**1. Introduction**

Microorganisms support essential roles in soil environment with important effects on ecosystem functioning and stability. They assure soil fertility, sustainability, and plant development [1]. However, global change pressures with increasing contaminant inputs and changing climate and environment have influenced native microbiota in different extent. Changes in soil microbiota community abundance, structure, and functioning could limit soil-provided ecosystem services that they mediate [2, 3].

Rhizosphere refers to the plant roots and soils adhering to them. It is considered the most dynamic and biologically active region of soil. Through the large variety and quantity of metabolites that are released by plant root fibrous system or root hair [4], rhizosphere sustains the large diversity of rhizobiota. This includes microorganisms such as algae, protozoa, slime molds, fungi, bacteria, archaea, viruses, etc. [5]. Most of these microorganisms are responsible for plant protection against pathogenic organisms, plant growth and development facilitation, and plant defense against abiotic stress factors [6].

Rhizobiota abundance and community structure modify once with plant root development and changes of soil environment property. Such changes could convert their functions either positively or negatively. Further, that potentially could impact the plant development [7]. There have been developed several approaches that allow assessment and monitoring of soil microbiota diversity and activity to better understand the soil ecology. These could be culture-based or culture-independent approaches. Culture-based techniques have been shown unable to isolate and grow a large domain of soil microorganisms [1]. Phospholipid-derived fatty acids (PLFA) profile analysis for monitoring soil microbiota phenotypic structure is a common culture-independent approach [8]. Additionally, in situ analysis of nucleic acids, direct analysis of DNA/RNA and polymerase chain reaction (PCR)-amplified segment of DNA molecules are frequently applied culture-independent methods [9, 10]. These culture-independent analytical tools are applied for microbial biomass, diversity, and activity assessment based on taxon richness and evenness. Commonly cited disadvantages are those related to sample storage and sample handling, which could limit results' accuracy. Soil samples' physicochemical properties also could restrict DNA/RNA extraction efficiency because of potential presence of inhibiting organic compounds or due to binding properties of nucleic acid molecules to soil particles. Further, DNase and RNase contamination could be easily acquired, which reduces results' accuracy too [1, 9]. Therefore, in the context of global changes that resulted in imminent abiotic and biotic pressures, as well of the importance of microorganism's key role in assuring soil-provided ecosystem services, it has become a requirement to find optimal evaluation tools for soil microbiota abundance, structure, and functioning assessment. Such biomonitoring tools help to improve ecosystem management strategies and consequently to protect biodiversity and conserve its functionality before loss of delivered ecoservices.

Biomonitoring tools are important to provide quick answer to changes in soil system offering insight on microbiota and its activity without disturbing soil. Gas chromatographic approaches could provide such information. Soil microbiota profiling based on phospholipids-derived fatty acids profile allows quantitative evaluation of living microbiota abundance and phenotypic structure. Bacterial released volatile organic compounds assessment permits evaluation of microbial metabolism status. Therefore, using such analytical approaches is possible to obtain a wider view on microbiota evolution and function under abiotic and biotic pressures raised by global change.

In the following chapter two chromatographic approaches will be presented that allow soil rhizosphere microorganisms' assessment and monitoring under a common abiotic pressure, the increased presence of pharmaceuticals in our surrounding environment.

#### **2. Rhizobiota functions and related ecosystem services**

Rhizosphere could comprise either free living or symbiotic microorganisms. Rhizobiota-related ecosystem services are the benefic outputs for human well-being *Gas Chromatographic: Mass Spectrometric Mining the Volatilomes Associated to Rhizobiota… DOI: http://dx.doi.org/10.5772/intechopen.102895*

resulted from microbial activities of the rhizosphere. These benefits are the end results of biotic and abiotic interactions and processes. Microbial communities are involved in organic matter decomposition, nutrient cycling, and pollutants degradation. They could stimulate or inhibit plants through the metabolites that they release. Those, they are directly involved in soil regulating, supporting, and provisioning services.

**Rhizobiota involvement in soil regulating services:** Main regulating services managed by soil microorganism are diseases and pest regulation, organic waste matter degradation, and pollutants degradation.

*Diseases and pest regulation*: Biological factors induced plant diseases cause decline of crop yields and quality. In the context of increased food demand once with global population increases, this resulted in frequent use of chemicals that prevent and control plant diseases and that warrant required fertilizers. Although extensive use of these chemicals has achieved the proposed objectives, their use has also resulted in unwanted side effects such as environment pollution, food products contamination and ecosystem alteration. The potential amplitude in time of these side effects ended in the necessity to find alternative eco-friendly solutions that minimize these associated health risks. Studies revealed that use of biological control agents could become a suitable alternative [11]. This started from the evidences that there are numerous mechanisms throughout microorganisms, including rhizobiota also, that influence directly or indirectly pathogen diseases. Soil bacteria and fungi life support functions could be summarized as antagonism, resistance, competition, and stimulation of plant defenses. At the moment is an increased interest in identifying and further the applying of beneficial plant-associated microorganisms instead of classical pesticides for pest and disease management. There are studies that identified different bacterial or fungal species that could control or act against several pests or diseases. *Pseudomonas* strains, which could be located also in rhizosphere, act against *Phytophthora infestans* oomycetes, which are a frequent damaging pathogen of potato [12, 13]. *Trichoderma harzianum* biocontrol *Rhizoctonia solani*, a soil-born pathogen, and *Fusarium oxysporum* f.sp., a fungus, act against crops of the Solanaceae family and other plants [12, 14]. The biocontrol ability of these microorganisms against pests and diseases is directly correlated with production of numerous organic and inorganic molecules.

*Organic waste degradation*: Organic waste degradation is considered a twostage biotic process. Through this process, organic waste is first fragmented into smaller pieces by deprives, followed by deconstruction of these fragments into organic and inorganic molecules by microorganisms [15]. Rhizosphere microbiota are involved in decomposition of organisms and plants waste. Obtained components after decomposition processes are easily taken up by living organisms or removed from soil environment through leaching and runoff processes. Their ability to enhance decomposition processes of organic wastes resulted in raising the use in different fields of organic waste management areas (municipal solid waste, agricultural waste, etc.). They started to be used successfully in different biotechnology fields as renewable biogas production or composting for soil fertility enrichment [16].

*Pollutant degradation*: Presence of pollutants increased over years in all environmental compartments. Although abiotic treatment processes (physical and chemical) are widely applied and considered most of the time efficient in decontamination processes, these processes are often associated with potential few constraints. One of such constraints is the generation of secondary pollutants through the decontamination process. Also, the high cost required in such treatment processes also limits their applicability in low-income regions. Use of biological treatment was found as an advantageous approach [17]. It is widely used all over the

world for emerging pollutants removal from wastewater. Also, different microbial strains started to prove their efficiency in degradation of different pollutants. Mycobacterium sp. and Bacillus megaterium, for example, are efficient in polycyclic aromatic hydrocarbons degradation in the presence of specific enzymes (e.g., ring hydroxylating and ring cleavage dioxygenase) [18]. *Acidisphaera*, *Burkholderia, Geobacillus, Pseudomonas,* and *Rhodococcus* bacteria are considered alkanedegrading bacteria [19]. *Sphingomonas* sp. and *Burkholderia* sp. degrade fenitrothion pesticide [20].

**Rhizobiota involvement in soil supporting services:** Supporting services are that services that hold up ecosystem functions that are indirectly used by humans. Soil microorganisms are critically involved in soil nutrients cycling and primary production.

*Nutrients cycling***:** Plant development and production require adequate nutrient resources. Rhizosphere bacterial and fungal community are involved in organic matter breakdown and recycling. Through their related catabolic reaction, they breakdown, transform, and mineralize macro- and micro-nutrients [21]. *Proteobacteria* and *Rhizobia* bacteria are involved in nitrogen fixation. *Cianobacteria* and *Eubacterium* enhance Zn and Fe translocation into plant.

*Primary production***:** Plant production is influenced by numerous microbial processes. *Proteobacteria* and *Firmicutes* enhance plant root system proliferation through produced organic compounds. *Rhizobium* sp., and *Frankia* sp. are involved in nitrogen fixation. *Streptomyces* and *Pseudomonas* produce iron-chelating compounds that facilitate Fe availability for plants. *Agrobacterium sp*. and *Bacillus* sp. are involved in phosphate solubilization. Numerous microorganisms increase plant stress tolerance through their produced organic and inorganic compounds [22].

**Rhizobiota involvement in soil provisioning services:** Provisioning services are those products that are obtained from ecosystem. Generally, these refer at food, fiber, genetic resources, chemicals, pharmaceuticals, etc. Microorganisms are considered important resources for numerous chemicals and pharmaceuticals with a broad range of applications.

*Bioresource***:** Bacterial and fungal population of rhizosphere influences plant communities, pathogens abundance, nutrient acquisition, and stress tolerance [15]. In most cases these are controlled by the produced bacterial and fungal origin molecules. Rhizosphere microorganisms were acknowledged as important bioresources for bioactive substances. They produce antibiotics, bacteriocins, lipopeptides, toxins, siderophores, enzymes, biosurfactants, osmoprotective substances, and other secondary metabolites [23].
