[first author] 2007 advances in applied microbiology

8/6/2019 [First Author] 2007 Advances in Applied Microbiology

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INDEX

A

AAD. See Antibiotic-associated diarrheaAcetobacterium woodii, 15Acetogenesis, 66, 76

Acidithiobacillus ferrooxidans, 92Acid mine drainage (AMD) systems

metagenomic analyses of biofilm from, 94microbes in, 93sulfur-oxidizing isolates from, 93

Actinobacteria, 250Actinomyces naeslundii T14V, 218Activated methyl cycle, 209211Acylated homoserine lactone, 194Acylated homoserine lactone antagonists,

226227Acylated homoserine lactone-degrading

enzymes, 224225

Acylated homoserine lactone-typeautoinducers, 195Adenine, 209Adenosine, 209Aerobic process, scale-up of, 106Agitation system

biological aspects of, 108mechanical damage due to, 112physical aspects of, 108

aerated power draw, 111air dispersion capability, 112

bulk fluid- and air-phase mixing,113114

heat transfer, 109110local specific energy dissipation rates,

variation in, 112mass transfer performance, 108unaerated power draw P, 110

turbulent flow field close to, 112Agrobacterium tumefaciens, 224AHL. See Acylated homoserine lactoneAlkylsulfate ester, 242

AMC. See Activated methyl cycleAmino acids, in rhizosphere, 240241Amino acids/peptides, as source of plant

sulfur, 240

Ammonium monooxygenase, 5amyE locus, 146, 151. See also

Integrative vectorsAnaerobic sediment microcosms, 10Antibiotic-associated diarrhea, 280Antibiotic resistance (AbR) bacteria, 270

in food animals, 271

in soils, 271272Antibiotic resistance (AbR) gene

dissemination of, 272273in environment, 272evolution of novel forms of, 278279in gut bacteria, 270, 278

Antibiotic resistance (AbR) gene transferbetween bacteria, 273275

in gut ecosystems, 276via transformation, transduction and

conjugation, 274

in vivo demonstrations of, 276277Antibiotics

and gut microbiota development, 282283and pro/prebiotics, 281

Antibiotic-selective pressure, 270, 272, 278

Antibiotic therapy, knockon effects of, 280Antibiotic use, 270273

in animal husbandry, 271in commensal gut microbiota, 280immune system develpoment and, 283

Anti-listeria bacteriocions. See Class IIabacteriocins

Antimicrobial peptides (AMPs), 197AP50, 130131aprE gene, 152, 158160, 167Arabidopsis rhizosphere, confocal

microscopy of, 239Archaea, 25, 8384, 95

Arrhenatherum elatius, 84Arthrobacter spp., 224, 274Arylsulfotransferase, 258

Ascomycota, 84ASD. See Autistic spectrum disordersATP-binding cassette (ABC)-type

transporters, 195

293


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Autistic spectrum disorders, 283Autoinducer-2 (AI-2), 193, 202

biosynthesis of, 199culture fluids from, 216

in E. coli, 214in foods, 220223formation of, 209molecular structure of, 203structure of, 214

Autoinducer-3 (AI-3), 208Autoinducer-2 (AI-2) detection assay,

220221Autoinducer-2 (AI-2)-mediated QS, 203

in Neisseria meningitidis, 217in non-Vibrio species, 204205

Autoinducer bioassay (AB) medium, 221Autoinducer-mediated regulation, of gene

expression, 200Autoinducers, 194

with antimicrobial activity, 196198extracellular concentration of, 201

Autoinducible promoters, 153154Autoinduction pathways, evolution of, 201Autotrophy, 29

Azospirillum, 25, 247

B

Bacillus amyloliquefaciens, 168Bacillus brevis, recombinant proteins

production in, 168169Bacillus licheniformis, 153, 159, 166, 171Bacillus megaterium, 151, 169171Bacillus species

sec system in, 154155in SRP system, 156157tat system in, 155156

Bacillus subtilis, 194batch fermentations of, 126citM gene of, 151degS-degUgenes of (see sacUh mutation)peptide pheromones from, 198

pst operon of, 153Bacillus subtilis, recombinant proteins

production in, 138chromosomal mutations impact on,

163168expression systems, 149160

in other Bacilli, 168171replication vectors and

bacteriophage, 148149integrative, 146148rolling circle-type, 139141

theta-type, 141146transformation systems, 160163

Bacillus thuringiensis, 159160, 225Bacterial communities, by PCR-DGGE of

16S genes, 255Bacterial conjugation, 276Bacterial detection, microarray technology

for, 86Bacterial fermentation, 107Bacterialfungusplant interactions, 258Bacterial population, physiological state of,

124Bacterial probiotics, 281Bacterial reporter strains, 239Bacteriocins, 197, 201

Bacteriophages, 148149, 274Bacteroides spp., 282Basidiomycota, 84Batch fermentation

ofBacillus subtilis, 126overflow metabolism in, 119

Bifidobacteria, 281282Biofilms, 226, 276Biogenic minerals, 95Bioluminescence

in V. fischeri, 194

in V. harveyi, 203, 221Bioreactor

agitation system in (see Agitation system)fluid mechanics in, 108mechanical agitation and aeration in, 115

Biotin, 51Brevibacterium flavium, mechanical agitation

on, 115Bromoethane-sulfonic acid (BES), 11Butyrivibrio fibrisolvens, 276

C

Calmodulin-binding peptide, 157Calvin-Benson-Bassham cycle enzyme,

27, 29Campylobacter coli, 221, 277Campylobacter jejuni, 203, 277Carbon and hydrogen fractionation

pattern, 13Carbon-bound sulfur, 242Catalyzed reporter deposition fluorescence

in situ hybridization (CARD-FISH), 96cat gene, 149, 158Cation diffusion facilitator (CDF), 41CDAD. See Clostridium difficile-

associated diarrhea

294 Index


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CFD. See Computational fluid dynamicsChemoorganoheterotrophic growth, 29Chemoorganoheterotrophs, 27. See also

Magnetospirillum spp.

Chemotrophic archaea, 92Chlorosis, 259Chromobacterium violaceum ATCC 12472, 226Chromosomal mutations, impact on

intra- and extracellular proteinscellular factors

cell wall, net charge of, 164165disulfide bond formation, 165extracellular proteases, 165167PrsA, 164

molecular chaperones, 163164

recombinant proteins production and,167168

Chytridiomycota, 84Class I bacteriocins. See LantibioticsClass IIa bacteriocins, 197Clean Air Act Amendments of 1990, 2Cloning vectors, rolling circle-type

plasmids and, 141Clostridia, 247Clostridium difficile, 276Clostridium difficile-associated diarrhea,

treatment of, 280Clostridium perfringens, 144, 173Clostridium symbosium, 277Clostridium tetani, 283Clostridium thermocellum, 148Cold sulfide springs, 94Comamonadaceae, 247ComGC, pseudopilin, 165Compound-specific stable isotope

analysis, 12Computational fluid dynamics,

120, 126, 132Conjugative gene transfer, 275, 278Conjugative transposons (CTns), 274, 278Contamination, sources of, 3Corynebacterium glutamicum, 116117, 274Crabtree effect, 11913C-RNA stable isotope probing, 247cryIIIA toxin gene, ofBacillus

thuringiensis, 159Crystal twinning, 33Cubitermes, 67, 75Cubitermes fungifaber, T-RFLP

foodsoil in, 73Cubitermes orthognathus, 65, 70

Cultured magnetite-producingmagnetotactic bacteria, transmissionelectron micrographs of, 28

CWBP52, cell wall-bound protease, 166

Cysteine, 240, 245Cytochrome P450 monooxygenases, 5

D

Deep sea hydrothermal vents, 9495Delisea pulchra, 223des gene, 153Desulfovibrio burkinensis, 26Desulfovibrio magneticus strain RS-1,

2526, 27Dihydroxyacetone phosphate (DHAP), 213Disulfide bond formation, 165DNA elements, recombinant proteins

production and30 and 5 stabilizers, 158159translation signals, 159160

DNA replication initiation, 123DNA transfer, 274Double-stranded labeled DNA, 50DPD, 209, 214, 218

E

Ectomycorrhiza, 258EHEC. See Enterohemorrhagic E. coliElectron-accepting process, 1415Electrotransformation, 162Enterococcus faecalis, 141, 274, 277Enterococcus faecium, 271, 277Enterohemorrhagic E. coli, 207209Environmental contamination, 4Environmental pollutants, in situ

biodegradation of, 12

Environment sensing theory, 200202erm family, of genes, 158159Erwinia carotovora, 194, 225Escherichia coli, 115, 138139, 141, 155, 159,

165, 194, 273, 276AI-2 in, 214detection and removal of cells of, 50fermentative metabolism in, 122GFP in, 156in HtrA-like serine proteases, 42lacIgene, 150lsr operon of, 213overflow metabolism in, 119pBR322 of, 146

Index 295


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Escherichia coli (Cont.)recombinant plasmids transfer from,

162163ribose-binding protein (RBP) from, 214

Escherichia coli fed-batch fermentation,124125, 128effect of dO2, glucose, and pH

fluctuations on, 129130, 130131small-scale experimental simulation

models of, 124126experimental results of, 128132experimental setup for, 126128

Escherichia coli fed-batch recombinantprotein process, 106

Escherichia coli fermentation, agitation and

aeration intensity, 116Escherichia coli O157:H7, 221Escherichia coli W3110 luxS-null mutant,

transcriptional response of, 207Ethyl tert-butyl ether (ETBE), 1, 9Eubacterium limosum, 15Euprymna scolopes, 193Euryarchaeota

in Cubitermes guts, terminal restrictionfragment length polymorphism(T-RFLP) analysis of, 74

in termite guts, 64, 67 (see also UnculturedEuryarchaeota)

Exoenzymes, 201Expression systems, recombinant protein

production in B. subtilis andDNA elements impact and, 158160promoter systems, 149154secretion systems, 154157tags addition and, 157158

Extant microbialites, 97Extracellular proteases, protein folding

and degradation, 165167Extremophiles, 92

F

Fed-batch bioreactors, large-scalepH controlling action at, 120spatial and temporal chemical gradients

in, 120Fed-batch fermentations, 114, 119120, 125Fermentation broth, oxygen transfer in,

108109Fermentation scale-up

engineering considerations in, 107process engineering considerations

for, 115

Fermenter, multiple Rushton turbineimpellers in, 107

Filamentous fungi, 247Flagellated protozoa, 65

Fluid mechanical stress. See Shear damageFluorescence resonance energy transfer(FRET) technique, 50

Folding catalystspeptidyl-prolyl isomerases (PPIases), 155quinone oxidoreductases, 165thiol-disulfide oxidoreductases, 155, 165

ftsZ mutation, 167168Fuel oxygenates. See also Methyl tertiary

(tert)-butyl etheras contaminants of water sources, 3

environmental fate of, 4structure of, 2

Fungal species, 84Fungi, sulfur transformations by, 247

G

Gasoline, 25Gastrointestinal tract (GIT), of animals and

humans, 275Geobacteraceae, 96

Geochemical environments,microorganisms in, 8889Geomicrobiological activities, 82, 98Geothrix fermentans, 97Glomeromycota, 84Glomus intraradices, 248Glomus mosseae, 258Glucose factor, 221Glucose oxidase and uricase,

immobilization of, 50Glutathione, uptake of, 240241

Glutathione S-transferase protein, 157Glycerol-3-phosphate, 213Glycine riboswitch, 151152Gnotobiotic mouse models, 277Green fluorescent protein genes (gfp),

37, 156Greigite, 23, 30

in MMP, 31morphology of, 33shapes of, 32transmission electron microscopy (TEM)

of, 32groE (groES-groEL) operon, 163Growth phase-and stress-specific

promoters, 152153GsiB protein, 153

296 Index


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H

Halobacteriales, T-RFLP analysis of, 75Halogenated furanones, 223Heavy metal pollution, 272Heptacistronic dnaKoperon, 163Hexahistidine tag, 157HI-reducible sulfur pool, 244

Hodotermopsis sjoestedti, 72Homocysteine, 209, 211212HtrA-like serine proteases, in E. coli, 42N-(3-hydroxybutanoyl) homoserine

lactone, 199, 203Hygiene hypothesis, 282

I

Impelleraxial flow hydrofoil, 113down-pumping, high solidity ratio

hydrofoil, 111hollow blade, 111low and high shear, 118mean specific energy dissipation rate

from, 110up-pumping, high solidity ratio

hydrofoil, 111Inducer-specific promoters, 150Inorganic sulfate, uptake and assimilation

of, 237240Integrative vectors, 146148Integrons, 274. See also Resistance integrons

(RI); Superintegrons (SI)Interferon-a2 (IFN-a2), 168Iron, forms of, 93Irons oxides, 23Iron sulfide-containing magnetosomes, 30

Iron sulfides, 23Isopropyl ether, 1Isopropyl thiogalactopyranoside (IPTG),

130, 138, 150

K

Kolmogoroff microscale of turbulence,115116

L

Laboratory-scale fermentation processes,scale-up of, 124, 128

lacA locus, 146. See also Integrative vectorsLaccaria bicolor, 248Laccaria laccata, 241

b-lactamase proteins, 257Lactic acid bacteria (LAB), 196Lactobacillus plantarum, 198Lactobacillus reuteri, 169, 217

Lactococcus lactis, 196197, 276lacZ, reporter gene, 146, 152, 158159Lantibiotics, 196, 197Lantibiotic subtilin, 152Large eddy simulation (LES), of glucose

concentration, 120121Leptospirillum group III strain, 94Lignosulfonate, 250Listeria monocytogenes, quorum-sensing

processes in, 193Listeria monocytogenes EGD-e, 210, 216

Lithobiotic microbial communities, 90Locus of enterocyte effacement (LEE),

207208lsrACDBFGE, transcription of, 213LsrB, 212213lsr operon, 212

ofE. coli, 213, 215ofS. typhimurium, 215transcription of, 220

LuxI and LuxR, 194LuxLM (AI-1 synthase), 216

LuxP, 212LuxS (AI-2 synthase), 203204

in cell physiology, 209212ecological performance of, 216pleiotropy of, 212ofS. typhimurium, 212

LuxS-dependent QS, in non-Vibriospecies, 207

LuxS-knockout mutation, 208, 216LuxS-null mutants

biofilm formation defect of, 217

characterization of, 205206culture fluids of, 210

Lysine riboswitch, 154

M

Mackinawite, 30Macrolidelincosamide-streptogramin (MLS)

antibiotics, 140, 158Macrolides, 271Magnetic antibodies, 50

Magnetic dipole moment, 3334Magnetite (Fe3O4), 23

biomineralization of, 27macroscopic crystals of, 32in magnetosomes, 31

Index 297


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Magnetite (Fe3O4) (Cont.)in magnetospirillum species, 32morphology of, 29shapes of, 32

transmission electron microscopy (TEM)of, 32

Magnetite magnetosomesapplications of, 50

biomineralization, 38, 47synthesis, physiological conditions of, 46

Magnetite precipitation, 39Magnetosome crystals

applications of, 5052composition of, 3031morphology of, 3133

size of, 31Magnetosome gene island (MAI), structure

of, 4546Magnetosome membrane (MM)

composition of, 38electron cryotomography (ECT) of, 39lipid analysis of, 38

Magnetosomes, 23, 29applications of, 5052arrangement of, 3334

biomineralization, steps in

iron uptake, 36vesicle formation, 36

downregulation of, 48in geology and paleomagnetism, 52greigite crystals in, 31magnetite crystals in, 31organization of, 44regulation of expression of, 4748

Magnetosome synthesischemical and molecular basis of, 35MM proteins in, 41

Magnetospirillum gryphiswaldense, 38gene transcription analysis of, 47iron uptake experiments with, 47magnetite synthesis in, 47magnetosome gene region in, 46MM proteins in, 41partial genome array for, 48

Magnetospirillum gryphiswaldense strainMSR-1, 26

genetic systems for, 37genome of, 36

Magnetospirillum magneticum, 36genome of, 41growth of, 47mamA in, 41

mass culture of, 4849MM proteins in, 39

Magnetospirillum magneticum strain AMB-1,27

genetic systems for, 37genome of, 36

Magnetospirillum magnetotacticum , 35, 38electron microscopy study of, 39growth of, 47magneto-aerotaxis for, 35mam22 of, 41MM proteins in, 39, 42

Magnetospirillum magnetotacticum strainMS-1, 26, 36

Magnetospirillum spp., 2527, 36

magnetite crystals in, 32MamB and MamM in, 41

Magnetostatic energy, 34Magnetotactic bacteria

applications of cells of, 49cultivated strains of, 23distribution and ecology of, 2324features of, 2223genetic systems and manipulations in, 37iron oxide-producing, 2325iron sulfide-producing, 2324, 26

magnetic polarities of, 34magnetite magnetosome

biomineralization by, 35magnetosome genes in, 40mass cultivation of, 4849nonmagnetotactic mutants of, 37at oxicanoxic interface (OAI), 23phylogeny and taxonomy of, 2526physiology of, 2630

Magnetotactic cocci, 2527Magnetotactic vibrios, 29

Magnetotaxis, biological advantage of,3435

mam and mms genes, 3944Many-celled magnetotactic prokaryote, 30

greigite crystals in, 3116S rDNAgene sequences from, 26

Martian meteorite ALH84001, 51MC-1, 2729

genome of, 37magnetic field with, 35magneto-aerotaxis for, 35

Medicago sativa, 258Megasphaera elsdenii, 279Metal-reducing bacteria. See Geothrix

fermentans

298 Index


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Metaproteonomics, 87Methane monooxygenase, 5

Methanobacteriaceae, 67, 73Methanobacteriales, 73

Methanobacterium bryantii, 72Methanobrevibacter, 67Methanobrevibacter arboriphilcus , 72Methanocorpusculum, 67Methanocorpusculum parvum, 72Methanogenic archaea, 64Methanogens, 11

Methanomicrobiales , 67, 73Methanomicrococcus-related clones, 75Methanosarcinaceae, 67, 73Methicillin-resistant Staphylococcus aureus,

278, 281Methionine, 240Methyl tertiary (tert)-butyl ether, 1

anaerobic biodegradation, 511carbon isotopic fractionation during,

1314by compound-specific stable isotope

analysis, 1213under methanogenic and suldfidogenic

conditions, 1011in natural attenuation

approaches, 1115under sulfate-reducing conditions, 9

annual production in United States, 23aqueous solubility of, 3carbon isotope ratios or hydrogen of, 12concentrations of, 9as contaminants of water sources, 34environmental fate of, 4as human carcinogen, 4as octane enhancer, 2O-demethylation of, 9

physical and chemical properties of, 4structure of, 2in surface water and groundwater, 4tertiary carbon structure and ether

linkage of, 5Methyl tertiary (tert)-butyl

ether-contaminated groundwater,technologies for remediation of, 5, 15

(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran (R-THMF), chemical structure of, 213

Microbesin acid mine drainage (AMD)

environments, 93in cave environments, 95

in deep subsurface, 96in iron- and sulfur-rich environments,

9395and minerals, 8788

in radioactive environments, 96in soil formation, 91

Microbial arylsulfatase expression, 246Microbial cells, physiological response

of, 122Microbial community

microarray technology for, 86sulfate-reducing bacteria living in, 94

Microbial diversityin geologic systems, 826S approaches of, 8485

Microbial involvement, in surfaceprocesses, 90

Microbial life, on Earth, 97Microbial linguistics, 194Microbial metabolism, 90Microbial metagenomic study, 87Microbial strains, high cell density

cultivation of, 119Microbial sulphur transformations

in nonaerobic soils, 246in soil and rhizosphere, 242

Microorganismsin environments, 87in extreme environments, 92in geochemical environments, 84, 8889metabolic activities of, 91and metals, 9192reduction and oxidation by, 93surface distribution of, 91

MM genes, 3944MMP. See Many-celled

magnetotactic prokaryote

MM proteins, 3944, 51MMS-1, 2526, 2930Mms16 protein, 42Molecular chaperones, 163164Molecular microbial world, 83Mosaic genes, evolution of, 278MRSA. See Methicillin-resistant

Staphylococcus aureusMTBE. See Methyl tertiary (tert)-butyl etherMultilingual bacteria, 215Multiparameter flow cytometry, 124Multiple quorum-sensing systems

ofP. aeruginosa, 199sensory information, integration

of, 198200

Index 299


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Multiple quorum-sensing systems (Cont.)ofV. harveyi, 199200, 216

MV-1 and MV-2, genomes of, 2526, 36Mycorrhizal fungi, 248

Mycorrhization, of plants, 258

N

Nasutitermes takasagoensis, 7273Natural rolling circle-type plasmids,

140141Neisseria meningitidis, in AI-2-mediated QS,

217nisABTCIP, 197Nisin gene cluster, transcription of, 198Nitrophenylsulfate, 258Nitrospira phylum, 25Nonfilamentous microbial cells, biological

behavior of, 117Nucleic acids, isolation of, 51

O

Odontotermes formosanus, 73Oligonucleotide probes, 96Omics analytical technologies, 122Organosulfur mineralization, 245

Oxalobacter formigenes, 280Oxicanoxic interface (OAI), magnetotactic

bacteria at, 2324Oxidized organosulfur, plant assimilation

of, 241N-(3-oxododecanoyl) homoserine lactone,

bactericidal property of, 196

P

P. fluorescens, HdtS from, 194Paraoxonases, 224

pAT187, mobilization of, 162163pBS72, 141pC194 plasmid, 140Pediocin-like bacteriocins. See Class IIa

bacteriocinspE194 plasmid, 140, 147148, 158Peptide-type autoinducers, 195Peptidyl-prolyl isomerases (PPIases),

folding catalysts, 155Pericapritermes nitobei, 73f105MU209, recombinant proteins, 148f105MU331, recombinant proteins, 148149PFR. See Plug flow reactorPhaeospirillum, 25Phages, f105 and SPb, 148

Phanerochaete chrysosporium, 247Phaseolus vulgaris, 241Phosphate, in soil, 237Phosphodiesterase (PhoD), 155

Phospholipid fatty acid analysis (PLFA), 255Phospholipids, 38Photorhabdus luminescens, 203pH-regulated fed-batch culture system, 49Pinus banksiana, 258Pisolithus tinctorius, 258Plantmycorrhiza interaction, 258Plant sulfate assimilation pathways, 237Plant sulfur, amino acids/peptides as source

of, 236Plasmid-encoded resistance genes, 278

pLS32, replication region of, 141Plug flow reactor, 126127, 130Polar magneto-aerotaxis, 27Polymeric sulfonates, 250Porcine kidney acylase, 224ppGpp and cAMP, 123pREP4 and pREP9, 150Prokaryotic communication, language

of, 194Prokaryotic diversity, 87Promoter systems, recombinant protein

production and, 149autoinducible promoters, 153154growth phase-and stress-specific

promoters, 152153inducer-specific promoters, 150152

Propanediol utilization pathway, 274Propane monooxygenase, 5Propylene monooxygenase, 5Protein-protein interactions, 87Proteobacteria, 2526b-proteobacteria, 250, 251

Proton-coupled amino acid transporters, 241Protoplasts, ofB. subtilis, 161162Protozoan grazing, 261PrsA, lipoproteon, 164Pseudomonas aeruginosa, 194, 195, 218

biofilms, 226LuxI/R-type QS systems of, 199sdsA1 gene of, 257

Pseudomonas putida, sulfatase-negativemutants of, 245246

Pseudomonas putida S-313, 249, 259atsK gene of, 257plant growth promotion by, 260

pst operon, ofB. subtilis, 153pT127 and pSN1 plasmid, 140

300 Index


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pTA1015 plasmid, 140pT181 plasmid, 140pUB110 plasmid, 140pUSH1, 158

Q

Quartz, 91Quinone oxidoreductases, folding

catalysts, 165Quorum quenching, practical applications

of, 223, 225226Quorum-sensing inhibitors (QSIs),

screening procedures for, 226227Quorum sensing (QS)

in gram-negative bacteria, 195in gram-positive bacteria, 196in Listeria monocytogenes, 193of sakacin K, 197in V. fischeri, 194ofV. cholerae, 199

R

Ralstonia species, 224Real-time polymerase chain reaction

experiments, 48Remanent magnetization, 31Resistance integrons (RI), 275Resistant bacteria

carriage of, 277spread of, 278

Reticulitermes flavipes, 67, 72Reticulitermes speratus, 67, 72Reverse transcriptase-PCR (RT-PCR), 85Rhizodeposition, 240Rhizosphere

amino acids in, 240241arylsulfatase activities in, 257desulfonation genes in, 250254GFP fluorescence in, 261nitrogen metabolism in, 261sulfatase genes in, 257sulfonate desulfurization by, 249sulfur supply with, 256

Rhodospirillum, 25Rhodospirillum rubrum, 42Ribosome protection-type tetracycline

resistance genes, 279Ribulose-1,5-bisphosphate carboxylase/

oxygenase (RubisCO) gene, 27Rock and mineral substrates, chemical

weathering of, 87, 90

Rolling circle mechanism (RCM), 139141Roseburia inulinivorans, 274RpoS, 123rpsF gene, 152

rRNAand mRNA, 8586PCR-based analyses of, 84

16S rRNA gene sequences, 85Rushton turbine, 111, 128

flooding-loading-complete dispersiontransitions for, 112113

radial flow, 119

S

Saccharomyces cerevisiae, 106, 116, 119sacUh mutation, 167S-adenosylhomocysteine (SAH), 212

detoxification of, 209recycling pathway of, 210

S-adenosyl methionine (SAM), 209, 212, 218Sakacin K, quorum sensing (QS) of, 198Salix mycorrhizosphere, 247Salmonella, 274Salmonella enterica, 194Salmonella genomic islands, 275

Salmonella typhimurium, 221galactose-binding protein from, 214lsr operon of, 214luxS of, 212

SCA. See Single-chain antibodyScrew dislocations, 33Secretion systems, recombinant protein

production in B. subtilis andSec system, 154155SRP system, 156157Tat system, 155156

Sec system, in Bacillus species, 154155Seed maturation, 237Serratia liquefaciens, 194Shear damage, 115, 118Shine-Dalgarno (SD) sequence, 150, 158Siderophores, 201Signal recognition particle (SRP) system, in

Bacillus species, 156157Silicate minerals, weathering of, 9091Single-chain antibody, 155, 163Single magnetic domains, 3132

Single nucleotide polymorphism, 50Single-stranded (ss) DNA, 139141, 16135S-labeled straw, 246SMD. See Single magnetic domainsS-methylmethionine, 240

Index 301


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Soil-derived humic substances, 243Soil-feeding termites, 64, 66, 75

archaeal diversity in, surveys of, 73methanogenesis in, 76

Soil fungi, 247Soil microbes, 241Soil organosulfur, 243, 259Soil S, classification by XANES

method, 244Soil S composition and S flux, 243Soil sulfatase enzymes, 246Soil sulfur, 237238, 240241

mineralization and immobilization of, 242transformations in bacteria, 248

Solanum tuberosum, 225

SP82, phage, 159160S-ribosyl homocysteine (SRH), 209210, 216ssuD and asfA gene, 249250Stable isotopes, fractionation of, 12Staphylococcus aureus, 140

biofilm formation in, 195virulence of, 217

Stirred tank reactorPFR scale-downexperimental model, 130

Stirred tank reactor (STR), 126127Streptavidin-modified magnetosomes, 51

Streptococcus, 274Streptococcus agalactiae, pIP50 1 of, 141Streptococcus oralis 34, 218Streptococcus pneumoniae, 168Streptococcus pyogenes

pSM19035 of, 141virulence factors in, 203

Stress-sensitive genes, mRNAconcentrations of, 122123

Stromatolites, 97Sulfate esters, 241242

hydrolysis of, 245transformations of, 245

Sulfate immobilization, 244245Sulfate transporters, 237Sulfonates, 241242

anaerobic desulfurization of, 247desulfurization, by rhizosphere bacteria,

249250

Sulfur, 93metal-chelating properties of, 236

microbial transformations of (seeMicrobial sulphur transformations)plant demand for, 237in plants (see Plant sulfur)in soil (see Soil sulfur)

Sulfur-containing amino acids, uptakeof, 240241

Sulfur cycle, plant growth promotionand, 259

Sulfur deficiency, in rice paddy soils, 246Sulfur supply

microbial community with, 255mycorrhizal interactions on, influence

of, 258rhizosphere community with, 256

Sulfur transformations, by fungi, 247Super integrons (SI), 275Superparamagnetic particles, 31Swiss-Prot protein database, 87Synbiotics, 281

Synthetic AI-2, 216219

T

TAA. See Tert-amyl alcoholTAME. See Tert-amyl methyl etherTat system, in Bacillus species, 155156TBA. See Tert-butyl alcoholTeichoic acid, 164165Termite guts

Euryarchaeota in, 64detection of, 6771diversity of, 67, 73

isolated Euryarchaeota from, 67role of methanogens in, 64structure and metabolism of, 6465

Termites, 63classification of, 64digestion in, 64methane emission from, 66

Tert-amyl alcohol, TAME biotransformationto, 910

Tert-amyl methyl ether, 1biodegradation of, under sulfate-reducing conditions, 9

biotransformation to TAA, 10O-demethylation of, 9

Tert-butyl alcohol, 1, 5, 9Tetracycline resistance genes, 277

mosaic forms of, 279recombinant forms of, 279ribosome protection-type, 279

Tetracyclines, 151, 271

Tetra-tricopeptide repeat (TPR), 41Thermoplasmalates, 69, 7374Theta-type replication vectors

cloning vectors from, 141146natural plasmids, 141

302 Index


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Thiobacillus species, 95Thiol-disulfide oxidoreductases, folding

catalysts, 155, 165Thiosulfate, 27, 2930

Toluene dioxygenase, 5Toluene monooxygenases, 5Toluenesulfonate, 242, 249Transformation systems, recombinant

protein production in B. subtilis andelectrotransformation, 162mobilization, from E. coli to B. subtilis,

162163natural competence, 160161protoplasts, 161162

Transposon mutagenesis, 37

Trichoderma reesei, mechanical agitationon, 115

Trichomitopsis, 72Trichonympha, 72tRNA genes, 46Turbohypobiosis, 115Tylosin, 271

U

Uncultured Euryarchaeota, in higher and

lower termite guts, 7273Uranium remediation strategies, 96US Environmental Protection Agency, 3US Geological Survey, 3U(VI)-reducing bacteria, 96

V

vanA resistance gene, 277Vancomycin, 281, 283Variovorax paradoxus, 224, 250

Vector systems, of recombinant proteinproduction in B. subtilis

bacteriophage vectors, 148149integrative vectors, 146148

rolling circle-type replication vectors,139141

theta-type replication vectors, 141146Vibrio cholerae, 199, 275Vibrio fischeri

AinS from, 194bioluminescence in, 194quorum sensing (QS) in, 194

Vibrio harveyibioluminescence in, 203, 221interspecies communication in, 215216

multiple QS systems of, 198, 216Vibrio harveyi BB170, AI-2-like activity

in, 222Vibrio harveyi MM30, 215

W

WB600, protease-deficient strain, 166Wood-feeding termites, 64, 6667, 72, 76

X

Xylose, as inducer, 151xylR gene, 151

Y

Yersinia pestis, 276

Z

Zootermopsis angusticollis, methane in, 72Zygomycota, 84

Index 303

[first author] 2007 advances in applied microbiology

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