Ecosystems consist of biotic and abiotic components, including flora and fauna, along with the conducive environmental factors of a particular place. These are imperative for maintaining the ecosystem's structure and energy flow between trophic levels and providing ecosystem services for the well-being of humans and other living organisms. However, ecosystems are being threatened by human activities, which disrupt the balance of nature. Thus, it impacts billions of people by causing economic loss and threats to the survival of terrestrial, aquatic, and other species. Climate change and increasing pollution also adversely affect the functions of the ecosystem. Microbes and microbiomes are reported to restore terrestrial, aquatic, and coastal ecosystems. The diverse microbes such as bacteria, archaea, algae, fungi, and protozoa help detoxify the polluted ecosystems through various physical, chemical, and biological mechanisms. They also help with the nutrient cycling and mineralization of nutrients from the soil to plants in their available forms. With the focus on ecorestoration, there is a need to take collective action to protect the environment and prevent ecosystem degradation worldwide.

Ecosystem degradation poses a significant and growing environmental threat. Restoring degraded ecosystems is vital to restoring their ability to provide essential services and benefits. In 2021, the United Nations declared the Decade of Ecosystem Restoration to emphasize the importance of coordinated efforts in this area. Microbes, with their stress tolerance, genetic diversity, adaptation to various conditions, and capacity to break down substances, are crucial for ecosystem sustainability. Their critical functions are vital in restoring ecosystem function and biodiversity. This chapter describes the role of microbes in a microbiome and their interactions, instilling optimism about their potential. It also covers how various factors shape the soil microbiome spatially and temporally. Soil microorganisms such as bacteria, archaea, and fungi are found around, on, and in plant roots, and they play an essential role in responding to abiotic stressors. Factors like soil conditions, geographical and climatic factors, and stressors like drought, pollutants, and salinity can result in distinct microbial compositions and characteristics. This chapter provides an in-depth overview of how these factors can impact soil microbial communities and their role in ecological restoration. This chapter also covers beneficial microbiomebased strategies, including microbial engineering for ecosystem restoration. These strategies are essential and a source of hope for the future.

Heavy metals (HMs) pollution is a major environmental concern, posing serious threats to human health and ecological systems. Anthropogenic activities have increased the levels of HMs in the environment, and their pollution is a major issue. Exposure to high levels of these metals can have harmful effects on human health, and they can also damage soil structure, diminish microbial biodiversity, and inhibit plant growth and development. In addition, traditional remediation methods for HMs contaminated soil are often expensive and negatively impact the environment. In recent years, microbial-assisted bioremediation has emerged as a promising and eco-friendly alternative for HM remediation. This approach utilizes microorganisms to transform, immobilize, or detoxify HMs, making them less harmful and more accessible for removal. This chapter highlights the eco-friendly use of microorganisms, the mechanisms that contribute to the bioremediation of HMs, and their potential use in the future. 

In 2050, 8.3 billion people will live on Earth, and 70 to 100% more food will be needed. Food and its products are available through agricultural practices. Soil biological systems play an essential role in food production. However, it is a complex process that leads to the stability of crop production and the maintenance of soil health. Healthy food with eco-friendly agriculture practices is required to sustain the soil ecosystem globally. Additionally, the continued depletion of the Earth's natural resources and the increasing use of harmful chemical fertilizers are significant concerns for agriculture's future. Biofertilizers are gaining popularity as a viable alternative to unsafe chemical fertilizers in the pursuit of sustainable agriculture. Biofertilizers have an important role in enhancing crop output and preserving long-term soil fertility, both of which are critical for fulfilling global food demand. Microbes can interact with agricultural plants to improve their resistance, growth, and development. Nitrogen, phosphorus, potassium, zinc, and silica are the fundamental elements needed for crop growth, yet they are normally present in insoluble or complex forms. Certain microbes dissolve them and make them accessible to plants.

Agriculture is our sensible recreation and the foremost food source for all animals and human beings. It gives laurels to us, but knowingly or unknowingly, agricultural systems face stress, resource quality degradation, and depletion by human activities. Abiotic stresses, such as nutrient deficiency, water logging, extreme cold, frost, heat, and drought, affect agricultural productivity. Biotic factors like insects, weeds, herbivores, pathogens, bacteria, viruses, fungi, parasites, algae, and other microbes limit good-quality products. Climate change leads to more complications when interpreting how plants and microbes interact to protect themselves from stress. Plants need water, carbon, and nutrients to grow. The extreme conditions mentioned restrict the growth of plants. Although plants can sense and exhibit natural mechanisms during stress conditions, increased non-sustainable agricultural practices and other human activities lead to highly stressful conditions for plant growth and yield. While in stressful situations, fungi play an essential role in energy transfer and uptake of nutrients by releasing the adverse effects of stress on plant growth. Many strategies in bacteria and fungi need to be addressed here, including stress conditions such as cysts and spore formation, cell membrane deformation, production of damage repair enzymes, and chemical synthesis to relieve stress. The mechanism of salt tolerance, symbiotic microbes, xenobiotics, and hazardous tolerance genes induces plant growth in unfavorable conditions. In recent days, technological improvements such as gene modification by genetic engineering have shown the potential to enhance the positive effects on agricultural production and products.

Industrial development improves our life quality. Nevertheless, the industries, such as those producing paper and pharmaceutical products, generate large amounts of industrial wastewater. This wastewater contains various pollutants, which are organic and inorganic. Various physical, chemical, and biological methods have been employed to eliminate the pollutants. Both physical and chemical methods involve more capital and produce secondary contaminants. During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of pathogens and parasites. For the purification of water and the preservation of the ecosystem, microbes in wastewater treatment are crucial. However, little is known about how microbial diversity is controlled and for what reasons. The varied microbial community supports flocculation, heterotrophic respiration, nitrification under aerobic conditions, and denitrification under anaerobic conditions. Although recycled water is reinstated for recreational and agricultural use, biomonitoring is vital for assessing treatment effectiveness. Microorganism-based biological treatment is developing as an effective and environmentally friendly method. This chapter thoroughly introduces biological wastewater treatment, growth and kinetics, and different microbial community types that include bacteria and fungus, actinomycetes, algae, plants, and the range of microbial wastewater treatment, among other topics.

Solid waste disposal is a major issue that is getting worse every day as more people move into cities. Solid waste disposal in India and other developing nations frequently involves open dumping and incineration. This practice increases both health risks and already existing pollution issues. To solve this issue with the least amount of environmental impact possible, it is urgently necessary to employ sustainable techniques. There are many environmentally friendly ways to manage solid waste, including composting, vermicomposting, and anaerobic digestion, with additional benefits like generating byproducts. Among them, biological agents play a significant role in solid waste management. This chapter overviews solid waste management and a long-term solution using biological agents and microbes. The distinctive characteristics of microorganisms can be effectively used to revive the environment. Microorganisms can be used as “miracle cures” for biodegradation and remediation of contaminated sites. Today, microorganisms and nanotechnology are used in nano-bioremediation to clean up radioactive waste effectively. Additionally, using genetically modified organisms (GMOs) in severely polluted areas makes the microorganisms beneficial for human welfare and ecosystem restoration. Numerous environmental phenomena, both natural and man-made, depend on microorganisms for maintenance. They perform beneficial roles that improve and optimize human life. Waste management is one of these areas where microorganisms are being used. The proper disposal of the vast amounts of waste that people produce throughout the course of a day presents a significant challenge, one that the government and environmental organizations are constantly looking for new solutions to. Utilizing microorganisms is a crucial component of effectively combating this threat. It discusses the numerous functions of microorganisms in the environment, such as the management of solid waste, and it concludes by highlighting some recent developments in microbiological solid waste management.

Ecosystem degradation through human actions is a global phenomenon. The international society has established goals to stop and reverse these trends, and the restoration industry faces the vital but difficult challenge of putting these goals into practice. Microbial communities are integral to all ecosystems because they perform critical roles like nutrient cycling and other geochemical processes. They are the indicators of the success of ecological restoration, including plantation forests, postmining areas, oil and gas activities, invasive species management, and soil stabilization. Since the last 2 decades, advancements in microbial genomics have allowed researchers to focus on microbial ecology and dynamics of environmentally balanced vis-a-vis damaged ecosystems. Advancements have significantly improved our capacity to define diversity in microbial ecology and its putative functions in metaomics methods brought about by developments in high-throughput sequencing (HTS) and bioinformatics. These tools may boost the likelihood that damaged ecosystems will be restored. The current article focuses on using meta-omics techniques to monitor and assess the outcomes of ecological restoration projects and to monitor and evaluate interactions between the various organisms that make up these networks, such as metabolic network mapping. We provide an overview of functional gene editing with the CRISPR/Cas technology to improve microbial bioremediation. The existing understanding will be strengthened by creating more efficient bioinformatics and analysis processes.

The geographical area where all the abiotic and biotic factors interact with each other to make the bubble of life is known as the ecosystem. While many natural and artificial calamities occur to destroy the ecosystem, microbial diversity plays a vital role in maintaining and functioning it. The microbes constitute one-third of the earth's biomass and are composed of enormous genetic diversity from extremely hot (thermophilic) and moderate (mesophilic) to extreme cold (psychrophilic) climatic conditions. Therefore, the principal objective of microbiome research is to elucidate the relationship between microbial diversity and its function in maintaining or restoring the ecosystem. Recent advances in microbial ecology and metagenomic approaches have enabled detailed assessment of the highly complex communities, allowing the establishment of the link between diversity and the function performed by microbes. In this chapter, we will explore some advanced bioinformatic tools for metagenomic studies that can provide quantitative insights into the functional ecology of microbial communities. The detailed study will help us understand the complex microbial diversity in tropical and temperate ecosystems and their functional aspects in ecosystem restoration.

The onset of the anthropogenic destruction of ecosystems is one of the ongoing problems that can threaten the existence of organisms, including humans. The emerging problem can be effectively addressed through restoration ecology, a naturebased solution that promises to be cost-effective. Microorganisms, including bacteria, fungi, and viruses, are omnipresent and provide numerous benefits to the ecosystem, such as sustainable plant productivity, enriched soil nutrients, increased soil carbon pool, decomposition, and a stable environment for human life. Soil microorganisms also play a fundamental role in ecosystem functioning and conserving plant diversity. Exploring voluminous beneficial microorganisms and promoting the reestablishment of these beneficial microbes in the soil will preserve Earth's diverse native plant populations, which, in turn, will help in improving soil and be a vital player in enhancing ecosystem primary productivity, food chain, and locking away atmospheric carbon into its plant body and soil. Microbial restoration can be achieved by basic and traditional methods, i.e., (i) by treating the soil with organic matter-rich manure harvested from bio piles, (ii) composting, (iii) graze manuring, (iv) natural manuring, and (v) plant-assisted microbial restoration technique. Regenerative/carbon farming can also be practiced in parallel to enhance the restoration rate and protect beneficial microbial life in the soil. However, the increasing use of microbial inoculants is also raising several queries about their effectiveness and their impacts on autochthonous soil microorganisms, which should be cautiously considered before introducing bioinoculants for restoration. Even if bioinoculants restore the microbial community, they have the following shortcomings: (i) prolonged persistence of microbial colonies and detection in soil; (ii) the monitoring of the impact of the introduced bioinoculants on native soil microbial communities, which needs to be monitored examined periodically. This chapter delves into fundamental and conventional techniques and approaches that can be employed to maintain soil microbial populations. Furthermore, the chapter investigates the possibility of creating protocols for regulatory or commercial objectives, emphasizing the significance of ecological restoration by using bioinoculants or microbial colonies in degraded sites.

A damaged ecosystem must be rebuilt to its original form, or a new ecosystem must be created in a degraded area. Ecosystem restoration is a complex procedure. Researchers can now investigate the structure and function of ecosystems at the molecular level thanks to the development of molecular techniques as a potent tool for ecosystem restoration. This chapter examines the application of molecular methods to ecosystem regeneration. The various available molecular methods and how they have been applied to monitor ecosystem health, identify microbial communities in ecosystems, and comprehend interactions between microbes and plants are discussed. The chapter also examines the application of molecular methods to the restoration of ecosystems that have been damaged, including the use of plant-microbe interactions to promote plant development in contaminated soils. The chapter emphasizes the significance of molecular methods in ecosystem restoration and their potential to offer a more precise and thorough comprehension of ecosystem processes. The conclusion highlights the importance of ongoing investigation into the use of molecular methods for ecosystem restoration, especially in creating novel methods and their incorporation with existing restoration techniques. In the end, applying molecular methods can help develop practices for ecological restoration that are more efficient and long-lasting.