Microbial Systematics: Taxonomy, Microbial Ecology, Diversity


Culture-Dependent and -Independent Strategies in Bacterial Diversity AppraisalIntroductionEcological perception of bacterial diversityRibosomal DNA based bacterial identificationCulture-dependent methods in microbial ecologyViable plate count and direct microscopic countPhospholipid fatty acid (PLFA) analysisCommunity-level physiological profiles (CLPP)Culture-based methods in microbial ecology: limitationsCulture-independent/molecular methods for microbial diversity analysesPCR based techniquesDenaturing or temperature-gradient gel electrophoresis (DGGE/TGGE)Terminal Restriction Fragment Length Polymorphism (T-RFLP)Automated ribosomal intergenic spacer analysis (ARISA)Amplified ribosoinal DNA restriction analysis (ARDILi)Single Stranded Conformation Polymorphism (,SSCP)Non-PCR based techniquesFluorescence in situ hybridization (FISH)DNA microairayNext-generation sequencing (NGS): a revolution in the era of microbial ecologyConcluding remarks and future directionsAcknowledgementsReferencesMethods for Isolation and Identification of MicroorganismsIntroductionCulture dependent identificationStreakingAxenic mediaMorphological characterizationSerological characteristicsBiochemical methodsPhysical testsIsolation and identification of anaerobesCulture independentNucleic acid techniquesElectrophoresis based methodsFluorescence in situ hybridization (FISH)Immunological based methodsSpectroscopy based methodsMethods for Isolation and Identification ofMicroorganisms 45MIDI SherlockConclusionsAcknowledgmentsReferencesApplication of MicroorganismsIntroductionApplication of microbes in various fieldsApplication of bacteria and fungi in soilApplication of bacteria and fungi in aquacultureApplication of bacteria and fungi in food industryApplication of bacteria and fungi in pharmacologyApplication of marine bacteria and fungiApplication of microorganisms in nanoparticle synthesisApplication of biosynthesized nanoparticles in soilApplication of biosynthesized nanoparticles in food industryApplication of biosynthesized nanoparticles in pharmaceutical industryConclusionReferencesMicrobial Cell FactoriesIntroductionApproaches for the production of enzymes and secondary metabolitesApplications of Penicillium chrysogenum, Trichoderma reesei, and Aspergillus nigerBiofuels production in cyanobacteriaCyanobacteria as sources of bioactive and value-added compoundsProduction of plant secondary metabolitesApproaches for developing algal cell factoriesAlgal cell factory potentialsBioenergy from microalgaeChallenges of CRISPR applicationsConclusionsFuture perspectiveAcknowledgmentsReferencesMetabolic EngineeringIntroductionWaste treatmentMicrobial cell factoriesBioremediationClimate changeEnergyReferencesComposition and Biological ActivitiesIntroductionAnti-microbial agentsAntibacterial agentsAntifungal agentsAntiviral agentsAntiparasitic agentsPharmacologically active substancesAntitumor agentsAntioxidant agentsAnti-inflammatoryImmunomodulatorsEnzyme inhibitionAgrochemicalsConclusionsAcknowledgmentsReferencesWaste TreatmentsIntroductionBiosorptionBioaccumulationBiotransformationBiodegradationPrinciples of biodegradationAerobic biodegradationAnaerobic biodegradationConclusionReferencesEnergyIntroductionBiofuelsBiogasMicroalgae as feedstockLignocellulosic biomassAnaerobic digesters for food waste as feedstockConclusionReferencesNext Generation Sequencing: Advances and Applications in the World of Bacterial DiversityIntroductionTransition from genome to metagenome (Sequencing to Next-Generation Sequencing)A brief history of DNA sequencingFirst-generation sequencing (FGS)The second/next-generation sequencing technologiesClonal in vitro amplificationEmulsion PCR (emPCR)Bridge amplification (Cluster PCR)Major NGS platforms/Roche SystemIllumina/Solexa genome analyzerIon Torrent/Semiconductor sequencingABI/SOLiD™ sequencerNext-generation sequencing technologies to assess microbial communityWhole genome sequencing (WGS)Third-generation sequencingNanopore sequencingConcluding remarks and future prospectiveAcknowledgementsReferences
 
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