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The Handbook of Microbial Bioresources

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Microbial technology plays an integral role in the biotechnology, bioengineering, biomedicine/biopharmaceuticals and agriculture sector. This book provides a detailed compendium of the methods, biotechnological routes, and processes used to investigate different aspects of microbial resources and applications. It covers the fundamental and applied aspects of microorganisms in the health, industry, agriculture and environmental sectors, reviewing subjects as varied and topical as pest control, health and industrial developments and animal feed.

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1: Microbial Resources for Improved Crop Productivity

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1  Microbial Resources for Improved

Crop Productivity

Javier Raya-González,1 Esmeralda Hernández-Abreu,2

Eduardo Valencia-­Cantero1 and José López-Bucio1*

1

Instituto de Investigaciones Químico-Biológicas, Universidad

Michoacana de San Nicolás de Hidalgo, Morelia, Mexico;

2

Centro de Bachillerato Tecnológico-­Agropecuario No. 7, Morelia, Mexico

Abstract

The ever-increasing human population and depletion of soil, nutrient and water resources make it necessary to ensure sustainability and genetic integrity of crops via exploitation of new technologies and through better agricultural practices. Many bacterial and fungal species may contain genes for plant resistance to biotic and abiotic factors and can produce metabolites that improve both the quality and the quantity of grains, fruits, fibre and nutritional energy. To ensure that beneficial microbes are available for commercial use, development of screening methods for identifying favourable traits is necessary. Recent advances in plant molecular biology, genomics and physiology using model plants and crop species together with improvements in microbial isolation, identification and culture techniques have provided the means to accelerate and strengthen the use of microbial formulations.

 

2: The Contributions of Mycorrhizal Fungi

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2 

The Contributions of Mycorrhizal Fungi

Marcela Claudia Pagano* and Ado Jorio

Department of Physics, Federal University of Minas Gerais, Brazil

Abstract

There is mounting research on microbial diversity and their products, especially those associated with soil amendments such as biochar and compost. There is increasing recognition of the beneficial effects of biochar, which, applied in suitable amounts and forms, can stimulate soil microbial activity, soil microbes and symbiotic microorganisms, and mycorrhizal fungi. Mycorrhizas may have an important role in determining the impact of biochar on plant communities. Biochar influences carbon (C) sequestration in soils as a simple instrument to counterbalance C emissions related to the burning of fossil fuels. Among soil microorganisms, most plant species associate with mycorrhizas and/or other symbionts. Mycorrhizas permit the plant to perform better under unfavourable conditions, mostly in the soil superficial layers. Due to their key position in the soil–root interface, the study of mycorrhizas in combination with biochar/compost has the potential to make a significant contribution to the biochar effect. The appreciation of alternatives to cope with environmental constraints, such as the use of soil amendments such as biochar and compost, is also of interest for understanding the effect of drought on crops. This chapter explores current information on mycorrhizas in agroecosystems with respect to the benefits of biochar/compost amendments.

 

3: Trichoderma: Utilization for Agriculture Management and Biotechnology

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3 

Trichoderma: Utilization for Agriculture

Management and Biotechnology

Pradeep Kumar,1* Madhu Kamle,2 Sarad Kumar

Mishra3 and Vijai Kumar Gupta4

1

Department of Biotechnology Engineering, Ben Gurion University of the

Negev, Israel; 2Department of Dryland Agriculture and Biotechnology,

Ben Gurion University of the Negev, Israel; 3Department of Biotechnology,

Deen Dayal Upadhyay Gorakhpur University, India; 4Department of

Biochemistry, National University of Ireland Galway, Ireland

Abstract

Plant diseases are the primary cause of reducing both the quality and the quantity of crop yields. Numerous synthetic products have been used to control plant infections; however, overuse of such products has favoured the development of strains of pathogens that are resistant to fungicides. Unfortunately, the more exact the impact of a synthetic product on a pathogen, the more likely it is that the pathogen will develop resistance to it. In addition, the widespread use of fungicides produces undesirable effects on non-target organisms. Concerns about nature, human well-being and other related hazards resulting from the overuse of synthetic chemicals have led to considerable interest in developing eco-friendly methods of biocontrol against plant pathogens.

 

4: The Role of Bacillus Bacterium in Formation of Plant Defence: Mechanism and Reaction

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4 

The Role of Bacillus Bacterium in Formation of Plant Defence:

Mechanism and Reaction

Igor Maksimov* and Ramil Khairullin

Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa, Russia

Abstract

This review analyses data on the physiological and biochemical influence of rhizospheric and endophytic plant growth-promoting rhizobacteria (PGPR) from the genus Bacillus on mechanisms of resistance of plants and considers the possibility of their use in agriculture for protecting crops against pathogens and pests. Published results showed that some strains of Bacillus spp. elicit significant reduction of incidence or severity of various plant

­diseases. PGPR-promoted defence of plants develops as a result of their endosymbiotic interrelationships. This mechanism is directly achieved by the bacteria producing peptide antibiotics and hydrolases of chitin and glucan and also because the plants form their own system of induced systemic resistance (ISR), accompanied by changes in the balance of defensive proteins, hormones and pro-/antioxidant status.

 

5: Biofilm Formation on Plant Surfaces by Rhizobacteria: Impact on Plant Growth and Ecological Significance

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5 

Biofilm Formation on Plant Surfaces by Rhizobacteria: Impact on Plant Growth and Ecological Significance

Mohammad Musheer Altaf and Iqbal Ahmad*

Department of Agricultural Microbiology, Aligarh Muslim University, India

Abstract

Microorganisms have historically been studied as planktonic or free-swimming cells, but most exist as sessile communities attached to surfaces, in multicellular assemblies known as biofilms. Biofilms on plant surfaces are of great importance to plant health. Plant growth-promoting rhizobacteria (PGPR) not only induce plant growth but also provide protection by the process known as biocontrol, whereas other bacteria in the biofilm mode of growth can create a nuisance for plants. Recent advances show that biofilm formation on plant roots is associated with the biological and pathogenic response, but its regulation by the plant is unknown. In this chapter we

­describe bacterial biofilm processes, the ecological significance and the microbes that form biofilms on plant roots, and the effect of root exudates on biofilms and plant health.

 

6: Biofilmed Biofertilizers: Application in Agroecosystems

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6 

Biofilmed Biofertilizers:

Application in Agroecosystems

Udugama V.A. Buddhika,1 Gamini Seneviratne,1* Ekanayake M.H.G.S.

Ekanayake,1 Dasanayake M.N. Senanayake,1 Avanthi D. Igalavithane,1

Nirodha Weeraratne,1 Asgiri P.D.A. Jayasekara,2 Wilfred L. Weerakoon,3

Amila Indrajith,3 Herath M.A.C.Gunaratne,4 Rambandi K.G.K. Kumara,1

Meragalge S.D.L. De Silva5 and Ivan R. Kennedy6

1

National Institute of Fundamental Studies, Kandy, Sri Lanka; 2Tea Research

Institute of Sri Lanka, Hantana, Sri Lanka; 3Center for Sustainable Agriculture

Research and Development, Rajagiriya, Sri Lanka; 4Plenty Foods Private Limited,

Madatugama, Sri Lanka; 5Tea Research Institute of Sri Lanka, Talawakelle,

Sri Lanka; 6Faculty of Agriculture and Environment, University of Sydney, Australia

Abstract

Certain soil microbiota naturally exists as surface-­attached microbial communities in a biofilm mode of growth.

They have been shown to be more effective at functioning than monocultures or mixed cultures of microbes.

 

7: Microbial Nanoformulation: Exploring Potential for Coherent Nano-farming

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7 

Microbial Nanoformulation: Exploring

Potential for Coherent Nano-farming

Sandhya Mishra,1 Chetan Keswani,2 Akanksha Singh,1

Braj Raj Singh,3 Surya Pratap Singh2 and Harikesh Bahadur Singh1*

1

Department of Mycology and Plant Pathology, Banaras Hindu University,

Varanasi, India; 2Department of Biochemistry, Banaras Hindu University,

Varanasi, India; 3Centre of Excellence in Materials Science (Nanomaterials),

Aligarh Muslim University, India

Abstract

Recently nanotechnology has emerged as the sixth revolutionary technology after the green revolution of the

1960s and the biotechnology revolution of the 1990s. Today when agricultural scientists are facing major challenges such as reduced crop production, nutrient deficiency and climate change, nanotechnology has offered promising applications for precision farming. This innovative technology embraces wide applications such as plant disease control, enhanced nutrient uptake, improved plant growth and sustained release of agrochemicals.

 

8: Bacillus thuringiensis: a Natural Tool in Insect Pest Control

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8 

Bacillus thuringiensis: a Natural Tool in Insect Pest Control

Javier Hernández-Fernández*

Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia

Abstract

Bacillus thuringiensis is a Gram-positive, ubiquitous, spore-forming bacterium that produces large amounts of proteins that crystallize inside the cell during the sporulation stage known as B. thuriniensis delta-endotoxins or

Cry proteins. The insecticidal Cry proteins produced by B. thuringiensis have provided a particular, secure and

­effective tool for the control of a wide diversity of insect pests around the world for over 70 years. The Cry proteins are lethal to insect larvae in the orders Lepidoptera, Diptera and Coleoptera. More recently, isolates have been identified with activity against the organisms in the orders Hymenoptera, Homoptera, Orthoptera and Mallophaga and also nematodes, mites, lice and protozoa. Furthermore, in the global biopesticide market B. thuringiensis represents nearly US$600 million/year. At least 900 different Cry toxin sequences have been found and classified into 73 family groups (by 2014). Biotechnology and genetic manipulation of cry genes present in B. thuringiensis can potentially improve the efficacy and cost-effectiveness of B. thuringiensis-based commercial products. The combination of genes from different B. thuringiensis strains to enhance their activity, extend their host range and improve the spectrum of insecticidal activity has been achieved with recombinant technologies. These genetically modified B. thuringiensis products are currently commercially available. It has been recently established that Cry hybrid proteins of B. thuringiensis, gained by domain swapping, resulted in enhanced toxicities when compared with wild-type proteins. Nowadays, B. thuringiensis insecticidal genes have been included in several of the most important crop plants where they provide a model for biotechnology in agriculture. The B. thuringiensis transgenic crop has received more attention in cases where cry genes have been brought together by a mixture of mutagenesis and oligonucleotide synthesis to produce synthetic genes. In this chapter, manipulation of Cry proteins from the soil bacterium B. thuringiensis and its biotechnological applications are described. The future prospects are also discussed.

 

9: Pleurotus as an Exclusive Eco-Friendly Modular Biotool

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9 

Pleurotus as an Exclusive

Eco-Friendly Modular Biotool

Ram Naraian,1* Simpal Kumari1 and Siya Ram2

Department of Biotechnology, Mushroom Training and Research Centre

(MTRC), Veer Bahadur Singh ­Purvanchal University, Jaunpur, India;

2

School of Biotechnology, Gautam Buddha University, Greater Noida, India

1

Abstract

The basidiomycete genus Pleurotus, commonly known as the oyster mushroom, is a well estabilished and recognized model biotool for many biochemical and biotechnological activities. Members of this genus are naturally widespread in temperate and subtropical environments throughout the world as decomposers of wood. Pleurotus is capable of growing on a wide range of lignocellulosic substrates, including various agricultural and forest wastes. Pleurotus spp. possess a cassette of genes producing important metabolites including lignocellulolytic

­enzymes which enables this group of fungi to be used as an ‘eco-friendly biotool’ for biodegradation, bioremediation, production of multipurpose enzymes, food derivatives, medicinal products, animal fodder, compost and an agent of biobleaching. This chapter compiles comprehensive and detailed accounts of several of the aforementioned activities. As a result of its remarkable characteristics, this fungus has now become an important biotool and the choice of biotechnologists for use as a model employed in innovative research studies, industries and various fields from the laboratory bench to large-scale activities.

 

10: Use of Biotechnology in Promoting Novel Food and Agriculturally Important Microorganisms

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10 

Use of Biotechnology in Promoting

Novel Food and Agriculturally

Important Microorganisms

Duraisamy Saravanakumar and Neela Badrie*

Department of Food Production, The University of the West Indies,

St Augustine, Trinidad and Tobago

Abstract

This chapter reviews the various applications of microbes in agriculture, characterization of novel microbial genes and enzymes useful in food and agriculture, and biotechnological tools used to augment the activity of microbes and their products. Microorganisms have many associations with plant communities such as commensalism, synergism, mutualism and antagonism. Some of these associations result in beneficial interactions between plants and microorganisms for various purposes, such as promotion of plant growth, guarding the plant from other harmful interactions and production of safer foods which are free from inorganic chemicals. In addition, microorganisms have been studied for their vital roles in various food production and fermentation industries. The utility of microorganisms demonstrated so far in the field of food and agriculture necessitates further characterization and identification of novel microbes and the untapped potential use of their enzymes and gene products. The availability of various traditional and classical approaches aid in the identification and characterization of microbes to some extent, however, conspicuously the advent of biotechnology has opened up many more techniques that can be used to characterize and promote agriculturally important beneficial microorganisms.

 

11: Endophytes: an Emerging Microbial Tool for Plant Disease Management

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11  Endophytes: an Emerging Microbial

Tool for Plant Disease Management

Dipali Majumder,1 Binalata Kangjam,1 Kongbrailatpam J. Devi,1 Domesticity

Lyngdoh,1 Janshame Tariang,1 Dwipendra Thakuria2 and Aakash Goyal3*

1

School of Crop Protection, Central Agricultural University, Umiam, India; 2School of Natural Resources Management, Central Agricultural University, Umiam, India;

3

International Center for Agricultural Research in the Dry Areas (ICARDA),

Rabat, ­Morocco

Abstract

In 1884, de Barry first used the term ‘endophyte’ to define bacteria or fungi that occur within asymptomatic plant tissues. Endophytes include bacteria, fungi and actinomycetes. These microorganisms live inside plant tissues for part of their life cycle or for their entire lifespan without showing their presence as the plants do not express any visible symptoms. They offer great-untapped potential, which can be exploited to maintain healthy crops. They exist inside living plant tissues in different relationships, such as symbiotic relationships where both the partners get benefit or as antagonistic relationships in which the growth of one partner is suppressed while the growth of the other is favoured. Endophytes have been reported as potential antagonists against several plant pathogens. The potential to colonize internal host tissues for the benefit of crop growth and disease suppression have made endophytes an important component to improve crop performance. Novel endophytes are also directly associated with the production of secondary natural products or with the processes involved. Therefore identification, understanding interactions and utilization of novel endophytes or their products to enhance crop productivity and for management of plant diseases are an integral part of sustainable agricultural production.

 

12: Role of Listeria monocytogenes in Human Health: Disadvantages and Advantages

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12 

Role of Listeria monocytogenes in Human Health: Disadvantages and Advantages

Javed A. Khan,1,2* Ram S. Rathore,2 Shaheen Khan,3

Fohad M. Hussain1 and Iqbal Ahmad1

1

Department of Agricultural Microbiology, Aligarh Muslim University, India; 2Indian

Veterinary Research Institute (IVRI), Izatnagar, India; 3Department of Biotechnology,

Doon (PG) Paramedical College and Hospital, Dehradun, India

Abstract

The genus Listeria consists of eight species: Listeria monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, Listeria welshimeri, Listeria grayi, Listeria rocourtii and Listeria marthii. Among Listeria species only

L. monocytogenes and L. ivanovii are pathogenic to humans and animals. Unlike L. monocytogenes which causes listeriosis in humans and animals L. ivanovii is solely an animal pathogen. The bacterium may be rod shaped, coccoid or filamentous depending on nutrients, environmental and cultural conditions. Among pathogenic bacteria L. monocytogenes is atypical as it has the ability to survive and grow in a broad temperature range

 

13 Natural Weapons against Cancer from Bacteria

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13 

Natural Weapons against Cancer from Bacteria

Smriti Gaur*

Jaypee Institute of Information Technology, Noida, India

Abstract

Cancer is an enduring disease responsible for numerous deaths worldwide. Currently resistance towards anticancer drugs and the side effects of chemotherapy are a major problem in the treatment of cancer, so there is an increased requirement for new effective antitumour agents that are active against fatal tumours but with fewer side effects. It has been known for more than two decades that there are a large number of natural compounds secreted by bacteria that exhibit anticancer activity. These alternative microbial agents can be exploited as antitumour agents. Antitumour compounds isolated from marine bacteria and the anticancer activity of lactic acid bacteria are particularly promising. This chapter presents an overview of the major compounds produced by bacteria that have potential as therapeutic agents in the treatment of cancer.

 

14: Giardia and Giardiasis: an Overview of Recent Developments

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14 

Giardia and Giardiasis: an Overview of Recent Developments

Sandipan Ganguly* and Dibyendu Raj

National Institute of Cholera and Enteric Diseases, Kolkata, India

Abstract

Giardia lamblia is one of the most common protozoan enteric pathogens that inhabits the upper small intestine of humans and several other vertebrates and causes giardiasis. Global prevalence of giardiasis has been estimated to be 300 million cases annually. To adapt in environments both inside and outside the small intestine of the host, this protozoan parasite undergoes significant developmental changes during its life cycle. It has been confirmed that G. lamblia has become drug resistant and biochemical studies have been undertaken to investigate the cause of resistance. This chapter focuses on the most current findings regarding the important advances in understanding the molecular mechanisms that regulate the antigen switching process, including oxidative stress and expressional modifications in Giardia, and potential drug targets for the treatment of giardiasis are discussed.

 

15: Power of Bifidobacteria in Food Applications for Health Promotion

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15 

Power of Bifidobacteria in Food

Applications for Health Promotion

Quang D. Nguyen,* Szilárd Kun, Erika Bujna, Petra Havas,

Ágoston Hoschke and Judit M. Rezessy-Szabó

Department of Brewing and Distilling, Corvinus University of Budapest, Hungary

Abstract

Bifidobacteria are the predominant bacteria in the normal intestinal biota of healthy breast-fed newborns (more than

95% of the total bacterial population), and represent approximately 20% of the microbiota in the gastrointestinal tract of adults. Nowadays, these bacteria are the second most commonly used microorganisms in the production of probiotic food products after members of the genus Lactobacillus. Bifidobacteria have been i­ntensively studied for the prevention and treatment of human and/or animal gastrointestinal disorders, such as colonic transit disorders, intestinal infections, colonic adenomas and cancer. The market of probiotic foods (an important segment of functional foods) is estimated to increase annually by about 6.8% from 2013 to 2018 and has an estimated total sales value of US$44.9 billion in 2018. This chapter focuses on the general characteristics and health effects of bifidobacteria as well as on potential applications of these bacteria in the production of different food products.

 

16: Probiotics and Dental Caries: a Recent Outlook on Conventional Therapy

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16 

Probiotics and Dental Caries: a

Recent Outlook on Conventional Therapy

Sarika Amdekar,1 Rakesh Kumar Patidar,1 Avnish Kumar,2

Vivek Kumar Shrivastav,3 Navneet Swargiri4 and Vinod Singh1*

1

Department of Microbiology, Barkatullah University, Bhopal, India;

2

Department of Biotechnology, Dr B.R. Ambedkar University,

Agra, India; 3Cancer Hospital and Research Institute, Gwalior,

India; 4Oil Hospital, Duliajan, India

Abstract

In the oral cavity several hundred species of microbe reside harmoniously. However, sometimes microorganisms that can cause inflammation and infection and induce demineralization of dental enamel can flourish. Such infection can destroy the dentin and the connective tissue of the tooth. Remedies include restoration, endodontic therapy and removal of the damaged tooth. These methods are not conclusively proved to be the best methods for preventing new primary caries or for treating secondary caries. Use of probiotic Lactobacillus spp. and Bifidobacterium spp. in treating or preventing dental caries and other related problems can change the conventional therapy of drilling, filling and billing. The mechanism of action of probiotic bacteria in the oral cavity may be direct, for example by replacing the pathogenic flora by competing for the adhesion site, nutrients and growth requirements and producing antimicrobial agents, thereby inhibiting growth of the pathogen. Some indirect mechanisms of action include: (i) modulating the systemic immune function; (ii) the effect on local immunity; (iii) the effect on non-immunologic/non-specific defence mechanisms; (iv) prevention of plaque formation by neutralizing free electrons and production of antioxidants; and (v) modifying the surrounding environment.

 

17: Human Microbiota for Human Health

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17 

Human Microbiota for Human Health

Maddur P. Raghavendra,1 Mudili Venkataramana,2 Basappa,3

Kesthur S. Girish4 and Siddaiah Chandranayaka5*

1

Maharani’s Science College for Women, Mysore, India; 2DRDO-BU

Centre for Life Sciences, Coimbatore, India; 3Department of Chemistry,

Bangalore University, India; 4Department of Studies in Biochemistry,

University of Mysore, India; 5Department of Studies in Biotechnology, University of Mysore, Mysore, India

Abstract

Microorganisms are considered to be absent in the human foetus during early development in the mother’s womb, but later after delivery the numbers of microbes exceeds the number of total human cells. This human microbiota has tremendous influence on human physiology, development, nutrition, immunity and resistance to pathogens and is also known to be associated with normal development and function of the mucosal and gut immune system. In health the microorganisms contribute to effective metabolism by producing enzymes such as

 

18: Biotechnological Production of Polyunsaturated Fatty Acids

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18 

Biotechnological Production of

Polyunsaturated Fatty Acids

Ederson R. Abaide, Juliana Bastos, Valeria Dal Prá, Lisiane de Marsillac Terra, Raquel C. Kuhn and Marcio A. Mazutti*

Department of Chemical Engineering, Federal University of Santa Maria, Santa Maria, Brazil

Abstract

The market for omega-3 fatty acids or polyunsaturated fatty acids (PUFAs) for biodiesel production is continuously increasing. The main source of omega-3 fatty acids is from the extraction of oil from cold-water fish that usually inhabit deep-water environments, whereas biodiesel is produced from vegetable oils. Microbial oil can be an interesting alternative for the production of PUFAs. This chapter reviews the production, extraction, chemical characterization and future trends on microbial oil production for applications in the food, pharmaceutical and chemical industries. From the analysis of several studies available in the literature, it has been shown that the production of lipids by the biotechnological route can be an effective way to complement the production of fatty acids for biodiesel production or to substitute the traditional extraction of fish oil for production of PUFAs. However, more technologies should be developed to enable the industrial production of microbial lipids.

 

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