Recent Advancements in Microbial Diversity

✍ Scribed by Surajit De Mandal (editor), Pankaj Bhatt (editor)

• Publisher: Academic Press
• Year: 2020
• Tongue: English
• Leaves: 623
• Edition: 1
• Category: Library

✦ Synopsis

Microorganisms are a major part of the Earth’s biological diversity. Although a lot of research has been done on microbial diversity, most of it is fragmented. This book creates the need for a unified text to be published, full of information about microbial diversity from highly reputed and impactful sources. Recent Advancements in Microbial Diversity brings a comprehensive understanding of the recent advances in microbial diversity research focused on different bodily systems, such as the gut. Recent Advancements in Microbial Diversity also discusses how the application of advanced sequencing technologies is used to reveal previously unseen microbial diversity and show off its function.

✦ Table of Contents

Cover
Front-matter
Copyright
Contents
Contributors
Chapter 1 - Biodiversity of microbial life: Indian Himalayan region
1 - Introduction
2 - Microbial diversity of IHR region
2.1 - Distribution and types
2.2 - Conditions
2.3 - Importance
3 - Indian Himalayan region (IHR): psychrophilic microorganisms
3.1 - Habitat
3.2 - Taxonomy of psychrophiles
4 - Applications of psychrophilic microbes
5 - Diversity of aquatic microorganisms in IHR
6 - Challenges for micro-diversity conservation
7 - Factors responsible for functioning of ecosystem of Indian Himalaya
8 - Conclusion and future vision
References
Chapter 2 - Microbial endophytes of plants: diversity, benefits, and their interaction with host
1 - Introduction
2 - Isolation of endophytes
3 - Biodiversity of endophytic microorganism
4 - Plant-microbe interactions and benefits to the plant
4.1 - Phytostimulation
4.2 - Pigment production
4.3 - Endophytes as a source of bioactive and novel compounds
4.4 - Enzyme production
4.5 - Role of endophytes in the field of biodegradation/bioremediation
4.6 - Endophytes with multiple roles
5 - Conclusion
References
Chapter 3 - A spotlight on the recent advances in bacterial plant diseases and their footprint on crop production
1 - Introduction
2 - Bacterial communities
2.1 - Bacterial community association
2.1.1 - With leaves
2.1.1.1 - Leaf spots
2.1.1.2 - Leaf blights
2.1.2 - With root
2.1.2.1 - Hairy root disease
2.1.2.2 - Granville wilt
2.1.2.3 - Root rot disease
2.1.3 - With fruit
2.1.3.1 - Fire blight disease
2.1.3.2 - Bacterial spot of stone fruits
2.1.4 - With bark
2.1.4.1 - Bacterial canker
2.1.4.2 - Bacterial wet wood
2.1.4.3 - Bamboo wilt disease
3 - Mechanisms of bacterial plant disease
3.1 - Overview of bacterial virulence factors
3.1.1 - Secreted proteins
3.1.2 - Small molecules as virulence factors
4 - Impact of bacterial disease in crop production
4.1 - Impact of bacterial disease on vegetables
4.2 - Impact of bacterial disease on cereal crops
4.3 - Impact of bacterial disease on Pulses
4.4 - Impact of bacterial disease on fruits
5 - Bacterial disease detection methods
5.1 - Direct methods
5.2 - Indirect methods
5.3 - Computational techniques
6 - Bacterial disease management and resistance
6.1 - Use of copper and antibiotics
6.2 - Biocontrol
6.3 - Antimicrobial peptides, SAR and induced systemic resistance (ISR)
7 - Recent techniques to overcome plant diseases
7.1 - Gene transfer
7.2 - Transcriptomics
7.3 - Genome editing
7.4 - RNA interference
7.5 - Proteomics
7.6 - Metabolomics
7.7 - Tissue culture as an approach for managing plant diseases
8 - Conclusion
References
Chapter 4 - Bacterial diseases of banana: detection, characterization, and control management
1 - Background
2 - Bacterial diseases of banana
3 - Isolation and identification of the causal bacterial agents of the diseased banana
4 - Control management
4.1 - Before planting
4.2 - During growth
4.3 - Chemical control
4.4 - Biological control
References
Chapter 5 - Toward an enhanced understanding of plant growth promoting microbes for sustainable agriculture
1 - Introduction
2 - Microbial communities
2.1 - Plant growth promoting rhizobacteria (PGPR)
2.2 - Plant growth-promoting fungi
2.2.1 - Arbuscular mycorrhizal fungi (AMF)
2.3 - Plant growth promoting algae
2.4 - Plant growth promoting protozoa
3 - Mechanistic approach of various PGPMs
3.1 - Siderophore production
3.1.1 - Siderophore production in gram-negative bacteria
3.1.2 - Siderophore production in gram-positive bacteria
3.2 - Phosphate solubilization
3.2.1 - Inorganic phosphate solubilization by PSM
3.2.2 - Organic phosphorus mineralization
3.3 - Phyto-hormone production
3.3.1 - Auxin
3.3.2 - Cytokinin
3.3.3 - Abscisic acid
3.3.4 - Gibberlic acid
3.3.5 - Ethylene
3.4 - Biological nitrogen fixation (BNF)
3.5 - Ammonia and hydrogen cyanide production
3.6 - Antibiotics and lytic enzymes
3.7 - Competition
4 - Applications of PGPMs
4.1 - As biofertilizers: for sustainable agriculture
4.2 - As soil fertility enhancers
4.3 - As phytoextractors and bioremediators
4.4 - As biofortifying agents: improving food quality
4.5 - As stress managers
4.6 - As phytostimulators
4.7 - As disease control agent
5 - Conclusion
References
Chapter 6 - Multifaceted beneficial effects of plant growth promoting bacteria and rhizobium on legume production in hill a...
1 - Introduction
2 - Rhizobium- legume symbiotic relationship
3 - Rhizobium-legume symbiosis: mechanism
4 - Legume –rhizobium interaction: advantages to non-legumes
5 - PGPR and its effect on rhizobial-legume interaction
6 - Effect of PGPRs on rhizobial- legume interaction
7 - Establishment of additional infection sites
8 - Release of plant growth-promoting substances
9 - Biological nitrogen fixation (BNF)
10 - Decreasing ethylene level (ACC deaminase)
11 - Nutrient solubilisation and its uptake by plants
12 - Siderophore production
13 - Biological control
14 - Improved water-use efficiency
15 - Conclusion
16 - Future perspectives
References
Chapter 7 - Role of rhizospheric microbial diversity in plant growth promotion in maintaining the sustainable agrosystem at...
1 - Introduction
2 - Microbial diversity at high altitude regions
3 - Microbial adaptations in cold high altitude regions
3.1 - Mechanisms involved in the endurance of cold
3.1.1 - Cell membrane-associated changes
3.1.2 - Cryoprotectants
3.1.3 - Cold acclimation proteins
3.1.4 - Cold-shock proteins
3.1.5 - Role of ice nucleators and antifreeze proteins
3.1.6 - Cold-adapted enzymes
3.1.7 - Role of RNA degradosomes
3.1.8 - Other substances
4 - Plant-microbes (PM) interaction
5 - The role of rhizosphere microorganisms in hilly agricultural area
6 - Enhancement of growth and yield of crops grown in hilly areas
7 - Mechanisms involved in plant growth promotions
7.1 - Biological nitrogen fixation
7.2 - Phosphate, potassium and zinc solubilization
7.3 - Phytohormone production (IAA production)
7.4 - ACC deaminase activity
7.5 - Siderophore
7.6 - Biocontrol activity
7.7 - HCN production
8 - Biofertilizers as a tool for sustainable agriculture
9 - Use of carriers for biofertilizers production
10 - Liquid bio-inoculums as biofertilizers
11 - The current status of effectiveness of bioinoculants developed from native PGPM
12 - Conclusion
References
Chapter 8 - Microbes adapted to cold and their use as biofertilizers for mountainous regions
1 - Introduction
2 - Mechanism of plant growth promotion at low temperature
2.1 - Phytostimulation and production of phytohormones
2.1.1 - Indole acetic acid
2.1.2 - ACC-deaminase
2.1.3 - HCN production
2.2 - Siderophore production
2.3 - Phosphate solubilization
2.4 - Nitrogen fixation
2.5 - Ice– bacteria for frost management
3 - Conclusion
References
Chapter 9 - Actinobacteria: diversity and biotechnological applications
1 - Introduction
2 - Occurrence and habitats
2.1 - Soil habitat
2.2 - Plant habitat
2.3 - Marine habitat
3 - Diversity of actinobacteria
4 - Biotechnology and importance of actinobacteria
5 - Actinobacteria as a source of natural products
5.1 - As a source of antibiotics
5.2 - As a source of insecticides
5.3 - As a source of bioherbicide and bioinsecticide agents
5.4 - As a source of antifungal and antibacterial agents
5.5 - Immunomodifers
6 - Actinobacteria as a source of enzymes
6.1 - Amylase
6.2 - Cellulase
6.3 - Xylanases
6.4 - Pectinases
6.5 - Proteases
6.6 - Chitinases
7 - Other aspects of actinomycetes having biotechnological applications
8 - Conclusion
References
Chapter 10 - Quorum sensing: the microbial linguistic
1 - The world of microbes
2 - Overview of Quorum sensing: social engagement of microbes
3 - Mechanism of Quorum sensing
3.1 - Quorum sensing in Gram-negative bacteria
3.2 - Quorum sensing in Gram-positive bacteria
4 - Biofilm: a shield against the challenging environment
4.1 - What are biofilms?
4.2 - How many archaea and bacteria live in biofilms?
4.3 - Archaeal biofilm production
4.3.1 - Archaeal biofilm and humans
4.3.2 - Cell-cell communication and signaling in archaea
5 - Applications of Quorum sensing
5.1 - Engineered QS system
5.2 - Biosensor
5.3 - Pathogen diagnostics and therapeutics
5.4 - Biocontrol
5.5 - Prevention of biofouling
5.6 - Biofilm in wastewater treatment
6 - Conclusion
References
Chapter 11 - Exploration of microbial communities of Indian hot springs and their potential biotechnological applications
1 - Introduction
2 - Hot springs: formation and distribution
2.1 - Formation
2.2 - Distribution
3 - India: a hot spring hub
4 - Microbial diversity of Indian hot springs
4.1 - Microbial diversity analysis via culture-dependent method from Indian hot springs
4.2 - Microbial diversity analysis via culture-independent method from Indian hot springs
5 - Biotechnological applications of thermophiles
6 - Conclusion
References
Chapter 12 - Microbial diversity and functional potential in wetland ecosystems
1 - Introduction
2 - Microbial communities in wetland
2.1 - Techniques to analysis the microbial communities in wetland
2.2 - Microbial diversity in wetland
2.2.1 - Archaeal diversity in wetland
2.2.2 - Bacterial diversity in wetland
2.2.3 - Fungal diversity of wetlands
2.2.4 - Algal diversity in wetlands
3 - Biogeochemical transformations driven by microbes in wetlands
3.1 - Methanogenesis in sediments of wetland
3.2 - Methane oxidation
3.3 - Sulfate cycle in wetland
3.4 - Metal reduction
3.5 - Denitrification
3.6 - Fermentation
3.7 - Role of phosphate solubilising bacteria in wetland
4 - Conclusion
Reference
Chapter 13 - Effect of climate change on microbial diversity and its functional attributes
1 - Introduction
2 - Climate change and its causes
3 - Impacts of climate changes on microbial diversity
3.1 - Terrestrial biome
3.2 - Aquatic ecosystem
4 - Conclusion
References
Chapter 14 - Spatial variation of the microbial diversity in the mangrove dominated Sundarban Forest of India
1 - Indian Sundarbans at a glance
2 - Physiography of the area
3 - Microbial diversities in Sundarban Biosphere Reserve (SBR)
4 - Study approach
5 - Results
6 - Discussion
7 - Future prospective
References
Chapter 15 - Microbe assisted plant stress management
1 - Introduction
1.1 - Salt stress
1.2 - Drought stress
1.3 - Flooding
1.4 - Nutrient stress
1.5 - Metal and other contaminants
2 - Fungi for mitigation of plant abiotic stress
3 - Microbes in mitigating biotic stresses
4 - Mechanisms of plant stress management through microbes
4.1 - Plant stress and ethylene
4.1.1 - ACC deaminase lowering of stress ethylene
4.1.2 - ACC deaminase
4.1.3 - ACC deaminase regulation
4.2 - Cellular level adaptation in microbes for abiotic stress
5 - Conclusion
References
Chapter 16 - Insect gut microbiome and its applications
1 - Introduction
2 - Structure of insect gut
3 - The gut as a medium for microbial colonization
4 - Insect gut symbionts
5 - Role of insect symbiotic microbiota
6 - Methods to investigate insect gut microbiome
6.1 - Metagenomics strategies
7 - The microbiome of common insects gut
7.1 - Cockroach
7.2 - Nematodes
7.3 - Aphids
8 - Applications of insect gut microbiome
8.1 - Cellulose and xylan hydrolysis
8.2 - Signal mimics
8.3 - Vitamin production
8.4 - Nitrogen fixation and phenolics metabolism
9 - Conclusion
References
Chapter 17 - Diversity and the antimicrobial activity of vaginal lactobacilli: current status and future prospective
1 - Introduction
2 - Normal vaginal flora
3 - Diversity in lactic acid bacteria (LAB)
3.1 - The genus Aerococcus
3.2 - The genus Carnobacterium
3.3 - The genus Enterococcus
3.4 - The genus Lactobacillus
3.5 - The genus Lactococcus
3.6 - The genus Leuconostoc
3.7 - The genus Pediococcus
3.8 - The genus Streptococcus
3.9 - The genus Bifidobacterium
3.10 - Glycogen metabolism by vaginal Lactobacillus
4 - Influence of age on vaginal microbiota
5 - Defense mechanism by LAB
5.1 - Bacteriocins
5.1.1 - Hydrogen peroxide (H2O2)
5.1.2 - Lactic acid
5.1.3 - Competitive adhesion
5.2 - Probiotic nature of LAB
6 - Current status and future prospective
6.1 - In urinary tract infections (UTIs)
6.2 - Bacterial vaginosis (BV) and lactobacillus
6.3 - Use of probiotic organisms in the human vagina
6.4 - Role of vaginal microbiome against cervical cancer
6.5 - Cancer and probiotics
Acknowledgments
References
Chapter 18 - Gut microbiota and brain development: A review
1 - Introduction
1.1 - Factors influencing colonization of bacteria
2 - Various pathways involved in a microbiota- gut communication
2.1 - Neural pathway/the vagal pathway
2.2 - Neuroendocrine gut hormone signaling
2.3 - Neuroendocrine- hypothalamic- pituitary- adrenal axis (HPA Axis)
2.4 - Development of HPA axis
2.5 - Gut microbiota and HPA axis
2.6 - Glucocorticoids and the HPA axis
2.7 - Interference with serotonin and tryptophan metabolism
2.7.1 - Indirect regulation
2.7.2 - Direct regulation
2.7.3 - Importance of serotonin for brain development
3 - Immune system
4 - Gut microbiome and microglia
5 - Synthesis of microbial metabolites
6 - Conclusion
References
Chapter 19 - Role of microbial communities in traditionally fermented foods and beverages in North East India
1 - Introduction
1.1 - Traditional Fermented foods and its history
2 - Various traditionally fermented foods consumed in North East India
2.1 - Fermented vegetables
2.2 - Fermented fish
2.3 - Fermented beans
2.4 - Fermented alcoholic beverages
2.5 - Fermented dairy products
3 - Health benefits and importance of different types of traditionally fermented foods
4 - Health risks of fermented foods
5 - Future aspects of microbes involved in fermentation
6 - Conclusion
References
Chapter 20 - Metagenomics: Applications of functional and structural approaches and meta-omics
1 - Introduction
1.1 - Metagenomics
2 - Culture-dependent approaches
3 - Culture-independent approaches ‘evolution of metagenomics’
4 - Next-generation sequencing
4.1 - Illumina platform
4.2 - Ion torrent-(Thermofisher)
4.3 - Pacific biosystems
4.4 - BGI
4.5 - Oxford nanopore
4.6 - Genia-Roche
4.7 - Bionano genomics
4.8 - RNAP sequencing technique
4.9 - FRET-based sequencing
5 - Enrichment of metagenome
5.1 - Bromo-deoxyuridine enrichment
5.2 - Stable-isotope probing (SIP)
6 - Taxonomic classification of metagenomes
7 - Binning
7.1 - Taxonomy-dependent methods
7.1.1 - Alignment-based methods
7.1.2 - Composition-based approaches
7.2 - Taxonomy-independent method
8 - Metagenomics approaches
8.1 - Sequence-based approaches
8.2 - Function-based approaches
8.2.1 - Functional screening
9 - “Meta-omics” approaches
9.1 - Low diversity environment
9.2 - Highly complex communities
10 - Conclusion
References
Chapter 21 - Metagenomics: a vital source of information for modeling interaction networks in bacterial communities
1 - Introduction
2 - Community level dynamics
2.1 - Exchange of metabolites
2.2 - Exchange of signals
2.3 - Horizontal gene transfer (HGT)
2.4 - Indirect interactions
2.5 - Spatial structure
3 - Mathematical modeling in bacterial systems
3.1 - Different models used to study microbial ecosystems
3.2 - Population and individual based models
3.2.1 - Dynamic models
3.2.2 - Evolutionary game models (EGM)
3.2.3 - Thermodynamically based models (TBM)
4 - Complexities in building predictive models for bacterial ecologies
5 - Metagenomics
5.1 - DNA extraction, sequencing
5.2 - Assembly
5.2.1 - Community composition
5.3 - Shot-gun metagenome assembly
5.4 - Annotation and functional metagenomics
5.5 - Single-cell metagenomics
6 - Metagenomics and bacterial evolution
7 - A metagenomics perspective on bacterial interaction
7.1 - Data processing
7.2 - Graph theory
7.3 - Predicting interactions
7.4 - Mathematical modeling
8 - Biodiversity analysis
9 - Experiments and metagenomics
References
Chapter 22 - Metagenomics based approach to reveal the secrets of unculturable microbial diversity from aquatic environment
1 - Introduction
2 - Cultivation- dependent methods in exploring bacterial diversity
3 - Cultivation-independent detection methods
4 - Need of metagenomics
5 - Metagenomics
6 - History of metagenomics
7 - Types of metagenomic approaches
8 - Metagenomics: aquatic ecosystem
9 - Bacterial biodiversity
10 - Fungal biodiversity
11 - Viral biodiversity
12 - Methodology
12.1 - Approach, strategy and tools for successful metagenomics analysis
12.2 - Sampling, isolation and cloning of metagenomic DNA
12.3 - Screening of metagenomic clones
12.4 - Sequencing and bioinformatics
12.5 - Current limitations of metagenomics
13 - Conclusion
References
Chapter 23 - Metagenomic-based approach to a comprehensive understanding of cave microbial diversity
1 - Introduction
2 - Cave–a unique natural habitat for microorganisms
3 - Taxonomic profiling analysis of microbial communities in the era of metagenomics and high-throughput sequencing
4 - Taxonomic distribution of cave microbiomes based on targeted 16S rRNA metagenomic sequencing
5 - Taxonomic distribution based on whole metagenome shotgun (WMS) sequencing
6 - Metabolic potential of cave microbiomes based on whole metagenome shotgun (WMS) sequencing
7 - The neglected world of fungi in cave microbiomes
8 - Concluding remarks
Acknowledgments
References
Index
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