envelope architecture (structural characteristic) or through their metabolism type (physiologic characteristic). Structurally, bacteria are grouped as Gram-positive (e.g., Bacillus, Clostridium, etc.) and Gram-negative (e.g., *Pseudomonas*, *Shewanella*). This difference mediates their survival in the environment.

*Gram-negative* bacteria cell envelope is a complex structure that allows them to interact with mineral surfaces and solutes from the environment. In that way, they obtain the required amount of nutrients for metabolism [17].

*Gram-positive* bacteria have a less complex cell envelope [18]. Their thick cell wall allows them to withstand challenging physical conditions of the soil environment [19].

*Actinomycetes* is a special group that now is classified as Gram-positive bacteria. These group differentiates by bacteria through their tendency to branch into small dimension filaments or hyphae that structurally resemble the hyphae of fungi [20]. They are widespread in soil environment and are recognized also as valuable antibiotic producers [21, 22]. Actinomycetes abundance increase with decomposed organic matter. However, they are strong pH-sensitive organisms, usually at pH below 5 pH units, their abundance decreases considerably. Contradictory with other bacteria species, their abundance increases once with soil depth. From ecological point of view, as growth strategy soil bacteria could be grouped as copiotrophs (e.g., *Betaproteobacteria*) and oligotrophs (e.g., *Acidobacteria*). Copiotrophs consume easily degradable organic C, while oligotrophs consume recalcitrant organic C. Although oligotrophs grow slowly but constantly, maximizing their yield under poor nutrient availability conditions. Copiotrophs to maximize their yield require high nutrient content. From bacteria metabolism point of view, considering the source of energy and C used for growth, Robert and Chenu [23] classified bacteria in several groups (chemoheterotroph, photoautotroph, photoheterotroph, etc.—see **Table 1**).

Therefore, according to their energy source, bacteria could be divided into four main groups (**Table 1**) as *phototroph* (energy is obtained from light—photosynthesis), *chemotroph* (oxidation of organic and inorganic chemicals), *autotroph* (carbon dioxide), *heterotroph or organotroph* (from organic compounds as glucose) [19]. Chemoheterotrophs (chemoorganotrophs) use organic compounds both as energy and as C source. Chemoautotrophs (chemolithotrophs) obtain energy from the oxidation of inorganic compounds and C from CO2. Photoautotrophs get energy from light and

*Global Change Drivers Impact on Soil Microbiota: Challenges for Maintaining Soil… DOI: http://dx.doi.org/10.5772/intechopen.111585*


**Table 1.**

*Bacteria classification based on their metabolism (modified after Pepper and Gentry, [19]).*

fix C from CO2. Photoheterotrophs obtain energy from light and C from organic compounds. Bacteria harvest energy either through respiration (aerobic or anaerobic process) or through fermentation (anaerobic process). *Archaebacteria* is a special heterogeneous group of bacteria that have the ability to leave even in extreme environmental conditions (e.g., environments with high sulfur or salt content). Usually, these organisms are classified either as *obligate anoxybiont* (total absence of oxygen in the media where they live) or *facultative anoxybiont* (they could survive in both aerobic and anaerobic environments, e.g., thermoacidophiles) [24, 25]. Obligate anoxynbionts include methanogen (produce CH4 from CO2) and halophile species

(live in extremely salt environment). Although there are bacteria in soils that can have a pathogenic effect on plant biodiversity, most bacteria are recognized that have important functions that assure soil health and functioning through decomposing organic matter and contributing to producing nutrients available for other living micro and macroorganisms.

#### *2.1.2 Archaea*

*Archaea*, although could appear similar to bacteria they differ from them genetically and biochemically. They appear both in extreme and nonextreme environments. Extremophiles could survive in environment with extreme temperature (hot, cold), salinity, alkalinity, or acidity [19]. Major divisions of archaea are *Crenarchaeota*, usually thermophiles (live in high-temperature environment), and *Euryarchaeota* that include haloarchaeans (live in saline environments) and methanogens (live in anaerobic environment at low temperature) [26]. Their major functions related to soil are those connected to horizontal gene transfer between archaeans and bacteria, and nitrification process control.

#### *2.1.3 Fungi*

*Fungi* with great biomass are physically the largest group of eukaryotic microorganisms. They are regnant in soil environment with high adaptability to various conditions. Are valuable components of soil biodiversity due to their essential function as decomposers [27]. Considering their morphological description, fungi are grouped as molds, mushrooms, and yeasts. *Molds*, filamentous fungi, are found in many fungal phyla. *Mushrooms*, filamentous fungi, are part of Basidiomycota. They form the large fruiting bodies known too as mushroom. Both molds and mushrooms are very important decomposers of natural products [19]. They produce also extracellular substances that bind soil particles, forming stable soil aggregates, reducing, therefore, soil erosion. *Yeast*, are unicellular fungi with the ability to ferment under anaerobic conditions. Some components through symbiotic relationships with algae and cyanobacteria form lichens [28]. These secrete organic acids that help rocks and inorganic surfaces in degradation. Fungi have chemoheterotroph metabolism. This supports biosynthesis and energy production based on simple sugars, but they produce also secondary metabolites. These metabolites (e.g., exoenzymes) produced during the stationary phase of growth are acknowledged that help to reduce the competition for nutrients from other microorganisms, and some of them have antimicrobial properties. Exoenzymes break down complex polymers into simple C compounds for cells [29]. Based on that, fungi could be grouped as saprophytic and mycorrhizae.

*Saprophytic fungi* are important organic material degraders (e.g., dead plants and organisms), especially of complex polymers associated with them (e.g., cellulose and lignin from plants; chitin from insects) [30, 31]. They are also able to degrade chemical pollutants [32]. *Mycorrhizae* form a symbiotic relationship with a large number of plants. Through that relation, these fungi increase plant roots' absorptive area and prevent desiccation, as well increase nutrient uptake (especially phosphate) [33, 34]. Similarly, plants furnish sugar (obtained through photosynthesis) to fungi. Mycorrhizal fungi could be divided into ectomycorrhizal and endomycorrhizal fungi group [32].

*Global Change Drivers Impact on Soil Microbiota: Challenges for Maintaining Soil… DOI: http://dx.doi.org/10.5772/intechopen.111585*

#### *2.1.4 Protozoa*

*Protozoa*, are eukaryotic microorganisms with fundamental genetic differences between species. Protozoa species are usually heterotrophic organisms and consume bacteria, yeast, fungi, and algae [35]. Usually habit the top part of soil (up to 20 cm depth) and are concentrated near roots (due to availability of the high quantity of prey). They are involved in soil organic matter decomposition processes.

### *2.1.5 Algae*

*Algae*, phototrophic organisms (metabolize in the presence of light for energy and CO2 for C), are located at the top surface of the soil or very close to it (green algae and diatoms, which are heterotrophs as well photoautotrophs). They are strongly involved in soil formation processes through their metabolism. Once through photosynthesis, they introduce C to the soil, and secondly through metabolizing processes produce and release into soil carbonic acid and polysaccharides [36]. Released carbonic acid help in weathering surrounding mineral particles, while extracellular polysaccharides facilitate soil particle aggregation [37]. Soil algae are seasonally variable, higher abundance having in spring and fall period. In winter and summer, their development and abundance are suppressed considerably due to water-induced stress—soil moisture and/or desiccation [36].

#### **2.2 Soil microbiota community structure and abundance: Role in soil processes**

Soil, the base of terrestrial ecosystems, is inhabited by a large diversity of organisms. Microbiota inhabitants are key actors in several essential processes in soil. Through their diversity and varied metabolism mediate biochemical reactions and take part in multiple interactions and reactions in and between surrounding microhabitats. Through these, soil microbiota contributes to and liaises essential functions of soil ecosystems. Thus, soil microbiota significantly influences the soil ecosystem in its ability to provide ecosystem services.

#### *2.2.1 Bacteria role in soil processes*

Bacteria are recognized as primer decomposers of both organic matter and organic wastes. They change compounds and elements from inaccessible to usable forms for higher trophic components, thus significantly contributing to the cycling of essential elements and providing the nutritive resources required by below- and aboveground organisms. Geddes et al., [38] with others [39–42] revealed that *Rhizobium sp*. and *Bradyrhizobium sp*., bacteria present inside the host root system (leguminous plants root nodules) fix atmospheric N, the primary nutrient that influences plant growth and development. Arashida et al., [43] showed that *Pseudomonas sp*., *Bacillus sp*., *Azotobacter sp*., and *Azomonas sp*., bacteria from the proximity of plant root system, fix atmospheric N usable form as ammonia. Less frequent bacteria phyla in soils, such as *Verrucomicrobia*, is also involved in N fixation and associative activities [44]. Cyanobacteria are recognized as important improvers of C, N, and exopolymeric substances content in the soil. They release into soil amino acids, proteins, polysaccharides, carbohydrates, vitamins, and phytohormones as elicitor molecules that

promote plant growth. Kumar et al., [45] (2013) also reported that cyanobacteria could facilitate plant resistance against both biotic and abiotic stresses. Actinobacteria species have also multiple roles in soil, such as fixation of atmospheric N (*Arthrobacter sp., Rhodococcus sp.*), minerals solubilization (*Ferrobacter sp.*), increase of antagonistic efficiency against different fungal root pathogens (*Streptomyces sp*.) as well as plant growth hormones production (*Frankia sp*.). They are also responsible for soil odor. Studies on dominant culturable bacteria, *Arthrobacter sp.*, *Streptomyces sp*., *Pseudomonas sp*., and *Bacillus sp.* revealed their involvement in nutrient cycling and biodegradation [46], degradation of recalcitrant organic compounds [47], and production of antibiotics [48] and biocontrol agents [49]. Functions in the soil of important autotrophic and heterotrophic bacteria are summarized in **Table 2** [19].
