The Role of Microbes and Microbiomes in Ecosystem Restoration E-Book
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- Herausgeber: Bentham Science Publishers
- Kategorie: Wissenschaft und neue Technologien
- Serie: Microbes and Microbiomes for Clean and Green Environment
- Sprache: Englisch
The Role of Microbes and Microbiomes in Ecosystem Restoration provides an in-depth exploration of how microbes and microbiomes can drive sustainable environmental recovery. It covers key topics from microbial roles in pollution remediation, biofertilizer production, and waste management to advanced microbial techniques for ecosystem resilience. Key chapters discuss microbial-assisted bioremediation, agriculture support through biofertilizers, waste treatment systems, and the restoration of polluted soils. With a special focus on the latest advances, including microbial genomics and metagenomics, the book highlights practical applications for mitigating climate impacts and promoting a greener future.
Key Features:
- Explains microbial and microbiome roles in restoring ecosystems.
- Covers practical applications for agriculture, waste management, and pollution control.
- Introduces advanced microbial techniques in environmental management.
- Provides insights into sustainable practices for reducing greenhouse gases and improving soil health.
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Seitenzahl: 523
Veröffentlichungsjahr: 2024
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PREFACE
The book “Role of Microbes and Microbiomes in Ecosystem Restoration” focuses on basic to advanced techniques in various roles of microbes and microbiomes in the abatement and restoration of polluted ecosystems, climate change, production of renewable energy sources, and waste management. It covers ecosystem sustainability, the UN decade of ecosystem restoration, efficient utilization of microbes and microbiomes and their role in socio-economic development, and the current status of polluted and degraded ecosystems.
Stepping into an unusual era of concurrent buffer leads to a shifting global climate. At the beginning of the twenty-first century, one of the active concerns in the human ecological background is the destruction of ecology and ecosystems. Human actions have evolved a remarkable power to affect the ecosystem. To address this developing issue, the science of restoration ecology and its applied practices provide a potentially cost-effective, buoyant answer. The notion of restoration has emerged as the dominant subject in the global environmental context. One of the most important goals of the UN Convention on Biological Diversity from 2011 to 2020 is to restore at least 15% of the world's damaged ecosystems. World leaders adopted the “Bonn Challenge” in 2011, which is a global commitment to rehabilitate 150 million hectares of deforested and damaged land by 2020. Most significantly, in 2015, the UN formalized these worldwide pledges by endorsing the 2030 Sustainable Development Goals, one of which focuses on ecological restoration. Microbes are ubiquitous, providing many critical services to the ecosystem, such as sustainable plant productivity and a stable environment for human life. They help to keep atmospheric CO2 and nitrogen levels stable, which are now reduced due to greenhouse gases and other hazardous pollutants. On a global scale, microbial organisms are extremely strong. Bacteria create approximately 50% of total oxygen, 75% of added nitrogen to the atmosphere, and 92% of nitrogen removal from the environment. As a result, this book covers the potential of bacteria and microbiomes in many ecosystems.
In Chapter 1, Prasad et al. provide an overview of the causes of ecosystem destruction, the need for ecosystem restoration, the significance of microbiome in biomining, restoration of farm and degraded land, control of heavy metals, production of renewable energy, crop growth, biofertilizer production, mitigation of greenhouse gases, and waste management. It also encompasses the role of molecular techniques in ecosystem restoration and the challenges involved in adopting microbiomes for ecosystem restoration.
Microbes are the crucial living elements of soils that contribute to the sustainability of ecosystems because of their capacity for stress tolerance, vast effective genetic pool, ability to survive in various conditions, and capacity for catabolism. However, various factors like soil conditions, geographical and climatic factors, and soil stressors (drought, submersion, pollutants, and salinity) may result in distinct microbial composition and characteristics, as well as its mechanism to support ecosystem restoration and defense against all of these stressors. Hence, Pooja et al., in Chapter 2, deliver the vital edaphic (pH, temperature, oxygen, nutrients, and moisture), geographical, climatic (UV radiation, elevated CO2, temperature, permafrost thaw), and abiotic factors (drought, submergence, salinity, pollutants) involved in the establishment of microbes and microbiome.
In Chapter 3, Sinduja et al. discuss the ecological role of microorganisms participating in biogeochemical cycles, hoping to delineate the role of microbes and microbiomes in biogeochemical cycles. Microorganisms play an essential role in moderating the Earth's biogeochemical cycles; nevertheless, despite our fast-increasing ability to investigate highly complex microbial communities and ecosystem processes, they remain unknown. Hence, this chapter covers the strategies for proper management of prevailing natural resources, considerations for management, its role in the biogeochemical cycle, and the influence of beneficial soil microbes, such as plant growth promoting rhizobacteria and cyanobacteria, on natural resource management, with special emphasis on the role of soil enzymes in nutrient cycling.
Bioleaching (microbial leaching) is being studied intensively for metal extraction since it is a cost-effective and environmentally benign technique. Bioleaching with acidophiles involves the production of ferric (Fe III) and sulfuric acid. Cyanogenic microorganisms, in particular, can extract metal(s) by creating hydrogen cyanide. Besides, bioremediation is one of the most effective approaches for reducing environmental contaminants since it restores the damaged site to its original state. Hence, Chapter 4 by Poornima et al. provides a baseline on bioleaching, its types, microbes involved in bioleaching, bioleaching pathways, and the role of microbes in the bioremediation of polluted habitats.
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. Hence, Naik et al., in Chapter 5, highlight the eco-friendly use of microorganisms, their mechanisms that contribute to the bioremediation of HMs, and their potential use in the future.
In Chapter 6, Sajish et al. present the basic principle of an MFC and the role of microbes in a microbial fuel cell, genetic engineering, biofilm engineering approaches, and electrode engineering approaches for increasing the overall efficiency of an MFC for its practical implementation. Microbial fuel cell, a type of BES, is a budding technology that exploits the potential of electroactive microorganisms for extracellular electron transfer to generate electricity. Hence, this chapter encompasses the history of MFC, bio-electrochemically active microorganisms, electroactive microbial genera in microbial fuel cells, factors affecting the development of anode biofilm, biofilm engineering, and the recent advances in strain improvement for improved MFC performance.
Energy crises resulting from the depletion of petroleum resources, hikes in the price of fossil fuel, and unpredictable climate change are some of the recent concerns that have provoked serious research on alternative energy sources that will be sustainable. In this regard, biofuels are a straightforward substitute for fossil fuels. Renewable feedstocks are suitable ingredients that sustainably produce biofuels using microbial-based bioconversion processes. Industrially important enzymes are capable of degrading long-chained biopolymers into short-chained monomeric sugars and fermenting them into energy-dense biomolecules. Hence, Chapter 7, authored by Oyelade et al., comprehensively reviews how sustainable bioenergy production through microbes using feedstocks can provide clean and green energy that can consequently facilitate ecosystem restoration. Feedstocks are pivotal to this biotechnological process.
In recent decades, biofertilizers have gained popularity as a viable alternative to unsafe chemical fertilizers in pursuing sustainable agriculture. They have an essential role in enhancing crop output and preserving long-term soil fertility, both of which are critical for fulfilling global food demand. Therefore, Chavada et al., in Chapter 8, deliver the various microbes involved in nitrogen fixing, phosphorus and potassium solubilizing and mobilizing, sulfur oxidizing, and zinc solubilizing. The role of arbuscular fungi and plant growth-promoting rhizobacteria in biofertilizer production is also discussed.
Knowingly or unknowingly, agricultural systems face stress and resource quality degradation and their depletion by the activities of humans. Abiotic stresses, such as nutrient deficiency, water logging, extreme cold, frost, heat, and drought, affect agricultural productivity. Similarly, biotic factors like insects, weeds, herbivores, pathogens, bacteria, viruses, fungi, parasites, algae, and other microbes also limit good-quality products. Thus, Vijayalakshmi et al. discuss the application of microbes and microbiomes in biotic and abiotic stress management in Chapter 9. This chapter especially discusses the adaptive mechanisms of salt tolerance in plants, tolerance to abiotic stress, the emerging microbiome in soil biota, and nanomaterials' efficacy on stress.
Microbes play a significant role as either generators or consumers of greenhouse gases such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) through various processes. Sethupathi et al., in Chapter 10, discuss the role of microbes and microbiomes in the emission of major greenhouse gases like CO2, CH4, N2O, and NH3. The potential of the microbiome in mitigating these greenhouse gases is also delivered in this chapter.
Given that there is potential for warmth to boost the release of carbon dioxide from dirt to the atmosphere due to better microbial disintegration of dirt raw material, the impact of environmental change on the soil carbon sink remains uncertain. If forecasted climate modification situations are precise, this boost in soil carbon loss might significantly worsen the dirt carbon cycle responses. Therefore, Chapter 11 by Al-Jawhari introduces us to the soil CO2 balance, environmental effects, and the significance of the soil carbon cycle and microbial decomposers, carbon cycle in soil, ocean, and ecosystem restoration under climate change perspective.
The generation of wastewater increases multi-fold because of industries and the overexploitation of freshwater resources. Wastewater treatment is always linked with waste recovery and its optimum utilization, which broadens the amplitude of wastewater treatment, enhancing the quality of the byproducts and as an efficient alternative for non-potable purposes. Microbiomes are crucial in biological wastewater treatment methods such as activated sludge, anaerobic digestion, and bioelectrochemical systems. The microbial population's activity and resilience in the microbiome significantly impact the performance and stability of these activities. Suganthi et al. present the biological wastewater treatment, growth and kinetics, and different microbial community types, including bacteria and fungus, actinomycetes, algae, plants, and the range of microbial wastewater treatment in Chapter 12.
Solid waste disposal is a significant issue that worsens daily as more people move into cities. In Chapter 13, Velusamy et al. provide the status of solid waste management in India, sources and types of solid wastes, various conventional solid waste management techniques, and the role of microbes in solid waste management through composting and anaerobic digestion.
Microorganisms are pervasive and genuinely make up the “unseen majority” in the marine environment. Although marine isolates have been the subject of laboratory-based culture methods for more than ten years, we still do not completely understand the ecology of marine microorganisms. Thus, in Chapter 14, Poornachandhra et al. explore marine microbial diversity, its utilization in bioremediation, and understanding their role in ecosystem sustainability.
Mangroves and wetlands are critical intermediary ecosystems between terrestrial and marine environments. These ecosystems offer a wide range of invaluable ecological and economic services. However, under the influence of natural and anthropogenic threats, mangroves and wetlands face rapid degradation. Hence, Chapter 15 by Haghani et al. is dedicated to enlightening us regarding the most critical features of microbial groups, including archaea, bacteria, algae, and fungi in mangroves and wetlands. Moreover, the biochemical transformations brought about by wetlands' microbial groups and the degree of complexity in microbial interactions are explained.
Jerome et al., in Chapter 16, articulate the significance of forest microbiomes in ecosystem restoration and sustainability. Generally, forest microorganisms are essential to how plants interact with the soil environment and are necessary to access critically limiting soil resources. This chapter focuses on the ecosystems below and above ground level of a forest microbiome, including the soil microorganisms, their importance, and the diverse interrelationships among soil microorganisms (parasitism, mutualism, commensalism).
Employing field-based monitoring and restoration assessment techniques, surveying microbes or microbial populations is challenging or impossible. In contrast, it is now possible to precisely and quickly describe and quantify these diverse and functional taxonomic groups by sequencing large quantities of environmental DNA or RNA utilizing genomic and, in particular, meta-omic technologies. Hence, Nagendran et al., in Chapter 17, throw light 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. An overview of functional gene editing with CRISPR/Cas technology to improve microbial bioremediation is also provided herewith.
Chapter 18 by Satpathy et al. provides details on metagenomic approaches like Multi-Locus Sequence Typing (MLST), MOTHUR, Quantitative Insight into Microbial Ecology (QIIME), and PHAge Communities From Contig Spectrum (PHACCS) in the restoration of the temperate and tropical ecosystem.
Soil microorganisms also play a fundamental role in ecosystem functioning and conserving plant diversity. Exploring voluminous beneficial microorganisms and promoting the reestablishing of those beneficial microbes in the soil will preserve Earth's diverse native plant populations. Hence, Prasad et al., in Chapter 19, delve 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.
In Chapter 20, Shivakumar et al. examine 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 discusses 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 sustainable industrial revolution is the way forward to help humankind to prolong its existence on Earth. John et al. enlighten us with the role of the microbiome in a sustainable industrial production system. In Chapter 21, they disclose the energy sector's current status, microbes' role in organic and amino acid production, and the role of microalgae in sustainable agriculture.
The human microbiome plays a vital role in human development, immunity, and nutrition, where beneficial bacteria establish themselves as colonizers rather than destructive invaders. In Chapter 22, Pradyutha et al. introduce microbes' role in human and animal health security. The various human and animal diseases and the potential of microbiota, such as probiotics, in disease treatment are also discussed in this chapter.
List of Contributors
Part 1: Introduction to Microbes and Microbiomes in the Ecosystem Restoration and Green Environment
Overview of Microbes and Microbiomes in the Restoration of Terrestrial, Aquatic, and Coastal Ecosystems
Shiv Prasad1,*,Sangilidurai Karthika2,Murugaiyan Sinduja3,Ramesh Poornima2,Govindaraj Kamalam Dinesh1,4,5,Velusamy Sathya6Abstract
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.
INTRODUCTION
The ecosystem is the complex of living organisms and non-living things interacting with each other in their physical environment called habitat, and all the interrelationships between organisms occur in a particular space unit. It is divided into (i) terrestrial, e.g., desert, forest, grassland, taiga, and tundra, and (ii) non-terrestrial, e.g., aquatic, marine, and wetlands. Ecosystems play a vital role in balancing the natural phenomenon, structural organization, energy flow, and nutrient cycling and provide various ecosystem services and benefits to human society. However, human activities negatively influence the well-being of 3.2 billion people. These activities cost more than 10% of the annual global gross product by losing biodiversity and vital ecosystem services. Human activities are reported to reduce productivity in 23% of global terrestrial areas [1]. Vegetation cover is decreasing, influencing grasslands, croplands, woodlands, and rangelands, particularly in vulnerable regions. Desertification has severe consequences for 38% of the global population. Wetlands have declined 70% over the previous century [2]. The global forest area has decreased by 100 million hectares since 2000 [3]. Reversing this fact can have substantial advantages. It can help improve the food and water supply, reduce GHG emissions, and mitigate adverse effects related to climate change.
The restoration of ecosystems is vital across global international conventions and agreements to achieve their goals and priorities regarding biodiversity, climate change, desertification, and a sustainable future. Global action is required to restore ecosystems and enhance positive global impact. Investment in ecosystem restoration projects can deliver many advantages to society, including biodiversity conservation [4]. At an international level, restoring the ecosystem degradation is essential to maintain temperatures below 2ºC [5, 6]. IUCN calls for collective action to set the world on a transformational trajectory in the UN Decade on Ecosystem Restoration, enabling the implementation of the Post-2020 Framework [7]. The UN also calls for accelerated and scaled-up ecosystem restoration by 50% to reverse loss in the area by 2030. They focused on spatial integrated planning in all ecosystems to cover 50% of the land, freshwater, and ocean regions by 2030 to reduce pressure on ecosystems and maximize biodiversity and ecosystem services.
Microbes and microbiomes are vital in ecosystem restoration [6, 8]. They contribute to nutrient cycling, decomposition of organic materials, soil fertility maintenance, and crop productivity enhancement [6]. Bacteria, archaea, and fungi exhibit distinct assemblies along vertical and horizontal profiles in reforested ecosystems. The diversity of bacteria and fungi decreases with increasing soil depth while archaeal diversity increases. As reforestation progresses, bacterial communities' vertical and spatial variation declines while archaeal and fungal communities proliferate. The distribution patterns of soil microbes are linked to the soil's physical and biochemical properties and the existence of plant roots. Bacterial and archaeal communities play influential roles in deep and superficial soil layers in multi-nutrient cycling. Soil fungi comprise various dynamic kingdoms of eukaryotes and are vital for maintaining ecosystem processes and functions [6].
Understanding microbial community assembly processes and biogeochemical cycling during ecosystem restoration is critical for optimizing management strategies [9]. Factors such as variation in community assembly processes, measurable microbial community attributes, and linkages to ecosystem function must be considered. By examining microbial succession, insights can be gained into microbial community structures in various ecosystem recoveries. They can help determine the success of ecosystem restoration efforts and maintain ecosystem stability [10]. Native mycorrhizal fungal communities play a significant role in restoring native plants [11]. Understanding microbial community assembly processes, managing microbial contamination risks, and identifying effective bio-indicators of soil health are crucial for optimizing ecosystem restoration efforts and promoting ecosystem stability and resilience. This chapter discusses an overview of microbes and microbiomes' role in ecosystem restoration.
CAUSES OF ECOSYSTEM DESTRUCTION AND THEIR IMPACTS
Ecosystem degradation is defined as a long-term reduction in the structure and functionality of the ecosystem or loss in delivering services and proficiency to benefit people. The significant causes of ecosystem destruction and their impacts are overviewed in the following sub-headings. The essential causes of ecosystem destruction are shown in Fig. (1), which is happening at an alarming rate due to various anthropogenic activities such as changes in land use practices, unrestricted natural resources utilization, deforestation, habitat loss, climate change, warming ocean waters, ocean acidity, and pollution.
Resource Exploitation
Resource exploitation, particularly mining and extraction activities, can positively and negatively impact ecosystems, socio-economics, and the environment. Saputra and co-workers [12] investigated the effect of sand mining in Indonesia and reported its promising impact on the socio-economics and environment. They also stated that the river deepens after sand mining, enabling it to hold considerable water and control overflow during the rainy season. Similarly, exploiting mineral resources like coal can impact local communities and ecosystems. Aigbedion and Iyayi [13] highlighted the negative impacts of mineral exploitation and its processing, which disturbed environmental settings and ecosystems, devasted natural flora and fauna, polluted air, soil, and water, and caused many other hazards. These impacts can worsen poverty and income inequality in resource-rich regions.
Fig. (1)) Causes of ecosystem degradation.Industrial enterprises associated with resource exploitation, particularly in Arctic regions, can also contribute to environmental pollution and safety concerns [14], including global warming and irreversible ecosystem damage. Expanding mining areas to exploit mineral and other natural resources causes ecological damage. In mining areas, authorities must focus on reducing environmental impact, health and risk assessment, and ecosystem services valuation for effective ecosystem restoration planning [15] to minimize implications in biodiversity conservation and the balance of native ecosystems [16]. Adopting these approaches, we can enhance the food resources base and promote ecosystem restoration by exploiting the potential of novel microbes and conserving threatened species [17].
In the Arctic tundra, the exploitation and depletion of scarce resources, including pasture grasses, can contribute to the irreversible degradation of grasslands. Animal husbandry, which heavily relies on pasture grasses, is a principal economic activity for indigenous peoples in the Arctic. However, the unique Arctic ecosystem requires special attention to prevent over-exploitation and degradation of these valuable resources [18]. The impact of resource exploitation on ecosystems is not limited to environmental factors but also extends to social and cultural aspects [19]. The effect of resource exploitation on ecosystems can also be influenced by factors such as tree diversity and the positive relationship between tree and fungal diversity in subtropical Chinese forests. Greater fungal diversity promotes better resource exploitation and confers higher resilience due to functional redundancy, which helps ecosystem service [20].
Climate Change
Climate change dramatically impacts ecosystem functions and their services [21]. Its impact assessment on ecosystem services has many challenges due to long time scales and high uncertainties [22]. However, climate change affects both abiotic and biotic elements of ecosystems, leading to changes in ecosystem functions and processes. Climate change can impact tropical and subtropical forests due to temperature increases, ecosystem structure, and function alterations. Its impacts on the hydrological cycle and the availability of water resources can reduce ecosystem services and freshwater supply [23]. Coastal habitat is highly vulnerable to climate change and is expected to be negatively impacted.
Climate change can alter biodiversity and species distribution, functions, and productivity [24] and negatively impact human well-being. Climate change affects water sources, leading to water quality and availability alterations, affecting human and ecosystem health. Temperature elevation and changes in precipitation resulted in extreme weather conditions, which directly and indirectly affect biodiversity and ecosystems. Studies show that the economic value created by ecosystem service functions of rivers has declined due to climate change and human activities [25, 26]. Climate change can disrupt biodiversity, change ecosystem structure and functions, alter water sources, and impact human well-being. Understanding climate change's effects on ecosystems and their services is crucial for effective conservation and adaptation strategies.
Increasing Environmental Pollution
Environmental pollution is a leading cause of many disturbances and destruction in the ecosystem and adversely affects its components. Significant air, water, and soil pollution sources are biomass burning, fossil fuel combustion, trash, toxic gaseous emissions, oil spills, agricultural chemicals, and pesticides. Pollution significantly impacts ecosystems, affecting the organisms and the environment's health. Various types of pollution, such as organic, chemical, heavy metal, and plastic, can harm ecosystem health. These pollutants can enter ecosystems through different pathways, including wastewater discharge, industrial activities, agricultural practices, and urbanization. The consequences of pollution on ecosystems can be wide-ranging, including changes in biodiversity, disruption of ecological processes, and degradation of water and soil quality [27, 28].
Polycyclic aromatic hydrocarbons (PAHs) are another pollutant type that can significantly impact marine ecosystems. PAHs are widespread in marine environments and can enter the ecosystem through chronic or acute pollution by oil spills [29]. Pollution derived from both point and non-point sources can transform aquatic ecosystems and impact the structure of local communities, including zooplankton communities. The interactions between multiple environmental factors and ecological processes determine different local communities' structures in contaminated river ecosystems. Understanding these interactions is crucial for assessing the impact of pollution on zooplankton communities and developing effective management strategies for polluted river ecosystems [30].
Microplastic pollution is a growing global problem that threatens marine ecosystems. Plastic production has increased significantly recently, accumulating plastic litter in marine environments. Plastic pollution and other artificial impacts, such as global heating, ocean acidification, eutrophication, and chemical pollution, can push marine ecosystems to the brink and harm ecosystem functioning and services. The persistence of plastic in the environment and its ability to accumulate in ecosystems make it a particularly concerning pollutant. Efforts to reduce and remove plastic litter from marine ecosystems are crucial for mitigating the impacts of plastic pollution on marine ecosystems [31].
Various strategies and technologies have been proposed to mitigate pollution's impacts on ecosystems. Bioremediation, which utilizes the capacity of microorganisms to degrade pollutants, is a promising approach for the recovery of contaminated environments. Microorganisms play a crucial role in the degradation of organic pollutants and can be harnessed to remove pharmaceutical compounds and other organic contaminants from impacted environments [29]. Rhodococcus spp., a microorganism, has shown potential for degrading pharmaceutical pollutants and producing valuable products. The use of Rhodococcus spp. and other microorganisms in biodegradation processes and biotechnology can contribute to the remediation of polluted environments and the production of targeted pharmaceutical products [14]. Coral reefs, for example, are highly vulnerable to climate change impacts and marine pollution. Evaluating the resilience of coral reefs and implementing management strategies to protect them is crucial for their conservation and the sustainable use of natural resources. Indicator frameworks incorporating various dimensions, such as coral diversity, biodiversity, and environmental factors, can provide suitable methods for decision-makers to make better management strategies to protect coral reefs and use natural resources strategies effectively [32].
Deforestation
Deforestation significantly impacts ecosystems, affecting various aspects such as biodiversity, carbon cycle, hydrological regimes, indigenous populations, and human health [33]. It can change atmospheric circulation patterns and rainfall distribution, affecting climate locally and in other regions [34]. Reducing forest cover can decrease evapotranspiration and moisture availability, reducing rainfall and longer dry seasons. Studies have shown that deforestation in the Amazon basin can reduce dry-season rainfall by up to 20% in regions far from the deforested area [35]. These climatological effects can have long-term consequences, potentially leading to large-scale forest loss and ecosystem degradation.
Loss of species due to deforestation can reduce functional redundancy, making ecosystems more vulnerable to further species loss. Functional redundancy refers to multiple species that perform similar ecological functions, providing a buffer against the loss of individual species [36]. The impacts of deforestation extend beyond terrestrial ecosystems to aquatic ecosystems as well. Deforestation in the catchment area can disrupt the structure and processes of riparian ecosystems, leading to changes in aquatic assemblages. These changes can occur through direct and indirect pathways, affecting the abundance and structural composition of benthic macro-invertebrate assemblages [37].
Studies have shown that deforestation increases the risk of vector-borne diseases, such as malaria, by enriching human exposure to mosquito vectors [38]. In addition to the direct impacts on ecosystems and human health, deforestation also affects the provision of ecosystem services. Ecosystem services are the benefits humans have by providing clean water, climate regulation, and nutrient cycling. Deforestation can disrupt the provision of these services, potentially leading to negative consequences for human well-being. For example, deforestation in Indonesia, one of the world's mega-biodiversity countries, has been severe and threatens the future provision of ecosystem services [39].
Habitat Loss and Destruction
Habitat loss and destruction significantly impact ecosystems, biodiversity, ecosystem services, species abundance reductions, species extinction, and disruptions to species interactions. When habitats are destroyed or fragmented, it can lead to a regime shift in the ecosystem, where reinforcing feedback mechanisms intensify and result in a new community configuration with ecological, social, and economic consequences. Habitat destruction can also lead to the erosion of environmental resilience, making ecosystems more vulnerable to disturbances [20]. One of the critical impacts of habitat loss and destruction is biodiversity loss. Biodiversity refers to an area's variety of species, genes, and ecosystems. Habitat destruction can result in the loss of species, as well as the loss of interactions between species. This biodiversity loss can have cascading effects on ecosystem functions and vital services. For example, losing keystone species, various ecosystem engineers species, and habitat-forming species can significantly damage functional redundancy, ecosystem resilience, and habitat complexity. Additionally, habitat loss can lead to the loss of carbon stored in vegetation biomass, contributing to climate change [20].
Urban green spaces (UGS) are crucial in promoting resilience and health in urban areas. UGS provides numerous benefits, including improved mental and physical health, increased social cohesion, and enhanced resilience to climate change and other stressors. Studies have shown that UGS positively impacts the promotion of resilience and health in urban citizens. However, the extent of the relationship between UGS and health and resilience is still being explored [40]. Habitat loss and destruction can also have specific impacts on marine ecosystems. For example, in temperate rocky reefs, habitat destruction can lead to the transition from kelp habitats to sea urchin barrens. This phase shift is commonly linked to destructive overgrazing behavior by sea urchins and developing urchin consumer fronts along the edges of kelp beds. This shift in ecosystem structure can have significant ecological consequences and reduce the resistance of the ecosystem to invasion, overgrazing, and the downfall of turf dominance [41].
The impacts of habitat loss and destruction are not limited to individual species or specific ecosystems. They can also have broader effects on ecological processes and dynamics. For example, habitat destruction can alter the coevolutionary trajectories of species and their response to habitat loss. Coevolution, the reciprocal evolutionary change between interacting species, can mitigate the adverse effects of habitat devastation in mutualistic networks. However, the impact of coevolution on antagonistic communities' persistence tends to be minor and less predictable. Additionally, habitat loss can simplify and destabilize soil microbial networks, affecting ecosystem functioning [42].
Humans’ Activities
anthropogenic activities have a significant impact on ecosystems, including both marine and terrestrial environments [43]. In terrestrial ecosystems, For instance, human activities such as land use change and forage harvest in grassland ecosystems can lead to changes in net primary productivity (NPP) and grassland degradation [44]. Human activities can also, directly and indirectly, impact specific ecosystems, such as mangrove forests [45]. Activities adjacent to mangrove forests, such as land use changes and pollution, threaten the ecosystem. The cumulative impact of these activities on mangrove forests can be quantified using models that overlay human activities onto maps of mangrove coverage [46].
The impacts of human activities on ecosystems are not limited to specific regions or ecosystems. They have global implications and can contribute to the emergence of zoonotic diseases. Human activities, such as deforestation, urbanization, and wildlife trade, disrupt the wildlife balance and can fuel zoonotic disease's emergence [47]. The COVID-19 pandemic exemplifies relationships between human activities and zoonotic epidemics. Understanding and mitigating the impacts of anthropogenic activities on ecosystems is crucial for preventing future outbreaks of zoonotic diseases. Understanding the cumulative effects of anthropogenic activities on ecosystems is essential for conservation and management strategies. Sustainable practices and conservation efforts are needed to mitigate the adverse effects of human activities and ensure ecosystems' long-term health and resilience.
Disease Outbreaks
Disease outbreaks can significantly impact ecosystems, affecting various ecological factors such as population size, population structure, species interactions, and ecosystem functioning [48]. It can also have long-lasting effects on ecosystems, e.g., a decline of the coral cover due to bleaching events. These outbreaks are linked to significant ecological and structural changes in coral reef ecosystems [49]. Additionally, disease outbreaks can affect the dynamics of species interactions, altering predator-prey relationships and the composition and functioning of ecosystems [50]. Biodiversity plays a crucial role in shaping disease outbreaks. A meta-analysis of 61 parasites found broad evidence that host diversity inhibits parasite abundance, indicating that the dilution effect is robust across different ecological contexts; observational studies overwhelmingly documented dilution effects, including for zoonotic parasites of humans. Therefore, maintaining or restoring healthy ecosystems with high biodiversity can help prevent zoonotic diseases and mitigate their impact [51].
Climate change can also influence disease outbreaks and their impacts on ecosystems. Temperature and other climatic factors can alter pathogen evolution, host-pathogen interactions, and the range of pathogens, increasing plant disease's spread in new areas [52]. For example, warming temperatures have increased the prevalence of wasting disease in eelgrass meadows, which are essential coastal habitats. Changes in lake surface water temperatures can also impact the probability of cyanobacteria outbreaks, significantly affecting lake ecosystems [53]. Therefore, climate change mitigation and adaptation strategies are crucial for reducing the risks and impacts of disease outbreaks on ecosystems. It is important to note that disease outbreaks can also indirectly impact ecosystems through their effects on human activities. For example, the COVID-19 pandemic has led to social distancing measures and reduced economic activities, resulting in land use changes and reduced pollution levels. These changes may have positive and negative impacts on ecosystems. Reduced human activity can improve air and water quality, benefiting the urban ecosystem. On the other hand, changes in land use and human behaviour can also have negative consequences, such as increased deforestation or the disposal of sanitary consumables in natural environments.
Land-use Changes
Land use changes to satisfy the human population are increasing alarmingly—the development of more landscapes, clear land for housing, roads, and infrastructure projects enhancing ecosystem degradation. The conversion of natural habitats and land-use changes for agriculture, urbanization, and infrastructure development predominantly contribute to the destruction of ecosystems, shifts in species interactions resulting in habitat loss, and a decline in biodiversity, ecosystem services, and human well-being [44, 86]. Land-use changes have economic implications, as they can affect the availability of resources, such as water and timber, and impact local economies.
In order to address problems related to land-use changes, we need to promote sustainable development by coordinating resources, functional regions, and ecological development, including management of regional landfills and municipal waste management with concerned authorities [44, 86]. Some developing nations have successfully managed their land use change by executing farming intensification, land use zoning, forest site protection, and augmented reliance on imported products. Sound policies and innovations are crucial in achieving sustainable land use practices and mitigating ecosystem degradation [54].
ECOSYSTEM RESTORATION
Ecosystem restoration is crucial to managing biodiversity and ensuring ecosystem services are provided to humanity [57]. Restoration actions can be evaluated based on diverse metrics and indicators. In marine coastal ecosystems, short-term survival rates are typically used to assess restoration success. Diversity measurements, vegetation arrangement, and ecological processes are often used in terrestrial ecosystems. Pilot-scale restoration investigations can deliver valuable initial data to improve the efficacy and accomplishment of large-scale restoration projects. These investigations can assist in assessing habitat suitability and optimize site selection for restoration [55]. The cost of ecological restoration can differ depending on factors such as the ecosystem type, degradation level, and the restoration procedures employed [56]. However, a lack of knowledge of functional traits and their link to ecosystem services poses a barrier to operationalizing various ecosystem restoration approaches [58, 59].
Restoration Ecology
Restoration ecology is a field of study that focuses on assisting the recovery of ecosystems that have been damaged, degraded, or destroyed. It involves restoring ecosystems' ecological structure, function, and biodiversity to a more natural and sustainable state. The goal of restoration ecology is to reverse the adverse impacts of human activities and promote the recovery of ecosystems, thereby enhancing their resilience and ability to provide ecosystem services. One of the critical aspects of restoration ecology is understanding the factors that drive the success of restoration efforts. A global meta-analysis by Crouzeilles and co-workers [60] examined the ecological drivers of forest restoration success. The study found that forest restoration boosts biodiversity by 15-84% and vegetation cover structure by 36-77% compared to degraded or damaged ecosystems. The primary ecological drivers of restoration success were the time elapsed since restoration started, disturbance types, and various landscape contexts. The time that has elapsed since restoration significantly influenced ecosystem restoration achievement in secondary forests but not selectively in logged forest types. Landscape restoration was most fruitful after the earlier disturbance was less severe and reduced habitat fragmentation.
Microbe and Microbiomes in Terrestrial Ecosystem Restoration
Microbes and microbiomes play a crucial role in terrestrial ecosystem restoration. Several investigations have emphasized the extent of microbial diversity in keeping multi-functionality and delivering essential ecosystem services in terrestrial ecosystems. Microbial communities in the soil have been found to drive multi-nutrient cycling in reforested ecosystems, with different microbial groups showing distinct assemblies along vertical soil profiles. Artificial revegetation has been shown to promote soil microbial diversity and restoration community in degraded ecosystems, increasing the alpha diversity of soil microbes within restoration periods [61]. In ecological restoration, it is essential to conserve microbial biodiversity, especially in drylands, as it is vital to soil survival and ecosystem functioning. Incorporating the microbial component into ecosystem restoration planning is pivotal in rebuilding the disturbed ecosystem microbiome and enhancing land management practices. The response of soil microbial communities to grassland degradation has also been studied, with changes in microbial community structural compositions and diversity at diverse levels of ecosystem degradation [62].
Removing and storing topsoil can negatively affect soil microbial communities and nutrient cycling in mining and post-mining rehabilitation. Successful restoration of degraded terrestrial ecosystems needs effective soil microbial inoculum to restore their populations and promote plant community development. Additionally, the enhancement of soil phosphorus cycling has been observed following ecological restoration, with the relative abundances of critical genes and genomes leading to higher soil microbial phosphorus cycling at restored sites than at unrestored sites [63]. Global warming consequences in glacier-fed stream (GFS) ecosystems are irreversible, and the microbiome cannot be preserved, restored, or managed like the microbiome of terrestrial environments. However, microdiversity within microbial communities may mitigate the impacts of climate change on microbial life in GFSs [64]. Many studies highlight the importance of microbes and microbiomes in restoring terrestrial ecosystems and maintaining soil fertility, as shown in Table 1.
Microbe and Microbiomes in Aquatic and Coastal Ecosystem Restoration
Microbes and microbiomes are crucial in restoring and managing aquatic and coastal ecosystems [74]. In freshwater ecosystems, microalgae biofilms are essential as they contribute significantly to the primary productivity of shallow waters and stabilize sediments, encouraging the establishment of microbial communities that operate bio-geochemical cycles [75]. Sedimentary microbes also play vital roles in sustaining the functional resilience of aquatic ecosystems. Still, due to the environmental complexity, their taxonomic composition and community processes must be better understood in estuarine-coastal margins. However, investigations have revealed that the abundance, diversity, and composition of microbes in sediments vary spatially and are influenced by various factors such as salinity gradients [76].
Bacteria-derived vesicles have been notified to be abundant in coastal and open-ocean seawater and are implicated in marine carbon flux. However, investigations on bacteria-derived vesicles in freshwater ecosystems are limited. Microplastics, which act as novel substrates for microbial colonization, are a growing problem due to their potential to multiply foreign or invasive species across various aquatic ecosystems. Microbes on microplastics build biofilms, and salinity gradients and ecological processes influence their dynamics and capacity to displace microorganisms across diverse marine ecosystems [77]. When studying microbial communities in aquatic and coastal ecosystems for restoration purposes, it is essential to consider the risks of microbial contamination and take measures to mitigate them. Microbes are ubiquitous, and uncontrolled contamination can compromise sample integrity and research quality. Therefore, researchers should carefully plan and execute field sampling, transport, and storage of microbial samples to ensure accurate and reliable results [5].
The relationship between microbes and aquatic plants has been observed in coastal ecosystems. Cable bacteria, for instance, are associated with aquatic plant roots in diverse ecosystems, including marine coastal habitats, estuaries, freshwater streams, isolated pristine lakes, and intensive farming systems. This plant-microbe association is widespread and not species-specific, and it has implications for vegetation vitality, primary productivity, coastal ecosystem restoration practices, and gaseous balance. Anthropogenic activities, such as fishing, shipping, and tourism, can harm coastal ecosystems, including deterioration of water quality, habitat destruction, and biodiversity loss. Microbes in these ecosystems are sensitive to environmental changes and can respond to anthropogenic stress by activating various adaptation strategies. Understanding anthropogenic activities' impact on microbial communities is crucial for effective ecosystem restoration and management [78].
Coastal wetlands, which act as transitional zones between terrestrial and aquatic ecosystems, undergo habitat transformations that can affect soil microbial community system and their functions. The decline and deterioration of aquatic macrophytes in these wetlands can simulate root-linked microbial communities and the larger micro-eukaryotes that rely on these interactions. Further, coastal wetlands are significant sinks for nitrogen reduction, and microbial-mediated functions such as denitrification and anaerobic ammonium oxidation are paramount in decreasing nitrogen overload in estuarine and coastal ecosystems [79]. In ecosystem restoration, exploiting microbiomes, macroalgae, and seagrasses has been proposed as a nature-based solution to fight the negative impacts of global climate change and human perturbation on coastal ecosystems. These approaches can improve water quality, enhance carbon sequestration, and contribute to the restoration and conservation of coastal ecosystems [80].
SIGNIFICANCE OF MICROBIOME IN NATURAL RESOURCE MANAGEMENT
The microbiome refers to the microorganism community, which includes bacteria, fungi, and viruses that significantly participate in natural resource management. Their significance is shown in Fig. (2). The microbiome directly impacts plant health, productivity, and nutrient cycling. The composition and function of the microbiome are crucial for sustainable intensification strategies in agriculture, particularly in organic systems where natural resources are the primary source of crop growth, yield, and environmental sustainability [81]. Microbes play a significant role in renewable energy by employing cellulolytic fungal strains and fermenting yeast and bacteria [82]. Various types of microbes are reported to remove hexavalent chromium [Cr(VI)] form in both terrestrial and aquatic ecosystems [83]. Microbes play an essential role in biofertilizer formulations, which contain live or latent cells of effective microbial strains cultured in the lab and packed in appropriate carriers [84]. Organic manure amended with effective microbial biofertilizers is found to reduce greenhouse gases and global warming potential farming systems [85]. Microbes, particularly siderophores, are an efficient biomining agent in recovering rare earth elements (REEs) [86].
Fig. (2)) Microbes and microbiomes in natural resource management.Role of Microbes and Microbiomes in Biomining
Biomining is a biotechnological process that employs microbes to retrieve metals and metalloids from ores and industrial and municipal waste materials. It has gained attention due to its prospect of addressing pressing issues linked to climate concerns, such as habitat devastation induced by mining effluent-related pollution, metal supply chains, and growing needs for cleantech-critical metals. However, biomining's drawbacks hinder its commercial applications, including prolonged processing periods, low recovery speeds, and narrow metal selectivity [87]. Microbes and microbiomes play a vital role in biomining operations. Specific microbial species, such as Geobacter and Shewanella, depend on extracellular electron transfer (EET) to decrease minerals and sustain growth, which has essential biotechnological applications in biomining. EET can also be harnessed to create biofuels and nano-materials [56]. These metal-reducing bacteria have extracellular electron transfer pathways that can route electrons across cell membranes to change the redox state of exogenous metals, allowing microbial-driven mineral conversions and the extraction of metals from ores, industrial and municipal waste [86].
Microbes employ microbial consortia rather than individual species in biomining, providing stable and efficient mineral degradation. These consortia consist of various classes of acidophilic prokaryotes, including Fe-oxidizing microbes, S-oxidizing microbes, and janitors that help to degrade organic carbon-containing compounds. The synergistic impact of these microbial consortia promotes sulfur-containing minerals' degradation and produces sulfuric acid, which sustains the optimum acidity levels for the consortium [88]. Advancements in synthetic biology present options to engineer iron/sulfur-oxidizing microbes to manage the limitations of biomining, such as low recovery rates and metal selectivity. Synthetic biology can improve the abilities of microbes applied in biomining operations, permitting the engineering of distinctive traits and functionalities. For instance, the engineering of polyhistidine tags on surface proteins of Acidithiobacillus ferrooxidans improved the metal binding ability of the microbes, extending further opportunities for metal bioseparation and their recovery [89]. The use of extremophiles, microbes that flourish in extreme conditions, is another area of interest in biomining and bio-leaching study [90]. Extremophiles have been studied for in-situ
