Index. Index 419. B Bacillus mojavensis, Bacterial cells, 14, 17, 21, 103, 104, 147, 182, 183, 214, 354, 360, 370, 398 isolation, 14, 370

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1 Index 419 Index 13 C NMR, in vivo, , , 396, S rdna, 3 8, 25, 30, 31, 56 58, 159, 160, 235, 412 amplification, 23 27, 62, 78 81, , 325, 407, 408, 411 library construction, 78 A Aeromonads in environmental waters, aquatic systems, 97 Aeromonas spp., 100, A. allosaccharophila, 98 A. caviae, 98, 99 A. hydrophila, A. media, 98 A. salmonicida, 98, 100 A. schubertii, 98 A. sobria, 98, 99 A. trota, 98, 99 Alpha-galactosidase, 121 Archaea, 3, 23, 26, 27, , 284, 389, 408, 409 Aromatic compounds, bioremediation of, 379, 384 Assimilation tests, Azospirillum, 360 and DNA extract cell culture, cellular thermal disruption, 153 obtaining DNA from, RAPD technique, B Bacillus mojavensis, Bacterial cells, 14, 17, 21, 103, 104, 147, 182, 183, 214, 354, 360, 370, 398 isolation, 14, 370 from soil, 17 Bacterial strains, 15, 107, 164, 341, 354, 369 labeling, 12, 20 with CFDA/SE, 105 cell staining, 103 BCG-trehalose-MRS agar, Biochemical studies, 381 Biofilms, 1, , 412 Biological removal, see also Wood lipids, 191, Bioremediation, see also Aromatic compounds, 12, 255, , 412 C Cactoblastis cactorum, 85 Carboxylated microspheres, helper oligos, 56 hybridization, 56 Cellulose, 140, 143, 173, 177, 180, 219, , 281, 283, Chemical shift reagents, and 23 Na NMR, 393, 394, 399 sodium gradients in microorganisms, 389, 391, 401 calculation of, 397 use of ionophores, 395, 401 Chemically defined medium, 140, 141 preparation, 142 Chromatographic analysis, 191, 197 Confocal Laser Scanning Microscope (CLSM), 109, 114, 116 Copper-resistant microorganisms, see PCR Counting (of yeast and bacterial cells), 169, 170, 257, 259, 287 protein determination, 21, 173, 277,

2 420 Index Cross-hybridization, 11, 19, 20 Cultural characteristics, 98 D DGGE, , 414 as fingerprinting tool, DGGE/TGGE, 336, 407, principles, 408 applications, 412 DNA, 4, 7 8, 18, 39 50, 70, 72, 76 80, 86 88, 91 94, 151, 154, 155, 159, , 169, , , 323, 326, 329, 341, 344, 364, 367, 407, 408, 414 extraction techniques, 6, 26, 29 32, 78, 90, 152, 153, 156, 162, 236, 239, 240, 245, hybridization, 11 21, 54, 56, 58, 60, 62, 167, 168, 171, , 366, 411 analyte DNAs in environmental samples, 51, 59, 67, 69 quantification, 167, 170 ethidium bromide, 12, 15, 16, 20 DNA DNA hybridization, see Reverse sample genome probing Denaturing Gradient gel electrophoresis, 31, 236, 323, 336, 407 Detection methods, 99, 108, 167 E Escherichia coli, 26, 41, 44, 49, 56, 57, 77, 99, 105, 171, 236, 237, 243, 244, 329, 336, 367, , 391, , 400 DNA standard, 40, Eucalyptus globulus, 191 EDTA, 4, 5, 28, 70, 76, 87, 88, 153, 161, 237, 238, 244, 270, 272, 280, 326, 327, 398, 414 probe preparation, 169 prehybridization, 168 hybridization, 53, 69, 168 posthybridization, quantification, 12, 281 Exonuclease digestion, see PCR Exopolysaccharides (EPS), , 180 F Fibrobacter succinogenes, cellulose, 173, 177, 180 culture, 181 preparation of cells, 180, 182, 185 glucose, , 396 NMR, , 390, 391, , 402 Fermentation tests, 87, 89 Flow cell, Flow cytometry, 44, 45 49, 51 54, 60 72, 107 bead standards, 54, 60, 63, 65, 66 linear flow cytometry intensity, 54 Fluorescence intensity, 39 42, 45, 47, 63, 107 DAPI DNA complex, 41, 42, 45 Fluorescent staining, and 6-carboxyfluorescein diacetate, succimidyl ester (CFDA/SE), fx (calculation of), 19, 20 G Gas-liquid chromatogram of propolis, 210 GC and GC/MS analysis, 5, 7, 26, 27, 39, 42, 47, 76, 88, 161, 163, , 208, 213, 237, 240, 280, 281, , , 355, 408, 409 Genome probing, 11, 15 21, 167 Giant cacti, 85, 86 Glycogen flux, 179 Glycogen futile cycle, by 13 C NMR, , 396, 402 by 1 H NMR, 173, , 396, 402

3 Index 421 H Habitat and isolation, 3, 83, 85 88, 94, 97, 251, 252, 283, 284, 287, 343, 366, 389 Humic acids, 18, 20 removal from soil DNA, 15, 21 Hydrolytic enzymes and phytopathogenic fungi, 283, 287, 299, 300, 302 Hybridization, see DNA I In situ imaging, 115 In situ 1H NMR, 177, 184 L Lactic acid bacteria (LAB), 14, 121, , 146, 260, 263, 264, 266, 277 differential enumeration, 257 from wine, interaction with yeast, plasmid DNA isolation, purification, 269, 270 nutrition, 138 in functional foods, medium, Lactobacillus casei, 140 Lactobacillus helveticus, 140 Least squares, and evolutionary correlation, 339, 340, 348, 349 Lignocellulosic material, hemicelluloses, 300 Lignin, , 226, 228, Lindane determination, extraction, 280 Lipophilic extractives, , M MRS broth (medium), , 140, 143, 270 Maltodextrins, 174, 178, 179, 185, 186 Microbes, 3 8, 75, 257, 359, 374 populations, 3 8 Microbial community characterization, 3, 190, 235, 285, 367, 368, 374, 407 T-RFLP analysis, N Nutritional requirements, 129, 140, 250, 317 base, 143 vitamins, 139 interpretation, 146 O Oligosaccharides, 177, 284 determination by HPLC, 137 soymilk products, 135 P PCR, 6 8, 25, 51, 53, 66, 72, 77, 86, 93, 159, 160, 163, 246, 323, 324, 330, 331 amplification, 23 27, 52, 62, 78 81, 94, , , , 244, 245, , , 366, of 16S rdna, 24 27, 79, 81, , 408, 411 and copper-resistant microorganisms, primers, 5, 7, 26, 27, 28 31, 54, 55, 58, 59, 70, 71, 76, 79, 80, 88 91, 152, 153, 154, 156, 161, 171, , 243, 244, , , rrna gene, 7, 24, 30, 31, 52 55, 81, 328, 329, 413 product, 29, 32, 67 71, 332, 333, 409 exonuclease digestion of, 52, 58, 59

4 422 Index Pitch deposit control, 189, 190, 195, 199 Plasmid DNA, see also Lactic acid bacteria, Primers, see PCR Propolis, bee glue; hive dross, 203 bioactivity against pathogens, , 211 gas-liquid chromatography, pharmacological activities, 204, 205 thin-layer chromatography, 208 Q Quantification, see DNA R rrna gene, see also PCR, 4, 75, 237, 346, 363 copy number and ecology, PCR, 8, 23, 159 RAPD, 86, 151 assay, PCR reaction, 154 amplification program, 154 electrophoresis, 153, 154 profiles, Removal, see Humic acids, 171, 186, , 213, 251, 301, 306, 382 humic acids, soil DNA, 15, 21 Reverse sample genome probing (RSGP), 11 13, 20, S Solid-phase extraction (SPE) fractionation, 190, 193, 199 Seawater bacteria, 7 isolation, 3, 5 molecular characterization, 3 Sequential culture in liquid media, 276, 277 Silk, bacteriocin, Bombix mori L., 263 sericin, fibroin, 263 Simultaneous cultures in liquid media, Lactobacillus hilgardii, 276 Hanseniaspora uvarum, 276 Soymilk products, , 135 T Terminal restriction fragment length polymorphism (T-RFLP) analysis, see also Microbial community characterization, bacteria, community, ammonia oxidizers, 24 denitrifiers, 24, 27 mercury-resistant bacteria, 27 Trehalose-MRS agar, W Wood lipids, biological removal, 189, 190, 193 Y Yeast, 4, 77, 90, 94, 125, 126, 129, 131, 140, 144, 152, 195, 258, , , 307, 317, 354, 363, 381, 399 extracellular hydrolytic enzymes from, 283 from columnar cacti in NW Argentina, 92, 93 from Prosopis and Acacia spp., 85, 92, 93 heavy metal tolerance, mercury, 250, 254 chromium, 250 cadmium, 250 nickel, 250 qualitative and quantitative resistance screening, 252

5 Index 423 interactions with lactic acid bacteria, Ecology in Northwest Argentina, 83 86, 89, 91, 278 Pichia kluyveri, 84, 92 Pichia fermentans, 84 Torulopsis (Candida) stellata, 92, 93