Environmental Microbiology: Advanced Research and Multidisciplinary Applications

Environmental microbiology deals with the role of microorganisms in supporting a thriving, viable and inhabitable environment. It helps to figure out the nature and functioning of the microbial population residing in all parts of the biosphere, i.e., air, water, and soil. Microbes are known to affect the environment both negatively and positively, as their contamination may lead to serious health issues on one hand, whereas various welfare activities like degradation of organic material, being a source of nutrients in food chains, recycling of nutrients, and bioremediation of pollutants are also associated with them on the other hand. In a way, their practical importance makes them a special tool in the hands of environment microbiologists to lessen the deleterious impact of different environmental problems. The degradation potential of microbes earns them a place in treating wastewater, containing organic and inorganic impurities being originated in public and industrial arenas whereby minerals, nutrients, and a number of other eco-friendly by-products are also generated. Microbial species like Pseudomonas, Sphingomonas, and Wolinella are few among those species which are commonly engaged in this process of degradation of harmful effluents being continuously added into the environment, thus ensuring the safety and sustenance of the latter. Furthermore, their degradative abilities also help them to effectively confront and conquer the problem of oil spillage in sea waters resulting in less ecological damage. The manipulation of microbes in the present times has gained quite an important place in our lives in which this discipline of environmental microbiology contributes by unraveling all such possibilities of utilizing the microbes to our benefit. The present chapter provides a deep insight into this important branch of microbiology and its scope, which will help better understand its role in other fields such as agriculture, medicine, pharmacy, clinical research, and chemical and water industries.

Microbial diversity is an essential aspect of any ecosystem on earth. Microorganisms are the most common and diversified population in the soil. A microbe is a microscopic organism that can be studied in a single-cell or colony. On the other hand, microbes have a positive or negative effect on their surroundings. Microbial diversity plays an essential role in bioremediation, which is the method of detoxifying or neutralizing radioactive waste into less harmful or non-toxic compounds by secreting various bacterial and fungal enzymes. In this chapter, we focus on (i) the impact of microbial diversity on detoxifying pollutants (bioremediation), (ii) microbial role in biofuel production, (iii) microbial role in ore leaching (bioleaching), (iv) microbial role in controlling biogeochemical cycles (v) microbial role in soil quality and agriculture improvement (vi)

 Rhizospheric soil is enriched with diverse microbial communities, which give rise to sophisticated plant-microbes interactions via chemical communication. The bacteria attain communication through quorum sensing and lead to biofilm formation, developing connections between the cell density, and altering gene expression. Such processes include diffusion and accumulation of signal molecules such as autoinducer i.e. acyl-homoserine lactones, Autoinducer-2 (AI-2), QS pheromone, etc. in the environment and trigger the expression of the gene. Due to increment in cell density, bacteria produce the substances that inhibit the growth of pathogens, fix nitrogen and optimize nodule formation. Moreover, the adaptability of microbial communities under stress conditions directly/indirectly was correlated with host plant growth. The plants and soil microorganisms equally face the abiotic stresses and may cause environmental tolerance and adaptability via complex physiological and cellular mechanisms. The recent knowledge of the plant-microbe relationship and their communication mechanisms can be helpful in the development and commercialization of agricultural practices to improve desired crop health and productivity under various abiotic and biotic stresses. This chapter explores such habiting microbial communications in rhizosphere attributing to soil environment in various means. 

To understand the interaction between different microbes, it is important to understand how they communicate with one another in their adjacent environment. These interactions are beneficial because when different microbes interact, they stimulate specific mechanisms, release signals, and result in the production and synthesis of important vaccines, anti-bacterial and anti-fungal agents, and secondary metabolites. These metabolites are beneficial from a medicinal point of view as well. Many studies proved that specific metabolites are released only when they interact with other microorganisms in their adjacent environment. This is also proved through chromatography and co-culturing of these microorganisms.

 Nutrient cycling is an important environmental process and has been the focus of ecological research. Nutrient cycling refers to the sufficient supply of key elements provided through the ecological processes within and between various biotic or abiotic components of a cell, community, or ecosystem. Nutrient cycling also includes the recovery and reuse of industrial, agricultural, and municipal organic debris that are considered wastes. Nutrient cycles include biotic and abiotic components involved in biological, geological, and chemical processes known as biogeochemical cycles. Changes occurring in such cycles may indicate or even alter the functioning of the ecosystem. Plants take up soil nutrients in terrestrial ecosystems for healthy growth and development, wherein soil acts as a nutrient reservoir. Nutrients are lost from such sites due to soil erosion, denitrification, and food production, which cause reduced availability of nutrients. Therefore, analyzing nutrients’ assimilation, transport through biota, and their release for subsequent re-assimilation is mandatory. Nutrients to be recycled essentially for the survival of organisms include macronutrients (C, O, H, N, K, P, Ca, Mg, S, and Cl) and micronutrients (Fe, Mn, Mo, Cu, Zn, Bo, Ni, Co, Na, Se, and I). This chapter presents the role of nutrients and nutrient cycling for environmental sustainability

 Unchecked disposal of substances or compounds such as organic/inorganic heavy metals, polychlorinated biphenyls (PCBs), herbicides, pesticides, phenolic and nitrogenous compounds, and polycyclic aromatic hydrocarbons (PAHs) ubiquitously present in the environment poses a global concern. This requires constant monitoring of environmental pollutants. Biological-based monitors and biosensors with high specificity and sensitivity are applied to monitor and check the level of pollutants. These are biological-based methods used for the intervention of environmental pollutants as analytes. The widely used biosensors are made by immobilizing various enzymes, antibodies, whole cells in the devices, and transducers. Microbial biosensor devices sense the substances in the environment through the various biochemical reactions of the microorganisms incorporated in the devices. However, with the ease of genetic modification techniques like genetic engineering technologies, various microorganisms have gained immense popularity as ideal candidates for developing biosensors. The microbial biosensors' inexpensiveness, compactness, and portability offer advantages over conventional chemical sensors. The most significant aspect of microbial biosensors is the in situ detection capability, and real-time analysis has enhanced their acceptability and applicability in environmental monitoring. The following chapter deals with microbial biosensors to detect air, water, and soil pollutants

At present, the world is reeling under the problem of different environmental pollutions, viz., soil, water, and air pollution, as a result of anthropogenic activities, intensive inorganic agriculture, industrial revolution releasing a wide array of xenobiotics. Across the world, scientists are trying to overcome pollution through physical, chemical, and thermal processes. The major drawbacks of these methods include their labor-intensive nature, high cost, and undesirable changes in the treated soil's physical, chemical and biological characteristics. The only alternative solution to overcome this challenge is microorganisms. The microorganisms transform the various substances through their metabolic activity. It mainly depends on two processes. growth and cometabolism. Growth refers to the process which results in complete degradation (mineralization) of organic pollutants. Hence, the only source of carbon and energy in growth is an organic pollutant. On the other hand, cometabolism refers to the process in which the metabolism of an organic compound takes place in the presence of a growth substrate, which is used as the primary source of carbon and energy. For maintaining the global carbon cycle and renewing our environment, microorganisms have an essential role to play. The various microbial activities are comprehended in biodegradation, bioremediation, and biotransformation. Substances transformed by microorganisms include a wide range of synthetic compounds and other chemical substances like hydrocarbons and heavy metals, which have toxic ecological effects. However, in most cases, this statement is concerned with the potential degradabilities of microorganisms estimated under ideal growth conditions using selected laboratory cultures. 

Increased population and industrial revolution, alongside the wrong agricultural management systems, are putting massive pressure on the natural resources available for human beings. Several international organizations are raising flags and knocking the future risks and costs of exhausting the available natural resources. Soil is categorized as a slowly renewable resource to a limit that made soil experts classify soil as a nonrenewable natural resource. Therefore, soil pollution is among the most important issues discussed at the global level. However, soil remediation is very high costly, time-taking, and needs experts for handling. Bioremediation is considered one of the most promising methods of soil rehabilitation by simulating the behaviour of nature in curing it. With lower costs, noticeable results, and eco-friendly alternative solutions, bioremediation might be the most suitable strategy for polluted lands. 

Various types of toxic chemicals and waste materials generated from different industrial processes have created environmental pollution leading to a challenge for healthy human life globally. There is a need to develop strategies for environmental renewal and maintaining healthy life. Bioremediation has emerged as a promising and eco-friendly approach as microorganisms have vast potential to remove toxic pollutants from the environment. Microbial biofilms can be used successfully for removing environmental pollutants because of their ability to degrade, absorb and immobilize a large number of pollutants from various sources. During bioremediation, metabolic activities of biofilm-forming microorganisms are used for degrading toxic environmental pollutants. Though information on the use of microbial biofilms for bioremediation is limited, biofilms have proved to be highly effective in bioremediation. The present chapter focuses on the application and potential of microbial biofilms for the removal of environmental pollutants for sustainable development

Most of the waste generated from agriculture and other industries is a great source of soil and water pollution. The increase in agriculture waste across the globe is of great concern because of various environmental and economic issues. However, genetic engineering and microbial processing development have helped extract various valuable products from this waste. Microbes have the natural potential to degrade this organic waste. This chapter highlights the opportunities to bio-valorize agricultural waste through microbes and produces valuable enzymes, biofuels and bioactive compounds. This chapter highlights how microbes may decrease the ever-increasing waste to produce various valuable products for industrial use.