Geomicrobiology and Biogeochemistry

302 Pages·2014·3.167 MB·English

by  Nagina Parmar, Ajay Singh (auth.), Nagina Parmar, Ajay Singh (eds.)

Soil Biology
Nagina Parmar
Ajay Singh Editors
Geomicrobiology
and
Biogeochemistry
Soil Biology
Volume 39
Series Editor
AjitVarma,AmityInstituteofMicrobialTechnology,
Amity University Uttar Pradesh, Noida, UP, India
For furthervolumes:
http://www.springer.com/series/5138
ThiSisaFMBlankPage
Nagina Parmar (cid:129) Ajay Singh
Editors
Geomicrobiology and
Biogeochemistry
Editors
NaginaParmar AjaySingh
DepartmentofChemistryandBiology LystekInternationalInc.
RyersonUniversity Cambridge
Toronto Ontario
Ontario Canada
Canada
ISSN1613-3382 ISSN2196-4831(electronic)
ISBN978-3-642-41836-5 ISBN978-3-642-41837-2(eBook)
DOI10.1007/978-3-642-41837-2
SpringerHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2013956629
©Springer-VerlagBerlinHeidelberg2014
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Preface
Earth sustains an immense diversity of prokaryotic and eukaryotic organisms.
Microorganismsplayanessentialroleinthefunctioningandsustainingofallnatural
ecosystems including biogeochemical cycling of nutrients. Biotechnology has
becomeanimportanttoolformanipulatingandutilizingmicroorganismsandplants
andprovidingnewapproachesinvariousindustriesincludingpetroleum,food,feed,
pharmaceutical,detergent,andpulpandpaper.Newstrainsarecontinuouslybeing
exploredandgeneticorenzymaticfunctionsareoftenreconstructedthroughmolec-
ularrecombinationandproteinengineeringtechniquestoincreasethegeneexpres-
sion and metabolic productivity of industrially important organisms. The unique
characteristicsofthesemicrobesarewidelyutilizedforindustrialapplicationssuch
asenzymesandchemicalproduction,wastetreatmentandrecycling,bioremediation
of industrial pollutants in soils and aquifers, enhanced petroleum oil recovery,
biomining, and soil fertility. Biochemical and molecular tools are continuously
being developed in an attempt to evaluate community structures with ecosystem
functionsandtodevelopappropriateindustrialapproaches.
ThisvolumeoftheSoilBiologyseries,GeomicrobiologyandBiogeochemistry,
is a selection of topics related to biological processes with an emphasis on their
industrialapplications.Itgivesanoverviewofvariousaspectsingeomicrobiology
andbiotechnologyincludingtopicssuchasbiomining,bioremediation,biotechno-
logical applications of some extremophiles, subsurface petroleum microbiology,
enhancedoilrecoveryusingmicrobesandtheirproducts,metalextraction,andsoil
nutrientcyclingandplantnutrition.
Expertsintheareaofgeomicrobiologyandenvironmentalsciencesfromdiverse
institutions worldwide have contributed to this book, which should prove to be
usefultostudents,teachers,andresearchersinthedisciplinesofsoilandgeological
sciences,microbiology,environmentalengineering,andbiotechnology.
We gratefully acknowledge the cooperation and support of all the contributing
authors,theserieseditorProf.AjitVarma,andDr.JuttaLindenbornthroughoutthe
preparationofthisvolume.
Toronto,ON,Canada Dr.NaginaParmar
Cambridge,ON,Canada Dr.AjaySingh
v
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Contents
1 Geobiotechnology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
NaginaParmarandAjaySingh
2 NovelMolecularToolstoAssessMicrobialActivityinContaminated
Environments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
NadineLoickandChristopherWeisener
3 AdvancedMolecularandMicrospectroscopyToolboxfor
DecipheringSoilDiazotrophDiversity. . . . . . . . . . . . . . . . . . . . . . 37
AnuKaliaandVirR.Parshad
4 HaloalkaliphilicBacteria:MolecularDiversityandBiotechnological
Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
MeghaK.Purohit,VikramH.Raval,andSatyaP.Singh
5 RecentTrendsinBioremediation. . . . . . . . . . . . . . . . . . . . . . . . . . 81
AshaA.Juwarkar,RashmiR.Misra,andJitendraK.Sharma
6 HeavyMetalBioremediationandNanoparticleSynthesis
byMetallophiles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
ArvindSinha,RajeshwariSinha,andSunilK.Khare
7 MineralogicalandGeochemicalControlsinBiominingand
Bioremediation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
BernhardDold
8 MicrobialRecoveryofNickelfromLateritic(Oxidic)NickelOre:
AReview. . . . . . . . . .. . . . . . . . . . .. . . . . . . . . .. . . . . . . . . . .. . . 137
LalaBehariSukla,SunilKumarBehera,andNilotpalaPradhan
9 SubsurfacePetroleumMicrobiology. . . . . . . . . . . . . . . . . . . . . . . . 153
AjaySingh,JonathanD.VanHamme,RameshC.Kuhad,
NaginaParmar,andOwenP.Ward
vii
viii Contents
10 NutrientCycling:PotassiumSolubilizationbyMicroorganisms
andImprovementofCropGrowth. . . . . . . . . . . . . . . . . . . . . . . . . 175
SatyavirS.Sindhu,PriyankaParmar,andManishaPhour
11 PhosphorusCycling:ProspectsofUsingRhizosphere
MicroorganismsforImprovingPhosphorusNutritionofPlants. . . 199
SatyavirS.Sindhu,ManishaPhour,SitaRamChoudhary,
andDeepikaChaudhary
12 BiotechnologyinEnhancedPetroleumOilRecovery. . . . . . . . . . . 239
AjaySingh,NaginaParmar,andOwenWard
13 TheChemistryofRemovalofInorganicCompoundsfrom
theSoil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
InnocentOseribhoOboh
14 BioremediationofContaminatedSitesandAquifers.. . . . .. . . . .. 261
NaginaParmar,AjaySingh,andHammadKhan
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Chapter 1
Geobiotechnology
NaginaParmarandAjaySingh
1.1 Introduction
Earth has a large wealth of biodiversity with taxa including microorganisms, pro-
tozoa,microscopicandlargeinvertebrates,vertebrates,vascularplantsandlichens,
algae,andmosses.Manyofthesesmallergroupscanbefoundinahandfulofsoil.
Because of the abundance and diversity of the multiple taxonomic groups, identi-
fyingallspeciesandtheirinteractionsinasinglesoilsampleisnottrivial.Instead,
our understanding of soil biodiversity is largely based on trophic or functional
classifications. A further and critical recognition of the dependence of humans on
the benefits provided by soil biodiversity is the concept of ecosystem services
includingcarbonsequestration,generationandrenewalofsoilstructureandfertil-
ity, flood and erosion control, geochemical nutrient cycling, waste management,
bioremediation, and biocontrol of pathogens and parasites. Application of molec-
ulartechniquestothestudyofmicrobialdiversityhasrevealedtheexistenceofan
incrediblevarietyofgenotypesandspeciesinallknownhabitatsaboveorbelowthe
earthsurface(Croaletal.2004).Theoretical andempiricalanalysesofthemicro-
bialdiversityofsoilsindicatethatsoilsharborintheorderof7,000differenttaxaat
anabundanceofapproximately109cellspercm3.
Over the past 4 billion years, microorganisms have been helping to shape the
earth by making it more habitable for higher forms of life. Geomicrobiology has
becomeanimportantlearningtoolthatintegratesgeologyandmicrobiologystudy-
inginteractions ofsubsurfaceextremophilesandtheir environmentssuchassoils,
rocks,springs,aquifers,petroleumreservoir,etc.Biogeochemicalprocessescarried
out by the microorganisms in near or deep subsurface sediments have been the
N.Parmar(*)
DepartmentofChemistryandBiology,RyersonUniversity,Toronto,ON,CanadaM5B2K3
e-mail:[email protected]
A.Singh
LystekInternationalInc.,1425BishopStreetNorth,Unit16,Cambridge,ON,Canada
N1R6J9
N.ParmarandA.Singh(eds.),GeomicrobiologyandBiogeochemistry,SoilBiology39, 1
DOI10.1007/978-3-642-41837-2_1,©Springer-VerlagBerlinHeidelberg2014