1. INTRODUCTION
The development of human civilization is closely related to the environment. But with the emergence of a highly industrial society, the dangers of human interference with nature have increased sharply. The harmful impact on the environment is a general problem that affects biodiversity and human health.
The global nature of environmental pollution in recent years requires the adoption of adequate measures to prevent this process and eliminate existing sources of pollution. It is necessary to develop new approaches, including fundamentally new biotechnologies, based primarily on the use of microbiological methods.
Such an approach is the application of remediation processes in order to restore contaminated areas to their natural state. Existing technologies for the remediation of contaminated environments are divided into two main groups – in situ and ex situ. In situ technologies involve the treatment of contaminated material directly on site. Ex situ technologies are a remediation option in which the pollutant is removed from its original location and cleaned away from the contaminated area or outside the area. The remediation methods applied in each specific case of a contaminated environment are determined by the type and extent of the pollution, as well as the characteristics of the terrain itself.
Among the various methods of environmental remediation, bioremediation plays a leading role. Modern bioremediation practices include techniques for removing pollution or contaminants from soils (surface layer, subsoil and sediment), waters (both subsoil and surface) and air.
Bioremediation is a natural and sustainable process used to remove or reduce soil and water pollution by using living organisms such as bacteria, filamentous fungi, yeasts, algae and plants to treat, degrade or transform toxic compounds from water or soil. This effective and environmentally friendly approach to remediating contaminated regions is a branch of biotechnology that aims to overcome the limiting factors that slow down the rate of biodegradation.
Main methods of bioremediation:
- natural attenuation, where there is little or no human intervention;
- biostimulation – the addition of nutrients and electron donors/acceptors to promote the growth or metabolism of certain microorganisms;
- bioaugmentation – the deliberate addition of natural or artificially created microorganisms.
Main advantages of bioremediation:
- environmental friendliness: the method uses natural processes, which minimizes the need for chemicals and reduces secondary pollution;
- еconomic efficiency: compared to traditional methods such as digging up and removing contaminated soil, bioremediation is often cheaper and less invasive.
- sustainability: after successful application of bioremediation, affected areas can be restored and returned to normal use, which improves the quality of life and health of people.
Challenges facing bioremediation
- the application of microbiological processes in bioremediation is still limited due to the lack of sufficient knowledge about the microbial metabolic potential for environmental restoration;
- limiting the application of bioremediation due to the still poorly understood processes that control the development of microorganisms in contaminated areas.
2. FINDINGS
Environmental omics refers to the application of omics technologies to understand and model environmental and genetic factors, mechanisms of toxicity, and response pathways. It studies the characteristics of biomolecules in relation to exposure to various environmental factors and applies systematic approaches to advance the understanding of biological processes in the context of the environment. Such high-throughput studies can help identify new organisms suitable for bioremediation and discover effective degradation mechanisms at the molecular level.
2.1. Basic omics techniques related to environmental applications
Environmental omics aims to better understand the metabolic processes of a wide range of organisms and/or complex microbial communities to improve the phenotype-genotype relationship, thereby providing new insights into key molecules in response to environmental changes and invaluable information about microbial communities.
The main omics techniques related to environmental applications are (Fig. 11.1):
- Metagenomics– the science of genomes in a microbial community. This technique allows the identification of new species and functional genes that cannot be cultivated in laboratory conditions.
- Metatranscriptomics – sequencing of the entire (meta)transcriptome of the microbial community to reveal actively expressed genes and microbial functions under conditions and in a given time range.
- Metaproteomics – an emerging omics science providing information about all proteins present in microbial communities at a certain time interval.
- Metabolomics– identification and quantification of all metabolites in a sample, the most direct indicator of maintaining or altering homeostasis;
- Fluxomics– a new omics discipline that deals with the analysis of metabolic fluxes and the fluxome, captures the real and dynamic picture of phenotypes under given conditions.
Learn: Metagenomics principles and workflow (video)
Learn: Metatranscriptomics analysis: a tutorial: (video)
Learn: More about metaproteomics types (video)
Learn: More about metabolomics & environmental metabolomics (video)
Figure 11.1. Integration of omics techniques related to environmental applications (Source:Emwas et al., 2022 ).
Omics techniques provide invaluable information about microbial communities and their interactions with the environment, allow for comprehensive analysis of biological systems, and help discover new biomarkers and adaptation mechanisms. Combining different omics techniques has led to a more complete picture of ecosystem processes and the development of strategies for environmental protection and sustainable resource management.
2.2. A holistic multiomics approach to environmental research
Microbial communities are crucial for the functioning of diverse ecosystems and have a critical impact on nutrient cycling, agriculture and health. They are characterized by interconnectedness, which is evident in the symbiotic relationships, metabolic exchanges and communication networks that microbes establish. Understanding these complex relationships is crucial for deciphering the resilience and adaptability of microbial communities to environmental changes and preserving the balance and resilience of ecosystems. Through the lens of new omics approaches and bioinformatics, the roles of specific microbial species, their responses to environmental changes and their collective impact on biogeochemical cycles are revealed (Fig. 11.2). The multiomics approach allows researchers to gain a holistic understanding of microbial systems by elucidating gene expression, protein activities and metabolic pathways within complex microbial communities.
Figure 11.2. Ecosystem microbiome connectivity.
(Source:Zhu et al., 2023)
3. ALTERNATIVES
3.1. Biotechnological applications of ecological omics
Ecological omics, which uses omics technologies in an ecological context, has a wide range of biotechnological applications Martínez-Espinosa et al., 2023. The main ones are presented in Table 11.1.
Table 11.1. Main biotechnological applications of ecological omics
| Application | Essence |
| Bioremediation | Using microorganisms and enzymes to degrade hazardous waste, purify wastewater and soil, and improve aquaculture; an environmentally friendly method with low risk to human health. |
| Sustainable agriculture | Application of cell and tissue culture, gene recombination and microbial fermentation to create new plant varieties with increased productivity and resistance to stress factors. |
| Bioproduction and industrial biotechnology | Using microorganisms or their biological components to develop new production processes that require fewer resources and energy and generate less waste and polluting emissions. |
| Development of the bioeconomy | Integrating biotechnological approaches to create new value chains that support economic growth and employment while protecting the environment. |
4. SOLUTIONS – OMICS TECHNIQUES AND APPROACHES
Omics approaches with potential biotechnological application in environmental research support the understanding and optimization of metabolic pathways, which is essential for industrial biomanufacturing (Figure 11.3).
Figure 11.3. Omics approaches with potential application in environmental research.
(Source: Sharma et al., 2022)
4.1. Biodegradation of hazardous pollutants
The prevalence of carbon tetrachloride and trichloroethene as groundwater contaminants is largely due to their common use as dry cleaning solvents and metal degreasers and to their improper disposal. Biotechnology offers new opportunities for biodegradation of trichloroethene, trichloroethene and the toxic metabolite cis-dichloroethene (cDCE). An example is Polaromonas sp. strain JS666, which is the only bacterial isolate capable of utilizing cis-dichloroethene (cDCE).
Potential applications of Polaromonas sp. for bioremediation and biocatalysis: https://doi.org/10.1128/AEM.00031-09
4.2. Potential of omics technologies for bioremediation of heavy metals
Omics technologies play a key role in optimizing bioremediation techniques for removing or neutralizing heavy metals from the environment by:
- Discovery of resistant organisms: identification of genes responsible for resistance and accumulation of heavy metals.
- Uncovering detoxification mechanisms: elucidating the biochemical pathways by which organisms transform or sequester heavy metals.
- Genetic modification: creating genetically modified organisms with an increased ability to absorb and neutralize heavy metals.
- Better understanding and improving bioremediation processes: integrating omics technologies for the development of effective strategies for cleaning contaminated environments.
Table 11.2 shows various examples of applications of the haloarchaeal speciesHaloferax mediterranei.
Table 11.2. Some important applications of omics technologies with microorganisms for bioremediation of heavy metals
| Haloferax mediterranei | Application |
|
Llorca & Martínez-Espinosa, 2022 |
|
Torregrosa-Crespo et al., 2020 |
|
Wang and Zhang, 2021 |
|
Akmoussi-Toumi et al., 2018 |
|
Giani et al., 2021 |
4.3. Development of innovative biosensors
Lanthanides (Ln) are attracting researchers’ attention for their potential use in developing new green energy technologies. However, concerns about their environmental and human health impacts require the design of reliable biosensors to monitor their accumulation and identify the cellular and molecular mechanisms of their toxicity.
The application of omics approaches (genomic phenotyping, proteomic analysis and molecular physiology analyses) to a model organism Saccharomyces cerevisiae exposed to lanthanides reveals the genes and metabolic pathways influencing Ln resistance and toxicity. Using the combination of these omics approaches, it is found that cell wall components are not only involved in Ln adsorption, but are also active signaling effectors, allowing cells to distinguish between light and heavy Ln. These studies pave the way for a better understanding of Ln toxicity in higher eukaryotes [Grosjen et al., 2022].
4.4. Application of ecological omics in agrobiotechnology
The application of eco-omics approaches can be key to increasing crop yields without negative environmental impacts, through the development of biofertilizers or the production of biostimulants.
Rhizobacteria that promote plant growth can be used as biofertilizers. These microorganisms play an important role in creating a favorable ecological environment in the rhizosphere, reducing the use of chemical fertilizers and pesticides, inhibiting the occurrence of pests and diseases, and ensuring the sustainable development of modern agriculture, while achieving the goal of increased production. The application of omics techniques in recent years has revealed the main mechanisms by which rhizobacteria in the root system of plants stimulate their growth. Examples of the use of omics techniques to realize agriculturally significant plant characteristics are listed in Table 11.3.
Table 11.3. Applications of proteomic, transcriptomic and metabolomic techniques for studying rhizobacteria and increasing their efficiency.
| Microbial species | Application |
| Bacillus pumilus | Liu et al., 2020 – uncovering the mechanism for stimulating rice root growth. |
| Herbaspirillum seropedicae | Irineu et al., 2022 – elucidating the molecular mechanisms for stimulating the early stage of maize development and increasing yields when inoculated with the microbial species. |
4.5. Multiomics biotechnological solution to reduce oil pollution
Marine oil pollution, mainly caused by anthropogenic activities, is a serious environmental problem due to its negative impact on human health and ecosystems. For example, the incident caused by the explosion of the Deepwater Horizon oil platform located in the Gulf of Mexico in 2010 led to an ecological disaster with serious damage to the marine ecosystem. It was bioremediation approaches that helped to completely eliminate the oil pollutant.
Uncovering the genomic background of hydrocarbon-degrading microorganisms is of great ecological importance, as it contributes to the development of effective methods for reducing oil pollution and mitigating environmental damage. High-throughput sequencing provides new knowledge about the basic mechanisms in microorganisms that carry out oil degradation. To date, the genomes of several hydrocarbon-degrading bacteria have been analyzed in depth. These genomes show various characteristic differences (Table 11.4).
Table 11.4. Characterization of the genomes of different bacterial species with oil-degrading capacity and potential applications in bioremediation
| Bacterial species | Omics approach | Obtained characteristics |
| Alcanivorax borkumensis SK2 | de novo transcriptomics based on RNA-seq and metagenomic analysis |
|
| Achromobacter sp. HZ01 | de novo transcriptomics based on RNA-seq and metagenomic analysis |
|
5. RECOMMENDATIONS
In recent years, environmental pollution has already pushed the Earth beyond its state of homeostasis, demonstrating the need for rapid recovery and the development of strategies to achieve the UN Sustainable Development Goals by 2030. However, implementing new approaches does not come without challenges. The use of omics technologies in research generates a huge amount of scientific data, which significantly expands the available information. However, in the search for new knowledge, some interpretation challenges must be overcome. Due to the huge amount and complexity of the data, their analysis requires special techniques based on machine learning and large arrays. In the case of single-omics approaches, data processing must address issues of data filtering and cleaning, curation, transformation, normalization, and scaling. Multi-omics analysis must also overcome additional challenges related to data integration, fusion, clustering, visualization, and functional characterization.
Despite these potential difficulties, omics approaches have made it possible to observe and measure biological systems with unprecedented precision and at ever-decreasing costs, and it is only a matter of time before these approaches are fully integrated into environmental sciences.
6. REFERENCES
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