Current Developments in Biotechnology and Bioengineering: Filamentous Fungi Biorefinery

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Current Developments in Biotechnology and Bioengineering
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Contributors
Preface
World of fungi and fungal ecosystems
	Introduction
	Fungal morphology
		General aspects of reproduction
		Fungal nutrition
			Nutrient uptake
	Lifestyles of fungi
	Taxonomy of fungi
	Fungal diversity
	Fungal ecosystems
		Terrestrial ecosystems
		Aquatic ecosystems
		Extremophile environments
	Applications of fungi in biorefineries
	Conclusions and perspectives
	References
Fungal biotechnology
	Introduction
	Fungal cultivation and requirements
		Fungal cultivation medium
			Growth chemical requirements
			Design and preparation of culture medium
		Fungal fermentation process
			Inoculum preparation
			Types of fermentation processes
		Effects of process variables on growth and product formation
	Fungal biorefineries
		Fungal biorefinery-based industries
			Agriculture
			Food and feed
			Pharmaceutical
			Pulp and paper
			Textile
			Biotechnological industries for biofuels, biochemical, and biomaterial production
		Adding value to organic wastes through fungi
		Strategies to improve investment and productivity in fungal biorefineries
	Fungal metabolites
		Ascomycetes
			Ethanol
			Citric acid
			Gluconic acid
			Itaconic acid
		Zygomycetes
			Ethanol
			Lactic acid
			Fumaric acid
		Basidiomycetes
			Ethanol
		Pigments and enzymes
	Fungal biomass
		Ascomycetes
			Human food
			Animal feed
		Zygomycetes
			Food and feed applications
			Chitosan
		Basidiomycetes
	Conclusions and perspectives
	References
Fungal biology
	Introduction
	The fungal world
		Growth of fungi
		Nutrition and transport in fungi
		Fungal reproduction
			Unicellular yeast form
			Chytridiomycota
			Zygomycota
			Glomeromycota
			Ascomycota
			Basidiomycota
		Metabolic and genetic complexity in fungi
		Genome
	Classification of fungi
		Opisthosporodia
		Aphelidea
		Rozellidea
		Microsporidia
		Chytridomycota (Chytrids)
			Chytridiomycetes
				Batrachochytrium dendrobatidis
			Monoblepharidomycetes
		Neocalimastigomycota
			AGF protein domains and homologous genes
		Blastocladiomycota
		Zygomycetous fungi
		Zoopagomycota
			Entomophthoromycotina
			Zoopagomycotina
			Kickxellomycotina
		Glomeromycota
		Mucoromycota
			Mortierellomycotina
			Mucoromycotina
		Dikarya
			Ascomycota
			Basidiomycota
	Conclusions and perspectives
	Acknowledgments
	References
Mycotoxins
	Introduction
	Major groups of mycotoxins: chemistry and processing stability
	Occurrence of mycotoxins in food
		International regulation
	Toxigenic fungi and factors affecting mycotoxins production
		Intrinsic factors
		Extrinsic factors
	Prevention and reduction of mycotoxins
		Prevention of mycotoxins
			Good agricultural practices
			Controlling the fungi growth and the storage condition
			Networking
		Reduction of mycotoxins
			Reduction by physical methods
			Reduction by biological methods
			Reduction by chemical methods
	Detection and determination of mycotoxins
		Detection and determination by the spectrometric method
		Detection and determination by chromatographic method
		Advance technology
	Conclusions and perspectives
	References
Sampling, preservation, and growth monitoring of filamentous fungi
	Introduction
	Applications of filamentous fungi
	Isolation, identification, and sampling of filamentous fungi
		Isolation and purification of filamentous fungi
			Spore isolation
			Isolation of single spore
			Sampling and isolation of filamentous fungi from environments
			Sampling and isolation of filamentous fungi from fermented products
		Sampling procedures for filamentous fungi
		Identification of filamentous fungi
	Preservation of filamentous fungi
		Short-term preservation
		Long-term preservation
			Cryopreservation of filamentous fungi
			Freeze drying of filamentous fungi
		Quality control of preserved filamentous fungi
	Growth monitoring of filamentous fungi
		Direct methods for biomass evaluation
			Gravimetric method
			Cell count
			Optical density
			Imaging and microscopy
			Impedance and capacitance techniques
			Fluorescence techniques
			Near-infrared spectroscopy technique
		Indirect methods for biomass evaluation
			Adenosine triphosphate measurement
			Chitin measurement
			Calorimetric measurement
			CO2 production and oxygen uptake rate
	Conclusions and perspectives
	Acknowledgments
	References
Industrial wastes as feedstock for filamentous fungi growth
	Introduction
	Microbiology of filamentous fungi
	Diversity of filamentous fungi
	Wastes, residuals, and wastewater as nutrients
	Role of filamentous fungi in pollution reduction
	Removal of microplastic using filamentous fungi
	Conclusions and perspectives
	References
	Further reading
Filamentous fungal morphology in industrial aspects
	Introduction
	Industrial bioprocess with filamentous fungi
	Important factors for industrialization of bioprocess with filamentous fungi
		Strain screening and inoculum
		Morphology
		Rheology
	Applications of filamentous fungi in pulp and biofuel industries
		Pulp industry
			Bio-debarking
			Bio-pitching
			Bio-retting
			Biopulping
			Biobleaching
		Biofuels industry
	Conclusions and perspectives
	References
	Further reading
Bioreactors and engineering of filamentous fungi cultivation
	Introduction
	Engineering fundamentals in bioreactor design
		Medium viscosity and rheology
		Power consumed for agitation
		Medium aeration and kLa
		Shear forces and shear stress
	Traditional bioreactor designs for filamentous fungi cultivation
		Mechanically agitated stirred tank reactor
		Bubble columns
		Air-lift reactor
		Trickle-bed bioreactor
		Packed-bed bioreactor
		Fluidized-bed bioreactor
		Rotating-bed bioreactor
	Main reactor designs in solid-state fermentation processes
		Tray-like bioreactors
		Rotating/stirred drum
	Filamentous fungi morphology and reactor design
		Life cycle of filamentous fungi
		Macromorphology of filamentous fungi in submerged fermentations
		Link between morphology and productivity
		Effect of different reactor designs on morphology
			Stirred tank reactors
			Other designs
		Tailoring filamentous fungi morphology: Future perspectives
	Conclusions and perspectives
	Acknowledgments
	References
Filamentous fungi processing by solid-state fermentation
	Introduction
	Main filamentous species and substrates
	Bioreactors and process control parameters: Critical aspects
		Biological factors
		Physicochemical factors
			Moisture content and water activity
			Temperature
			pH
			Aeration
			Particle size
		Mechanical factors
			Agitation
		Heat and mass transfer in SSF
		Bioreactors
	Products and current industrial applications
		Enzymes
		Organic acids
			Citric acid
			Lactic acid
			Succinic acid
		Bioactive compounds/secondary metabolites
			Pigments
			Phenolic compounds
			Antibiotics
		Biological control agents/biopesticides
		Biofuels
			Biodiesel
			Bioethanol
		Biosurfactants
		Biopolymers
		Other secondary metabolites
			Phytostimulatory hormones
			Aroma
			Polyunsaturated fatty acids
	Conclusions and perspectives
	References
Production of industrial enzymes by filamentous fungi
	Introduction
	Applications of industrial enzymes
	Advantages of enzymes production by filamentous fungi
	Filamentous fungi in enzymes production
		Aspergillus
		Fusarium
		Penicillium
		Rhizopous
		Trichoderma
	Platforms for enzymes production by filamentous fungi
		Solid-state fermentation for enzymes production by filamentous fungi
		Submerged fermentation for enzymes production by filamentous fungi
		Comparison between solid-state and submerged fermentation in enzymes production by filamentous fungi
	Challenges for the development of industrial enzymes production by filamentous fungi
		Troubles in oxygen supply
		Toxin production
		Production and secretion of endogenous proteases and peptidases
		Lack of sufficient information
	Strategies to improve enzymes production by filamentous fungi
		Filamentous fungi morphology in enzymes production
		Agitation
		Fungal mycelia immobilization
		Feeding strategies and cultivation mode
		Fermentation pH
		Cultivation media
		Engineering of filamentous fungi
	Heterologous protein expression in filamentous fungi
	Economic aspects and filamentous fungal enzymes market
	A roadmap toward future research on filamentous fungal enzymes production
	Conclusions and perspectives
	References
Production of bioactive pigmented compounds by filamentous fungi
	Introduction
	New non-mycotoxigenic fungal work horses for the production of polyketide pigments as food colorants
	Focus on azaphilones
		Toward mycotoxin-free Monascus red
		Monascus-like pigments from non-toxigenic fungal strains
	Fungal hydroxyanthraquinoid (HAQN) pigments as potential food colorants
	Focus on anthraquinones
		Fungal natural red
		Other fungal anthraquinones
	Fungi from marine ecological niches as novel sources of chemically diverse pigments
	Conclusions and perspectives
	Acknowledgments
	References
Filamentous fungi for food
	Introduction
	Filamentous fungi as protein source
		Protein quality of various protein sources
		Proteins and environmental concerns
		Smart proteins
	Filamentous fungi in food applications
		Fungal filaments vs mushrooms
		Fermented food using filamentous fungi
			Tempe
			Soy sauce
			Oncom
		Natural food additives and metabolites from filamentous fungi
			Natural colorant from filamentous fungi
			Flavor enhancer from filamentous fungi
			Enzymes from fungi
			Other food ingredients
		Fungal mycelium-based food
	Nutritional consideration
		Proteins
		Vitamins
		Lipid
		Other health aspects/functional properties
	Safety of fermented foods using filamentous fungi
		Mycotoxins
		Other harmful contaminants
		Pathogenic bacteria in fermented food
	Industrial production of filamentous fungi-based food
		Traditional processes of food from filamentous fungi
			Tempe
			Soy sauce
		Modern processes
			Modern process of tempe production
			Production of Quorn
	Conclusions and perspectives
	Acknowledgment
	References
Filamentous fungi as animal and fish feed ingredients
	Introduction
	Animal compound feed
		Fishmeal
		Economic and environmental aspects of fishmeal as feed ingredient
		Alternatives to the fishmeal
	Single-cell proteins (SCPs)
	Fungi kingdom
	Fungal biomass composition as animal feed nutrient
		Protein and amino acid profile
		Fat and fatty acid content
			Arachidonic acid (AA)
			Linoleic acid (LA)
			Alpha linolenic acid (ALA)
			Oleic acid
		Cell wall components
			Glucans
			Chitin
			Chitosan
			Mannose
		Minerals
		Pigments
		Antioxidant agents
		Vitamins
		Nucleotides
		Prebiotics
	Animal feed
	Applications of fungal biomass as feed
	Economic and environmental aspects
	Conclusions and perspectives
	Acknowledgments
	References
Production of alcohols by filamentous fungi
	Introduction
	Feedstocks for fermentative production of alcohols
	Production of ethanol by filamentous fungi
		Production of ethanol by zygomycetes
		Production of ethanol by ascomycetes
	Metabolic engineering of filamentous fungi for production of ethanol
	Ethanol recovery and concentration
	Fermentative production of butanol
	Conclusions and perspectives
	References
Biological production of organic acids by filamentous fungi
	Introduction
	Itaconic acid
		Microorganisms, metabolism, and physiology of itaconic acid biosynthesis
		Production and process conditions
		Strain engineering and process modifications
	Gluconic acid
		Microorganisms, metabolism, and physiology of gluconic acid biosynthesis
		Production and process conditions
		Strain engineering and process modifications
	Citric acid
		Microorganisms, metabolism, and physiology of citric acid biosynthesis
		Production and processing conditions
		Genetic and process engineering strategies
	Oxalic acid
		Microorganisms, metabolism, and physiology of oxalic acid biosynthesis
		Production and process conditions
		Strain engineering and process modifications
	Conclusions and perspectives
	Acknowledgments
	References
Production of antibiotics by filamentous fungi
	Introduction
	History
	Filamentous fungi producing antibiotics
	Production of antibiotics
		Isolation and screening of microbes
		Antimicrobial assay
		Fermentation process
			Submerged fermentation (SmF) for the production of antibiotics
			Solid-state fermentation (SSF) for the production of antibiotics
		Extraction and purification
		Refining
		Quality control
	Examples of fungal antibiotics
		Penicillin
			Mode of action
		Cephalosporin
			Mode of action
		Fusidane
			Mode of action
		Asperchondols
		Aspochalasin
		Aspergillin
		Fumagillin
		Claviformin
		Tropolone derivative
		Other antibiotics from filamentous fungi
		Metabolic engineering
			Targeted approaches
			Untargeted approaches
			Metabolomics approaches
	Conclusions and perspectives
	Acknowledgment
	References
Production of fungal biopolymers and their advanced applications
	Introduction
	Fungal cell wall
	Fungal cell wall polysaccharides
	Effect of growing conditions on production of fungal polysaccharides
	Extraction and purification of fungal biopolymers
		Fungal chitin-glucan and chitin
		Fungal chitosan
	Applications of fungal biopolymers
		Bioemulsifiers and biosurfactants
		Wound healing materials
		Tissue engineering
		Antimicrobial and preserving agent
		Textiles (textile fibers, nonwoven textiles, and leather like materials) and paper like materials from fungi
		Biocomposites for construction and packaging applications
		Other applications of fungal biopolymers
	Conclusions and perspectives
	References
Versatility of filamentous fungi in novel processes
	Introduction
	Brewery waste
	Fruit industry waste
	Bioethanol industry wastes
	Fish processing industry waste
	Oil processing industry waste
		Olive oil processing industry
		Palm oil processing industry
	Potato processing industry waste
	Sugar processing industry waste
	Dairy processing industry
	Conclusions and perspectives
	Acknowledgments
	References
Index
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	C
	D
	E
	F
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	H
	I
	J
	K
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	M
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	O
	P
	Q
	R
	S
	T
	U
	V
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	X
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