Industrial Applications of Soil Microbes: Volume 1 E-Book
69,68 €
Mehr erfahren.
- Herausgeber: Bentham Science Publishers
- Kategorie: Wissenschaft und neue Technologien
- Serie: Industrial Applications of Soil Microbes
- Sprache: Englisch
This volume is a compilation of reviews on the industrial usage of soil microorganisms. The contents include 15 brief reviews on different soil microbe assisted industrial processes. Readers will be updated about recent applications of soil bacteria, fungi and algae in sectors such as agriculture, biotechnology, environmental management.
The reviews also cover special topics like sustainable agriculture, biodiversity, ecology, and intellectual property rights of patented strains, giving a broad perspective on industrial applications of soil microbes. The text is easy to understand for readers of all levels, with references provided for the benefit of advanced readers.
Sie lesen das E-Book in den Legimi-Apps auf:
Seitenzahl: 501
Veröffentlichungsjahr: 2002
Ähnliche
BENTHAM SCIENCE PUBLISHERS LTD.
End User License Agreement (for non-institutional, personal use)
This is an agreement between you and Bentham Science Publishers Ltd. Please read this License Agreement carefully before using the ebook/echapter/ejournal (“Work”). Your use of the Work constitutes your agreement to the terms and conditions set forth in this License Agreement. If you do not agree to these terms and conditions then you should not use the Work.
Bentham Science Publishers agrees to grant you a non-exclusive, non-transferable limited license to use the Work subject to and in accordance with the following terms and conditions. This License Agreement is for non-library, personal use only. For a library / institutional / multi user license in respect of the Work, please contact: [email protected].
Usage Rules:
All rights reserved: The Work is the subject of copyright and Bentham Science Publishers either owns the Work (and the copyright in it) or is licensed to distribute the Work. You shall not copy, reproduce, modify, remove, delete, augment, add to, publish, transmit, sell, resell, create derivative works from, or in any way exploit the Work or make the Work available for others to do any of the same, in any form or by any means, in whole or in part, in each case without the prior written permission of Bentham Science Publishers, unless stated otherwise in this License Agreement.You may download a copy of the Work on one occasion to one personal computer (including tablet, laptop, desktop, or other such devices). You may make one back-up copy of the Work to avoid losing it.The unauthorised use or distribution of copyrighted or other proprietary content is illegal and could subject you to liability for substantial money damages. You will be liable for any damage resulting from your misuse of the Work or any violation of this License Agreement, including any infringement by you of copyrights or proprietary rights.Disclaimer:
Bentham Science Publishers does not guarantee that the information in the Work is error-free, or warrant that it will meet your requirements or that access to the Work will be uninterrupted or error-free. The Work is provided "as is" without warranty of any kind, either express or implied or statutory, including, without limitation, implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the results and performance of the Work is assumed by you. No responsibility is assumed by Bentham Science Publishers, its staff, editors and/or authors for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products instruction, advertisements or ideas contained in the Work.
Limitation of Liability:
In no event will Bentham Science Publishers, its staff, editors and/or authors, be liable for any damages, including, without limitation, special, incidental and/or consequential damages and/or damages for lost data and/or profits arising out of (whether directly or indirectly) the use or inability to use the Work. The entire liability of Bentham Science Publishers shall be limited to the amount actually paid by you for the Work.
General:
Any dispute or claim arising out of or in connection with this License Agreement or the Work (including non-contractual disputes or claims) will be governed by and construed in accordance with the laws of Singapore. Each party agrees that the courts of the state of Singapore shall have exclusive jurisdiction to settle any dispute or claim arising out of or in connection with this License Agreement or the Work (including non-contractual disputes or claims).Your rights under this License Agreement will automatically terminate without notice and without the need for a court order if at any point you breach any terms of this License Agreement. In no event will any delay or failure by Bentham Science Publishers in enforcing your compliance with this License Agreement constitute a waiver of any of its rights.You acknowledge that you have read this License Agreement, and agree to be bound by its terms and conditions. To the extent that any other terms and conditions presented on any website of Bentham Science Publishers conflict with, or are inconsistent with, the terms and conditions set out in this License Agreement, you acknowledge that the terms and conditions set out in this License Agreement shall prevail.Bentham Science Publishers Pte. Ltd. 80 Robinson Road #02-00 Singapore 068898 Singapore Email: [email protected]
FOREWORD
I am indeed very happy that this book on the scientific and industrial aspects of soil microbes is coming up. Since the discovery of microorganisms like bacteria, fungi, mycorrhiza, etc., and their association with plants, scientists have been attracted to the microbial association with plants and their role in the ecosystem. Studies on plant-associated soil microbes and their use in the industry have been a fascinating area of research for the last two decades and also play a crucial role in plant growth and development, such as nutrient cycling, crop productivity, and nitrogen fixation. Nowadays, scientists and industries are exploring the use of microbes in the fields of agricultural and industrial production of secondary metabolites from these beneficial microorganisms. Several bio-products are available on the market, and many more are likely to come in the future.
This book, entitled “Industrial Applications of Soil Microbes”, Volume I, is a praiseworthy step towards popularizing the industrial applications of microbes inhabiting the soil environment. This volume contains fifteen contributed articles on various aspects of soil microbes, their industrial utility, and their role in improving soil quality and yield. The various chapters of the present book have been written by reputed scientists in the microbiology field. It will provide the most recent information on the uses of microorganisms and their applications in industry and agriculture in one place.
The authors have covered most of the interesting topics, like preliminary information about soil microbes to highly advanced technologies like degradation of inorganic wastes, bioremediation, nutrient transformation, and the role of nanotechnology in agriculture. Some information about IPR, its rules, and regulations is also discussed. The latest references used by the authors will also provide the most recent developments in the industrial/agricultural uses of soil microbes.
I do not doubt that this book will be a significant scientific contribution and a source of inspiration to students and scientists who are trying to understand the mechanism of interaction of microbes with soil as well as their industrial applications.
PREFACE
The rapid increase in the population, industrialization, and so many human activities are all interrelated with each other and cause harm not only to the environment but also to the soil ecosystem. The soil ecosystem comprises various microorganisms, which may be beneficial or harmful to plants, soil, animals, and human beings. Some microbes, such as algae, bacteria, fungi, protozoans, and mycorrhizae, inhabiting soil are highly important for living beings, including humans.
These soil microbes carry out different biochemical reactions, leading to beneficial products. The ability of soil microbes to decompose organic waste is one of the major important uses. Beneficial soil microbes are being utilized in various chemical reactions in industries to produce products, which can be directly used in agriculture to increase the yield of the crops.
Indiscriminate use of fertilizer in the soil, barren land, and various pollutants present in the atmosphere results in an unhealthy environment for living beings. Either using the soil microbes in modified or unmodified ways may enhance the production of agriproducts and cause a healthy environment. The beneficial soil microorganisms as such or their products can be used in agriculture to get a better yield. This will certainly be beneficial to the farmers.
Sometimes a crazy idea also means a new school of opinion. We have been emphasizing here the soil microbes and their uses in agriculture, and we found that the information is scanty and scattered about the soil microbes and their uses. Thus, students and researchers could not get all this information in one place. Therefore, we decided to come up with a book entitled “Industrial Applications of Soil Microbes”, which carries the latest information on the subject.
In this volume of the book, an attempt has been made to present the basic and applied aspects of soil microbes with the latest information about microbial diversity in soil, their involvement in different processes either directly or indirectly for enhancement of crop yield, maintaining the ecosystem, reducing the pollution, future applications of soil microorganisms as nanoparticles, intellectual property rights, and their management.
Although there are other textbooks on soil microbes, it is hoped that the present book will be highly helpful to the students, academicians, scientists, and entrepreneurs who are working in this field. Further, it may provide information to the growers of the crops, giving them some principled knowledge to enhance their crop productivity.
The editors will be pleased to receive comments on the style and content of this volume for inclusion in further editions.
ACKNOWLEDGEMENT
The authors are highly thankful to the researchers, authors, and editors who contributed their research in the form of chapters for this book. We are also thankful to the Hon’ble Chancellor, Mr. B.P. Soni and Pro-Chancellor, Er. Anant Soni, AKS University, Satna, MP, India for permitting us and providing the facilities and encouragement. The authors are highly thankful to our colleagues for their constructive suggestions. We are also thankful to Mr. Ashish Khare, Designer, AKS University, for editing the figures. We can not forget the help of our family members. Without their love, affection, and encouragement, we could not have completed this work.
The authors express thanks to Bentham Science Publishers, for allowing this project and especially to Humaira Hashmi for timely help and guidance.
List of Contributors
Soil Bacteria- Our Allies in Building Soil Health
Sneha S. Nair1,Prabha Susan Philip2,*,K.S. Karthika3Abstract
Microorganisms give life to the soil and provide a variety of ecosystem services to plants. Soil bacteria are the strongest candidates for determining soil health. Bacterial communities are important for the health and productivity of soil ecosystems. Therefore, we must have thorough knowledge of the diversity, habitat, and ecosystem functions of bacteria. In this chapter, we will discuss the functional, metabolic, and phylogenetic diversity of soil bacteria and highlight the role of bacteria in the cycling of major biological elements (C, N, P, and S), detoxification of common soil pollutants, disease suppression, and soil aggregation. This chapter also underlines the use of soil bacteria as indicators of soil health. We have concluded the chapter by taking note of the present agricultural practices that call for concern regarding the natural soil microflora and steps to return biological activity to the soil.
INTRODUCTION
Soil is a unique product formed by a combination of geological parent material, soil biota activity, land use pattern, and disturbance regimes. It is a niche for a diversity of microorganisms such as bacteria, archaea, fungi, insects, annelids, and other invertebrates, as well as plants and algae. Among various microbes present in the soil, bacteria are the most abundant. They provide a multitude of ecosystem services in the soil, such as nutrient cycling, disease suppression, soil aggregation, bioremediation, etc. The most critical function of bacteria in soil is the regulation of biogeochemical transformations. Soil is a complex medium rich in a variety of minerals and complex organic molecules.
A wide variety of bacteria, especially those belonging to actinobacteria and proteobacteria, can degrade complex organic molecules such as cellulose, hemice-
llulose, lignin, and chitin to simple sugars and amino acids, thereby leading to the formation and turnover of soil organic matter (OM) that includes mineralization and sequestration of carbon (C). The entire process of nitrogen fixation into the rhizosphere or plant compartment is mediated by soil bacteria. They also significantly contribute to phosphorus, sulphur, iron, and magnesium pools in the soil. Soil bacteria are also active agents of bioremediation and disease suppression. They use complex mechanisms such as biosorption, bioaccumulation, biotransformation, bioprecipitation, and bioleaching to reduce toxic metals in soil. Soil aggregate formation is a major function of these soil dwellers. They do so by producing extracellular polymeric substances (EPS), which act as gelling materials and help stick the aggregates together. This, in turn, helps in increasing the water-holding capacity of the soil. As the key producers of different enzymes in the soil, such as dehydrogenases, catalases, phosphatases, etc., soil bacteria are also commonly used as indicator organisms to assess soil health.
Bacteria serve numerous roles in the pedosphere. Being able to survive even in the extremes of the environment, they have become strong candidates for building soil health. For that reason, it is necessary to understand their soil habitat, diversity, and the ecosystem services they provide. Therefore, in this chapter, we will briefly consider diversity, abundance, distribution, and, in particular, their role in regulating ecosystem services.
SOIL AS A CULTURE MEDIUM FOR BACTERIA
Soil is the outer loose material of the earth’s surface, which provides mechanical support and essential nutrients to plants. The nutrients in the soil are obtained by physical, biological, and biochemical reactions related to the decomposition of organic weathering of the parent rock. The soil also acts as a niche for many microorganisms, especially bacteria, which are the most abundant microorganisms in the soil, providing them with sufficient nutrients and a beneficial microclimate for their survival. The diversity, abundance, and activity of bacterial communities are dependent on soil depth, soil pH, soil temperature, soil nutrients, soil moisture, etc.
Soil Depth
Soil is divided into different horizons based on its physical, chemical, and biological characteristics. Typical horizons that develop in agricultural soils include the A, B, and C horizons. Bacteria exist in all the horizons, but their abundance and diversity are highest in the top 10 cm of soil and decline with depth. According to Aislabie and coworkers [1], the A horizon has the highest density of soil microbes and plant roots because of its high organic matter content and is considered to be the site of humification in soil. As water infiltrates the A horizon, organic compounds and minerals like iron, aluminium, clay, etc., get leached out to the B horizon. The B horizon (subsoil) retains non-mobile constituents and thus tends to be enriched in minerals such as quartz. Below the B horizon are the partially weathered stones, forming a C horizon above the solid, unweathered bedrock. Fierer and coworkers [2] discovered that the maximum microbial biomass exists in the top 0–5 cm of soil depth. The reason for this might be the abundant availability of organic carbon in the A horizon. Bacteria that can grow facultatively with the help of inorganic ions mostly occupy the deeper horizons of soil. As one moves to the C horizon, nutrients, as well as water and oxygen, become deficient, leading to the habitation of certain extremophiles.
Soil pH
Soil pH also influences the occurrence and distribution of bacteria as it determines the chemical activity of protons in soil, which are the foundation for all enzymatic reactions, mineralization and precipitation, surface complexation, and other geochemical reactions in soil [3]. Based on optimal growth pH, bacteria can be distinguished into three groups: acidophiles that grow best at pH < 5, neutrophiles that grow optimally at pH between 5 and 9, and alkaliphiles that grow fastest above pH 9 (Table 1). For a microbe with a pH range spanning 4 pH units, assuming that its optimal pH is near the middle point of the pH range, a deviation of one unit from this optimal pH can reduce its growth rate by about 50% [4]. Therefore, soil pH is an important parameter that determines the bacterial population in the soil. Most soil bacteria show optimum growth at neutrophilic pH, but some bacterial species can thrive well under extremes of pH.
Soil Nutrients
Soil is biologically alive as it contains sufficient nutrients for microbial growth. Oxygen and hydrogen are abundantly present in the upper layers of soil. Nitrogen is abundant in the atmosphere as nitrogen gas but is unavailable to bacteria except to the few species of nitrogen-fixing bacteria, as rainwater fixes very little nitrogen as nitrates in the soil. The ultimate source of carbon in soil is carbon dioxide. Based on the nutrient requirements, bacteria in soil can be classified as phototrophs and chemotrophs. Photoautotrophs are organisms that carry out photosynthesis. Using energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions such as biosynthesis and respiration. Photoheterotrophs obtain their energy from sunlight and carbon from organic material, not carbon dioxide. They can be contrasted with chemotrophs that obtain their energy from the oxidation of electron donors in their environments. Chemoautotrophs can synthesize their organic molecules from the fixation of carbon dioxide. The energy required for this process comes from the oxidation of inorganic molecules such as iron, sulfur, or magnesium. Chemoheterotrophs, unlike chemoautotrophs, are unable to synthesize their organic molecules. Instead, they consume carbon molecules synthesized by other organisms. They do so, however, while still obtaining energy from the oxidation of inorganic molecules like the chemoautotrophs. Chemoheterotrophs can only thrive in environments that are capable of sustaining other forms of life due to their dependence on these organisms for carbon sources (Table 1).
Soil Moisture
The moisture content of the soil is correlated with the oxygen status. Soil water content is important in regulating oxygen diffusion, with maximum aerobic microbial activity occurring at moisture levels between 50% and 70% of the water holding capacity [5]. A high moisture content (metric potential > −0.01 MPa) can result in a low oxygen supply, leading to a decrease in the rate of organic matter decomposition. A low moisture content can decrease microbial activity, as water is an essential nutrient for the activation of most of the microbial enzymes. Although some bacteria can survive in extreme moisture conditions such as drought and waterlogged soils, the majority of soil bacteria prefer optimum moisture conditions of 50-70% water holding capacity. Drought-tolerant bacteria in soil include Pseudomonas, Enterobacter, Pantoea, Klebsiella, Arthrobacter, and Ochrobactrum. Whereas methanogens, denitrifiers, sulphate reducers, etc., dominate waterlogged soil [13].
Soil Aeration
Oxygen is an essential micronutrient for most of the bacteria in the soil as it acts as the terminal electron acceptor in the electron transport chain. Bacteria that cannot survive in the absence of oxygen are called obligate aerobes. They contain enzymes that can neutralize free radicals and peroxides of oxygen, such as catalase, peroxidase, and superoxide dismutase (SOD). On the other hand, bacteria that are killed in the presence of oxygen are called obligate anaerobes. They may live by fermentation, anaerobic respiration, bacterial photosynthesis, or methanogenesis. Facultative anaerobes are organisms that can switch between aerobic and anaerobic types of metabolism. Under anaerobic conditions, they grow by fermentation or anaerobic respiration, but in the presence of O2, they switch to aerobic respiration. Two more categories of bacteria exist in soils that can tolerate low levels of oxygen. They are aerotolerant anaerobes and microaerophiles. Aerotolerant anaerobes are indifferent to the presence of oxygen. They do not use oxygen because they usually have a fermentative metabolism, but they are not harmed by the presence of oxygen, as obligate anaerobes are, whereas microaerophiles require oxygen to survive, but require environments containing lower levels of oxygen than those that are present in the atmosphere (i.e. <21% O2; typically 2–10% O2). Obligate anaerobes usually lack all three enzymes. Aerotolerant anaerobes do have SOD but no catalase.
Soil Temperature
Bacteria are known to live at extremes of temperature (Table 1). Temperature has a direct effect on bacteria, as most enzymes get denatured at very high temperatures. Organisms have a specific range of temperature at which their biological activity operates, which is defined by cardinal points (minimum, optimum, and maximum temperature). Soil bacteria may be subdivided into several subclasses based on their cardinal points for growth. Bacteria with an optimum temperature (T) near 37°C are called mesophiles. Thermophiles are bacteria that thrive at temperatures ranging from 45 to 70°C. Bacteria (mostly Archaea) with an optimum T of 80 to 115°C are referred to as hyperthermophiles. Thermophiles possess several heat-stable enzymes wherein they showcase different critical amino acid substitutions at a few locations in the enzyme that allow the protein to fold in a unique, heat-stable way. Besides enzymes and other macromolecules in the cell, the cytoplasmic membranes of thermophiles and hyperthermophiles are counteracted by constructing membranes with more long-chain and saturated fatty acid content and lower unsaturated fatty acid content than is found in the cytoplasmic membranes of mesophiles. Thermophiles also have a high G+C content in their DNA, such that the melting point of the DNA (the temperature at which the strands of the double helix separate) is at least as high as the organism's maximum T [5]. The cold-loving bacteria, on the other hand, are psychrophiles, defined by their ability to grow at 0°C. A variant of a psychrophile (which usually has an optimum temperature of 10-15°C) is the psychrotroph, which grows at 0°C but displays an optimum temperature in the mesophile range, nearer room temperature. Psychrophiles have unsaturated fatty acids in their plasma membrane, which remain liquid at low temperatures but can also be denatured at moderate temperatures. Psychrophiles also have enzymes with a greater content of α-helix and a lesser content of β-sheet, which helps them function at temperatures of at or near 0 degrees.
The soil environment is very complex and provides diverse microbial habitats. It differs with regard to climate, vegetation, location, etc. Despite these factors, we now know that bacteria can survive harsh environments. Biological activity is an important fraction of soil, and the microbes that colonize these soils are influenced by the soil pH, moisture, temperature, aeration, etc. A combination of these factors influences the microbial community of any soil.
CLASSIFICATION OF SOIL BACTERIA
Bacteria are prokaryotic (without a true nucleus), single-celled organisms varying in size and shape. A single gram of soil may contain 103 to 106 unique species of bacteria [14]. Soil bacteria can be classified based on their shapes (rod, sphere, spiral and pleomorphic), size (varying from 0.5µm), cell wall structure (Gram-positive and Gram-negative), oxygen requirements (obligate aerobes, facultative anaerobes, microaerophilic and obligate anaerobes), nutritional differences (autochthonous and zymogenous) and growth and reproduction (autotrophic, chemotrophic and heterotrophic). With new advances in DNA sequencing, scientists have classified bacteria into closely related phyla. DNA sequencing technology can be used to study relationships between unknown and known organisms and provides an estimate of the genetic diversity of organisms in a given community. In this section, we will go through important bacterial classifications in soil microbiology.
Classification Based on Nutritional Differences
Soil bacteria are most commonly classified based on nutritional differences into autochthonous and zymogenous [15]. Autochthonous microbes are indigenously present in soil and have adaptive mechanisms to survive in natural conditions with extremely low nutrient supplies (oligotrophic environment) [16]. They are ecologically defined as k- strategists. In contrast, zymogenous bacteria, or r- strategists consist of actively fermenting forms, which require nutrients that are quickly exhausted for their activity. Under nutrient-sufficient conditions, these microbes increase to great numbers and then return to detectable numbers as nutrients diminish. Major differences between the two groups are listed in Table 2. R- and k-strategists have often been described in relation to ecological succession, with r-strategists being abundant in early successional stages and k-strategists prevailing in late successional stages [17]. In a nutshell, r-strategists are adapted to maximize their intrinsic rate of growth when resources are abundant, while k-strategists are adapted to compete and survive when populations are near carrying capacity and resources are limited [18].
Molecular Classification of Soil Bacteria
Soil bacteria were previously classified by studying individual strains through cultivation in laboratories. However, this approach neglects the vast majority of soil bacteria that are unculturable. Recently, molecular approaches have gained importance as a useful tool for the characterization of bacterial communities [20]. The estimated relative abundance of the major phyla varies between different soils (or samples). Jansen [21] identified the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes and highlighted members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria to be widespread and often abundant, whereas members of the Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Planctomycetes, and Gemmatimonadetes to be less prevalent (Table 3). The Proteobacteria are a metabolically diverse group of organisms in several subphyla, four of which, α-, β-, γ-, and δ-Proteobacteria are abundantly present in the soil. They play an important role in determining soil nutrient characteristics, as most of the bacteria in this phylum are involved in different biogeochemical cycles. These proteobacteria can be either r- or k-strategists. Adding low molecular weight carbon to soil increased the relative abundances of β- and γ-Proteobacteria while spiking soils with recalcitrant carbon increased the relative abundance of α-, β-, and δ-Proteobacteria [22].
Acidobacteria is a group of bacteria similar to Proteobacteria in their metabolic and phylogenetic diversity, ubiquitous nature, and abundance in soil habitats. Genome sequencing of three-cultured soil Acidobacteria suggests that bacteria belonging to this phyla may be oligotrophs that metabolize a wide range of simple and complex carbon sources [23]. They also appear well suited to low nutrient conditions, tolerate fluctuations in soil moisture, and are capable of nitrate and nitrite reduction, but not denitrification or nitrogen fixation.
Actinobacteria and Firmicutes contribute as major Gram-positive bacteria in the soil. Actinobacteria are aerobic and spore-forming bacteria, belonging to the order Actinomycetales, with most of them characterized by substrate and aerial mycelium growth. They are also responsible for the characteristically “earthy” smell of freshly turned healthy soil. The phyla include soil actinobacteria (such as Frankia), which live symbiotically with the plants whose roots pervade the soil, fixing nitrogen; Streptomyces, known for their ability to produce antimicrobial compounds; and members of the genus Mycobacterium, which are important pathogens. They are metabolically diverse aerobic heterotrophs, playing an important role in the cycling of carbon, nitrogen, phosphorus, potassium, and several other elements in the soil [24]. The relative abundance of Actinobacteridae in the soil increases following the addition of labile carbon sources [22].
Firmicutes include heat-stable endospore formers in soil and are aerobic to facultatively anaerobic (genus Bacillus) and anaerobic (genus Clostridium). Bacillus species are known for their plant growth-promoting activity, besides their antagonistic activity against many pathogens. The most abundant bacilli in soil include Bacillus subtilis, B. cereus, B. thuringiensis, B. pumilus, and B. Megaterium.
Bacteroidetes are another group of bacteria present in the soil. They are involved in the aerobic degradation of complex organic molecules such as starch, proteins, cellulose, and chitin. They are Gram-negative, non-spore-forming, anaerobic or aerobic, and rod-shaped bacteria, whereas Verrucomicrobia is characterized as an unculturable soil microbiota. The most abundant verrucomicrobial class, Spartobacteria, contains free-living taxa. Verrucomicrobial isolates display a wide variety of features, such as methanotrophy, nitrogen fixation, pathogenicity, etc.
Another ubiquitous organism on the list is Planctomycetes. Examples of these include Singulisphaera acidiphila, S. rosea, and Paludisphaera borealis, which are psychrotolerant and can grow at low temperatures, down to 4–6°C [25]. They are most commonly known in soil for their ability to perform anaerobic ammonium oxidation (anammox) [26]. Planctomycetes possess distinctive phenotypic features that are highly unusual among bacteria. These include the lack of peptidoglycan in their protein cell walls (as reproduction mostly by budding process), resistance to antibiotics that inhibit cell wall synthesis, such as the β-lactam and vancomycin (due to lack of peptidoglycan) and synthesis of sterols [27].
Classification Based on Soil Functions
Bacteria perform many important ecosystem services in the soil, such as improved soil structure, soil aggregation, nutrient cycling, etc. (Table 4). Even though phylogenetic classification is the most accurate method of classification, as soil microbiologists, we need to ponder upon a much more diverse division of soil bacteria as they have numerous ecosystem functions in the soil. Therefore, the whole chapter about soil bacteria will be dealt with keeping in mind the ecosystem functions of the bacteria in the soil.
ROLE OF BACTERIA IN SUSTAINING SOIL HEALTH
The soil microbial community is fundamental in any ecosystem because it takes part in organic matter decomposition and nutrient cycling, influencing the chemical and physical properties of the soil and, consequently, primary productivity. In the subsequent sections, we will discuss in detail the ecosystem services that soil bacteria provide.
Nutrient Cycling
Nutrient cycling is the whole process of use, movement, and recycling of nutrients within the ecosystem and is one of the most important ecosystem functions that soil bacteria execute. Most of the elements on earth are nutritionally essential and are prerequisites for living organisms to complete their life cycle. For the growth and development of higher plants, 17 nutrients are considered essential as per criteria developed by Arnon and Stout [39]. These include both macro and micronutrients derived mainly from the atmosphere- carbon (C), hydrogen (H), oxygen (O); primary nutrients- nitrogen (N), phosphorus (P), potassium (K); secondary nutrients- calcium (Ca), magnesium (Mg), sulphur (S); and micronutrients- iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), boron (B), molybdenum (Mo), chlorine (Cl) and nickel (Ni). All these nutrients play a key role in a plant’s life cycle. Therefore, these nutrients must be cycled in a way to make them available for plant uptake. Nutrient cycles are complex processes
involving biological, geological, and chemical processes, and for this reason, the term “biogeochemical cycle” is often used.
These circuits are completed and connected by various nutrient transformation steps wherein some or whole steps are microbe mediated. Nutrient transformation is a key process that makes nutrients available for plant uptake. Microorganisms, especially bacteria, provide a notable contribution to nutrient cycling. As a part of this chapter here, we discuss four important nutrient cycles, which play a significant role in soil ecosystem balance.
Carbon Cycle
Carbon is the structural component of organic molecules like carbohydrates, proteins, and lipids that build living tissues. It is the backbone element for all life forms in the biosphere. The element is of great relevance as the major greenhouse gases that regulate the pace of global warming and climate change are carbon compounds; carbon dioxide (CO2) and methane (CH4). Organic compounds released in the form of root exudates, lysates, secretions, and other organic residues serve as the energy sources for belowground microfauna, especially the soil bacterial community.
The global carbon cycle describes the complex transformations and carbon fluxes between the major components of the Earth’s system. Carbon is stored both as organic and inorganic compounds in four major Earth reservoirs, including the atmosphere, lithosphere, biosphere, and hydrosphere [40]. Two important processes of the C cycle are photosynthesis and respiration. Through the process of photosynthesis, CO2 marks its entry into the biosphere, and through respiration it exits and leaves back into the atmosphere. The C cycle begins with biological C fixation, i.e., CO2 from the atmosphere is fixed as complex organic molecules in the terrestrial system (plants and microorganisms) by the process of photosynthesis. The processed form of C by photoautotrophs is utilized by heterotrophs as their energy source.
Carbon is released back into the atmosphere from the terrestrial ecosystem through several processes, like the burning of fossil fuels and crop residues, the decomposition of dead and decaying organic matter, and respiration by living organisms and roots. Decomposition by saprophytes (bacteria and fungi) is the breakdown of dead and decaying organic residue and the release of carbon and other nutrients back into the environment, and it is one of the most important roles of bacteria. By way of the decomposition process, nutrients or minerals are released back into the soil system; hence, this process is often referred to as mineralization.
The C:N ratio is a fundamental indicator of biogeochemical cycles in ecosystems. Any shift in C:N stoichiometry could pose great impacts on the nutrient cycling and the composition and structure of plant communities, affecting ecosystem service functions at local, regional, national, and global scales [41]. Carbon is important for bacteria as it is an energy-producing factor, and nitrogen for building microbial body tissues. There is always a narrowing of the carbon-nitrogen ratio when organic matter decomposes. Bacteria maintain a C: N ratio of 4:1 to 8:1, less compared to other microorganisms. This stoichiometry is important as it determines the direction of nutrient fluxes in the soil system.
Methane production, or methanogenesis, is also a crucial step in the carbon cycle. Reduced compounds like methane accumulate in certain anaerobic environments when CO2 is used as a terminal electron acceptor in anaerobic respiration by archaea called methanogens. Methanogens in both natural anaerobic soil and aquatic environments lead to methane accumulation and cause serious environmental concern as CH4 is a greenhouse gas involved in global warming. Biological oxidation of this methane in the soil can be carried out by methanotrophs, thereby reducing the atmospheric methane levels.
N-Cycle and Microbial Nitrogen Transformations
The N-cycle begins with the inert dinitrogen (N2) form and follows it through the processes of fixation, mineralization, immobilization, nitrification, ammonia volatilization, leaching, runoff, plant assimilation, and completion with denitrification. Microorganisms, especially soil bacteria, are involved in all major aspects of the cycle. Plant available N in soil depends on the balance between rates of mineralization, nitrification, and denitrification. On earth, N is distributed in two large pools – as an inert form of atmospheric molecular nitrogen and a biologically reactive form of nitrogen, namely, NO3, NH4, and organic nitrogen. These two large pools are interconnected and controlled by microbially mediated processes of nitrogen fixation and denitrification [42]. The entire process of fixing N2 into the rhizosphere or plant compartment and the transformation of one form into the other comprises the nitrogen cycle.
N Fixation
The N-cycle starts with biological N fixation, wherein gaseous inert N from the atmosphere is made available to plants by bacteria such as Rhizobium (in legumes). Microbial mediated nitrogen fixation is one of the prime mechanisms contributing to large additions of mineral nitrogen into the soil ecosystem. In 1888, Dutch microbiologist Martinus Beijerinck was the first to identify Rhizobium, a class of bacteria for its ability to fix elemental N from the atmosphere into the roots of leguminous plants by forming nodules. Several scientific reports disclose the roles of bacterial members from the families Azotobacteriaceae, Spirillaceae, Enterobacteriaceae, Bacillaceae, Pseudomona-daceae, and Achromobacteriaceae in nitrogen fixation. As plants cannot take up N in its atmospheric form, it needs to be transformed to either as nitrate (NO3-) or ammoniacal (NH4+) form to facilitate its uptake by plants [43]. Biological N fixation includes the processes through which atmospheric N is converted to ammonia with the involvement of nitrogenase enzymes by symbiotic N fixers, associative N fixers, and free-living N fixers [44].
Symbiotic N Fixation
Symbiotic N fixation is a well-known example of the symbiotic association that exists between the roots of leguminous crops and N-fixing bacteria. This results from the complex interaction between the host plant and rhizobia (Rhizobium, Bradyrhizobium, Sinorhizobium, and Mesorhizobium) [45]. Rhizobium and Bradyrhizobium belonging to α proteobacteria are the main N fixers that inhabit the root nodules of leguminous crops.
Non-Symbiotic N Fixation or Associative N Fixation
The method of N fixation also termed associated N fixation refers to the process in which bacteria fix nitrogen by using carbon compounds as an energy source, and bacteria release the fixed nitrogen at the root surface and in the cellular interstices of root tissue only after lysis of the bacterial cells [46, 47]. Azotobacter, Azospirillum, and Enterobacter are major soil bacteria involved in non-symbiotic N fixation. Associative N fixation in plant root interiors has gained high significance and agronomic importance in sugarcane, sweet potato, and rice, etc.
Free Living Nitrogen Fixation
In free-living N fixation, the fixation of N occurs without a formal microbe plant symbiotic relationship. The process is ubiquitous in terrestrial ecosystems and the major free-living N fixers include many bacterial phyla such as Alphaproteobacteria (Bradyrhizobium and Rhodobacter), Betaproteobacteria (Burkholderia and Nitrosospira), Gammaproteobacteria (Pseudomonas and Xanthomonas), deltaproteobacteria, firmicutes, cyanobacteria, etc.
N Mineralization
The majority share of N in the soil is present as complex organic molecules, which need to be converted into plant-usable forms by microorganisms present at the soil-root interface. Mineralization of organic nitrogen is a three-step process, namely aminization, ammonification, and nitrification. These processes are governed by the carbon: nitrogen (C: N) ratio of the organic substrate present. In the case of fresh and easily decomposable organic material with a narrower C: N ratio (for legumes, 30:1), mineralization takes place faster, whereas for high molecular weight compounds like lignin and humus with a wider C: N ratio (for sawdust, 600:1), mineralization is very slow [48].
Aminization
Heterotrophic bacteria, actinomycetes, and fungi are capable of enzymatically digesting proteins and other proteinaceous compounds released from roots or organic residues into amino acids and amines, and the process is known as aminization.
The amino acids so produced are either utilized by microbes (immobilization) or mineralized to NH3 by ammonification. Amino acids act as an important source of N uptake for plants under some circumstances, and the existence of amino acid uptake systems in plant roots has also been reported.
Ammonification
In this process, amino acids or amines released by root exudation are transformed into ammonia by ammonifiers (bacteria, fungi, and actinomycetes) using enzymes.
Nitrification
This process involves two-step oxidation processes wherein the oxidation of ammonium ion (NH4+) is converted to nitrate ion (NO3-) by nitrifying organisms. In the first step, NH4+ is converted to nitrite (NO2-) by Nitrosomonas, Micrococcus, and Nitrospira, and then the conversion of NO2- to NO3- is mediated by Nitrobacter and Nitrocystis.
Immobilization
Soil microorganisms utilize inorganic N forms for building up their body tissues, thereby leading to the temporary unavailability of nitrogen for plant uptake. This process of conversion of inorganic nitrogen into organic forms is termed immobilization. It is a reversal of the mineralization process. The main factor governing the immobilization process is the C: N ratio of the substrate available for bacteria. The more complex the organic substrate, the wider the C: N ratio, leading to a higher N demand by saprophytes feeding on it. To meet their elevated N demand, decomposers utilize either added or native N sources immediately available to them. The process of immobilization leads only to the short-term unavailability of N for plants.
Denitrification
The process of denitrification mainly happens under anoxic conditions in which bacteria of the genera Thiobacillus denitrificans, Thiobacillus thioparus, Pseudomonas, Micrococcus, Achromobacter, and Bacillus reduce NO2- and NO3- leading to the release of gases NO, N2O, and N2 back into the atmosphere.
These microorganisms use organic compounds as their energy source, which are available in plenty in the soil. Favourable conditions for the denitrification process include limited O2 supply, high concentration of NO3-, presence of soil moisture, carbohydrates source and warm temperatures [49, 50]. Nitrate and nitrite act as electron acceptors instead of O2 for respiration by microorganisms in denitrification.
Losses of mineral N from terrestrial ecosystems are mainly through microbial-mediated processes of nitrification and denitrification. Dissimilatory nitrate reduction (DNRA) is a process mediated by bacteria and fungi wherein the respiratory reduction of nitrate to a more stable ammonium form takes place, thereby limiting losses of N from the soil system.
Phosphorus Cycle
Phosphorus (P) is a primary nutrient element vital for plant growth and development. It plays an important role in energy transfer, root formation and growth, photosynthesis, the translocation of sugars and starches, etc. Microorganisms, specifically bacteria, are integral to phosphorus transformation in soil and play a key role in mediating its availability to plants. Knowledge regarding the microbial contribution and opportunities for manipulation of the specific microbial communities to enhance P availability and use efficiency is important as global phosphorus reserves are limited and getting exhausted day by day. The best option available is to increase P use efficiency by employing a specific microbial community capable of doing so [51].
Phosphorus in the soil solution is mainly brought about by the weathering of minerals (apatites), the application of phosphatic fertilizers, and organic manure addition. The added P in the solution gets transformed through adsorption and precipitation processes into P products of varying degrees of solubility. Soil bacteria are capable of mineralizing a fraction of such chemically immobilized P and bringing it to the soil solution pool for plant uptake. During this process, a portion of it gets tied up in microbial tissues for a short period, which upon decaying of microbial tissues gets released into soil solution [48].
Bacteria secrete organic acids like lactic and glycolic acids that aid in the solubilization of immobilized inorganic phosphates, thereby enhancing P availability to plants. P solubilizing bacteria are cultured and available for commercial application as biofertilizers or as plant-growth promoting bacteria (PGPRs). Several Pseudomonas spp. are also associated with P mobilization [52].
C:P Ratio
Net mineralization of organic P happens if the organic residue added to soil has a carbon to phosphorus (C:P) ratio below 200:1, while net immobilization of soluble P occurs at a C:P ratio above 300:1.
Sulphur Cycle
Sulphur (S) is the 10th most abundant element in the universe and the sixth most abundant element in microbial biomass [53]. It is a constituent element of many vitamins, proteins, and hormones that play critical roles in both climates and the health of various ecosystems. The majority of the Earth’s sulphur is stored underground in rocks and minerals as sulphate salts buried deep within ocean sediments. The transformation and fate of this element in the environment are critically reliant on microbial activities.
The S cycle is both atmospheric and terrestrial. Similar to N, the majority of S exists as organic sulphur compounds. Since elemental S has the ability to exist in a wide range of stable redox states, it is involved in various oxidation and reduction biochemical reactions. Within the terrestrial portion, the cycle begins with the weathering of rocks, S then comes into contact with air where it is converted into sulphate (SO4). Organic S compounds upon mineralization under aerobic upland conditions to SO4 by the action of S oxidizing bacteria, Thiobacillus.
The sulphate is taken up by plants and microorganisms and converted into organic forms; animals then consume these organic forms through the foods they eat, thereby moving the sulphur through the food chain. The addition of bulky organic manures low in S content leads to a microbial proliferation, which tends to meet their S requirement from inorganic SO4-S, leading to immobilization and rendering S temporarily unavailable to plants. Later, as these microbes die, microbial S is again mineralized to provide the plant with usable SO4. Under reduced conditions, SO42- ions are reduced by anaerobic bacteria, Desulphovibrio and Desulphotomaculum, to sulphite and sulphide, respectively. In the redox process, the SO42- ion is the last one to undergo reduction because of its low redox potential value of -215 mV. There are also a variety of natural sources that emit S directly into the atmosphere, including volcanic eruptions, the breakdown of organic matter in swamps and tidal flats, and the evaporation of water. Besides this, SO2, as a part of industrial pollution, also reaches the atmosphere and is brought back to the atmosphere in the form of acid rain. Thus, S eventually cycles back into the Earth or comes down in rainfall. A continuous loss of sulphur from terrestrial ecosystem runoff occurs through drainage into lakes, streams, and eventually oceans.
C:S Ratio
S in the soil is associated with organic carbon in a fixed carbon to sulphur (C:S) ratio and maintenance of the C:N:S ratio at favourable levels of about 125:140:1 is essential to ensure S availability to plants. Otherwise available S in the soil, which is subjected to various microbial transformations, may lead to temporary unavailability to crops.
RECYCLING WASTES AND DETOXIFICATION
Worldwide, contamination of soil due to natural geogenic sources such as volcanic releases, forest fires, erosion and anthropogenic activities such as mining, industrial activities, activities linked to transportation in and around urban centers, waste and sewage disposal, warfare, agricultural and livestock activities, etc., has resulted in an increased release of a wide range of xenobiotics. The main source of soil pollution is anthropogenic [54]. The major pollutants in soil include heavy metals, nitrogen, phosphorus, pesticides, polycyclic aromatic hydrocarbons, persistent organic pollutants (POPs), per- and polyfluorinated alkyl substances (PFAS) and radionuclides. Soil pollution is an alarming issue as it threatens food security both by reducing crop yields due to toxic levels of contaminants and by causing the produced crops to be unsafe for consumption [55
