Microbial Genomics in Sustainable Agroecosystems: Volume 1

293 Pages·2019·5.186 MB·English

by  Vijay Tripathi, Pradeep Kumar, Pooja Tripathi, Amit Kishore

Vijay Tripathi · Pradeep Kumar 
Pooja Tripathi · Amit Kishore Editors
Microbial
Genomics in
Sustainable
Agroecosystems
Volume 1
Microbial Genomics in Sustainable
Agroecosystems
(cid:129) (cid:129)
Vijay Tripathi Pradeep Kumar
(cid:129)
Pooja Tripathi Amit Kishore
Editors
Microbial Genomics in
Sustainable
Agroecosystems
Volume 1
Editors
VijayTripathi PradeepKumar
DepartmentofMolecularandCellular DepartmentofForestry
Engineering,JacobInstituteof NorthEasternRegionalInstituteofScienceand
BiotechnologyandBioengineering Technology(DeemedToBeUniversity-MHRD)
SamHigginbottomUniversityof Itanagar,ArunachalPradesh,India
Agriculture,TechnologyandSciences
Prayagraj,UttarPradesh,India AmitKishore
DepartmentofBotany
PoojaTripathi KamlaNehruP.G.College
DepartmentofComputational Raebareli,UttarPradesh,India
BiologyandBioinformatics,Jacob
InstituteofBiotechnologyand
Bioengineering
SamHigginbottomUniversityof
Agriculture,TechnologyandSciences
Prayagraj,UttarPradesh,India
ISBN978-981-13-8738-8 ISBN978-981-13-8739-5 (eBook)
https://doi.org/10.1007/978-981-13-8739-5
#SpringerNatureSingaporePteLtd.2019
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Foreword
Microorganisms are found ubiquitous in nature, and studying the microbiota of
plant, soil, ocean, and human body using omics approaches represents the
metagenomes by sequencing techniques. The exponential advancement of the
next-generation sequencing-based techniques, i.e., the microbial diversity analysis,
hasreachedamilestoneingenomics.Frommicrobialevolutiontomicrobialdiver-
sity, host-pathogen interactions to disease-causing genetic variation, and microbes
producing industrially important enzymes to plant growth-promoting microbes,
genomicshasprovideddeepinsightsintothemicrobialworld.
Thepresentbook,MicrobialGenomicsinSustainableAgroecosystemsVolumeI,
primarily gives insights from the microbial taxonomy to pathogen detection along
with their applications and updated information. Genomic techniques enable com-
parativeanalysisofmultiplegenomesandmetagenomesofcomplexagroecosystem
environment. This book packs comprehensive information on the present omics
technologiesemployedtorevealthemicrobialcommunitiespresentinthedifferent
agroecosystemsforsustenance.
Iamhappytonotethattheeditors haveframed aconceptualbookandeditedit
with updated information and precise language. I am sure this book will unfold
existingdoubtsandbottlenecksonmicrobialgenomics.Thebookdrafthas14well-
written chapters starting from bacterial pan-genomics, functional genomics, to
CRISPR-Cas9forpathogendetection.
Although the main emphasis of this book is microbial genomics insights in
different agroecosystems,itcontainsvastinformationwith easyandunderstanding
language. I am confident that this book has tremendous potential to attract a wide
groupofresearchers,students,academicians,andfacultywork.
ProfessorandHead,Departmentof Dr.PramodW.Ramteke
BiologicalSciences, FNAAS,FAMSc,FNABS,FLS,FBRS
Dean,PostgraduateStudies
SamHigginbottomUniversity
ofAgriculture,TechnologyandSciences
Allahabad,UttarPradesh,India
v
Preface
Overthepastseveraldecades,high-throughputsequencingtechnologieshavebeen
used for the detection of different microbial species which are fundamentally
important in understanding human infections, development of diagnostics and
vaccines,biodefensestudies,antimicrobialtargetidentification,anddrugdesigning.
The rapid advancement of next-generation sequencing platforms has reduced the
timeandcostandprovidesthecapabilitytoproduceseveralhundredsofprokaryotic
genomeseachyear.
Thecurrentbook,MicrobialGenomicsinSustainableAgroecosystems,isacom-
prehensivetextbookthathighlightstheroleofmicrobialgenomictechniquesinvarious
disciplines of science. Complementary chapters focus on the microbial genomic
approachestounderstandtheagroecosystems,bioremediationofsoilandwaterfrom
organic pollutants, characterization of microbial communities, carbon management,
andenergyproduction.Thishighlightsthelatestdevelopmentsofmicrobialgenomic
approachesintheunderstandingandanalysisofdifferentmicrobialgenomes.
The overall objective of this book is to cover the importance of microbial
genomics in agriculture, environment, and food technology. The book not only
deciphers the importance of microbial genomics but also makes the reader and
researchersinthepresentscenarioofmicrobialgenomicsandmetagenomicsfamiliar
with the existing techniques and tools. Chapter 1 discusses the role of functional
genomics and systems biology in the bioremediation process of organic and inor-
ganic wastes generated from various sources including agriculture. Chapter
2 describes the application and use of pan-genome in different areas. The
pan-genomehelpsresearcherstodifferentiatepathogenicisolatesinalargepopula-
tion and understand their pathology. The pan-genome can also be applied as a
reference to find genes or sequences that are significantly linked to the particular
phenotypessuchasinvasivenessorantibioticresistance,thuscrucialforfacilitating
bacterialdiseasecontrol,vaccinedevelopment,anddrugdesign.Chapter3describes
factorsallowingthesuccessfulestablishmentofthephyllospheremicrobialpopula-
tionandthemethodusedfortheirroleinplantfitnessandhealth.Pathobiomestudy
and the potential use of phyllosphere monitoring are important in sustainable
agriculture practices (e.g. biocontrol agents, plant growth stimulators, and
biofertilizers). Chapter 4 discusses the role of functional genomics to study the
effectofstressonplants.Variousapproachesandtoolsofsystemsbiology,required
vii
viii Preface
foralterationinbiologicalnetworksincludinggeneregulatory,protein-protein,and
metabolic network, are also discussed in detail. Chapter 5 elaborates the available
genome in public databases and the role of next- and third-generation sequencing
technologyinthegrowthofgenomeandmetagenomesequencinganditsassociated
projectsandtheirtechnologyandfunctionalcharacterizationthroughbioinformatic
analysis.Chapter6detailsthecomputationalmethodsincorporatedwithsequencing
techniques in the viral genome. This chapter mainly focuses on how the computa-
tional method incorporated with sequencing technique is made easy for microbial
detection and characterization. Therefore, Chap. 7 discusses the importance of
whole-genome sequencing techniques with great potential in the food safety and
surveillance against foodborne pathogens and antimicrobial resistance. Chapter 8
comprises the understanding of taxonomic and functional microbiome profiles
caused by the occurrence of microbial pathogens in the food production system.
Thiscanleadtovaluableinformationtounderstandthenegativeeffectofpathogens
oncrops.Chapter9describesthepotentialofmicrobesforenergyproductionsothat
thismayleadtolimitedusageoffossilfuelsinthenearfuture.Thebriefsectionof
therolemicrobialworld,ecosystem,andtheirrelationshipwiththeclimaticchange
is also discussed in this chapter. Therefore, Chap. 10 summarizes the different
methods to get the microbial diversity that may eventually enhance plant growth
insustainableagriculture.Thischapteralsohighlightsthemoleculartechniquesfor
theidentificationandgenotypingofmicroorganism,andthesetechniquesdeveloped
forsequencingareabreakthroughformicrobialsystematics.Therefore,Chap.12is
dividedintotwosections:thefirstsectionexplainsthemolecularmechanismofthe
naturally occurring CRISPR-Cas9 systems, and the next section elaborates the
applicativepartofCRISPR-Cas9-basedtools/systemsinarangeofmicroorganisms
and parasites. Chapter 13 discusses the brown algae and its characteristics as
bio-sorbent for the removal of heavy metals from industrial effluent. Chapter 14
discusses the use of microbial genomics approach in renewable energy production
andglobalcarbonmanagement.Thechapteraddressedtheglobalenergycrisesand
suggests various omics technologies develop a better understanding to harness
differentrenewableandcarbon-neutralenergysourceslikelignocellulosicbiomass,
microalgae,andcyanobacteriatoovercomethisproblem.
Thisbookprovidescomprehensiveknowledgeabouttheuseofmicrobialgeno-
micsapproachinsolvingthevariousresearchquestionsrelatedtoagroecosystems.
At the same time, it explains to the biologist some of the basics behind the next-
generation sequencing techniques that are necessary for research in this field. The
book will be mainly useful for the students, research scholars, academicians, and
scientistswhoarestudyingandworkinginthefieldofgenomics.
Prayagraj,UttarPradesh,India VijayTripathi
Itanagar,ArunachalPradesh,India PradeepKumar
Prayagraj,UttarPradesh,India PoojaTripathi
Raebareli,UttarPradesh,India AmitKishore
Contents
1 FunctionalGenomicsandSystemBiologyApproach
inBioremediationofSoilandWaterfromOrganic
andInorganicPollutants. . . .. . . . . .. . . . . . .. . . . . .. . . . . . .. . . 1
SumanYadav,YashpalBhardwaj,Neha,andAbhishekSingh
2 BacterialPan-Genomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
ArashIranzadehandNicolaJaneMulder
3 PhyllosphereandItsPotentialRoleinSustainable
Agriculture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
GulabChandAryaandAryeHarel
4 FunctionalGenomicsandSystemsBiologyApproach
forUnderstandingAgroecosystems. . . . . . . . . . . . . . . . . . . . . . . . . 67
BirendraSinghYadavandAshutoshMani
5 AdvancementsinMicrobialGenomeSequencing
andMicrobialCommunityCharacterization. . . . . . . . . . . . . . . . . 87
BhaskarReddy
6 BioinformaticsandMicroarray-BasedTechnologies
toViralGenomeSequenceAnalysis. . . . . . . . . . . . . . . . . . . . . . . . 115
MayankPokhriyal,BarkhaRatta,andBrijeshS.Yadav
7 ApplicationofWholeGenomeSequencing(WGS)Approach
AgainstIdentificationofFoodborneBacteria. . . . . . . . . . . . . . . . . 131
ShivBharadwaj,VivekDharDwivedi,andNikhilKirtipal
8 FunctionalMetagenomicsforRhizosphericSoil
inAgriculturalSystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
EstefaníaGaribay-Valdez,KadiyaCalderón,
FranciscoVargas-Albores,AsunciónLago-Lestón,
LuisRafaelMartínez-Córdova,andMarcelMartínez-Porchas
9 MicrobialGenomicsinCarbonManagementandEnergy
Production. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
ShatabishaBhattacharjeeandTulikaPrakash
ix
x Contents
10 MicrobialGenomeDiversityandMicrobialGenome
Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
AditiJangidandTulikaPrakash
11 MolecularBiologyTechniquesfortheIdentification
andGenotypingofMicroorganisms. . . . . . . . . . . . . . . . . . . . . . . . 203
NisargGohil,HappyPanchasara,ShreyaPatel,andVijaiSingh
12 RNA-GuidedCRISPR-Cas9SystemforRemovalofMicrobial
Pathogens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
GargiBhattacharjee,KhushalKhambhati,andVijaiSingh
13 Biosorption-Cum-BioaccumulationofHeavyMetals
fromIndustrialEffluentbyBrownAlgae:DeepInsight. . . . . . . . . 249
PriyankaYadav,JyotiSingh,andVishalMishra
14 LinkingMicrobialGenomicstoRenewableEnergy
ProductionandGlobalCarbonManagement. . . . . . . . . . . . . . . . . 271
Neha,AbhishekSingh,SumanYadav,andYashpalBhardwaj
Editors and Contributors
About the Editors
VijayTripathi iscurrentlyworkingasanAssistantProfessorattheDepartmentof
MolecularandCellularEngineering,SamHigginbottomUniversityofAgriculture,
Technology and Sciences, Prayagraj, India. He was previously awarded an ARO
Post Doctoral Fellowship at the Department of Soil, Water, and Environmental
Science, Agricultural Research Organization, Bet Dagan, Israel. He has also
receivedtwoprestigiouspostdoctoralfellowships(Indo-IsraelGovernmentFellow-
shipandPBCOutstandingPostDoctoralFellowship)andworkedwithProfEdward
TrifonovasapostdoctoralfellowattheInstituteofEvolution,UniversityofHaifa,
Israel. Dr Tripathi began his research career as a doctoral student at the Center of
Bioinformatics, University of Allahabad, India. During his doctoralthesis work he
wasalsoawardedaMUIRfellowshipandvisitedtheUniversityofCagliari,Italy.
PradeepKumar iscurrentlyworkingasanAssistantProfessorattheDepartmentof
Forestry, North Eastern Regional Institute of Science and Technology (NERIST),
Nirjuli,India.BeforejoiningNERIST,heservedasanInternationalResearchProfes-
sor/Assistant Professor at the Department of Biotechnology, Yeungnam University,
SouthKorea.HewasawardedaPBCOutstandingPostDoctoralFellowshiptowork
formorethanthreeyearsasaPostdoctoralResearcherattheDepartmentofBiotech-
nologyEngineering,BenGurionUniversityoftheNegev,Israel.Heistherecipientof
manybestpaperpresentationsandtheNarasimhanAwardfromtheIndianPhytopath-
ologicalSociety,India.Hehaspublishedfourbooksandmorethan50researchand
reviewarticlesinpeer-reviewedjournals,aswellasseveralbookchapters.
PoojaTripathi iscurrentlyworkingasanAssistantProfessorattheDepartmentof
ComputationalBiology&Bioinformatics,JIBBatSamHigginbottomUniversityof
Agriculture,TechnologyandSciences,Prayagraj,India.ShecompletedherPhDin
BioinformaticsattheUniversityofAllahabad,Prayagraj.Shewasalsoawardedthe
prestigiousPBCOutstandingPostDoctoralFellowshipfromtheMinistryofHigher
Education, Israeli Government, to pursue her postdoctoral research at the Depart-
mentofPlantandEnvironmentalScience,WeizmannInstituteofScience,Rehovot,
Israel. She also received an ARO Post Doctoral Fellowship and joined the
xi