Heritage Microbiology and Science: Microbes, Monuments and Maritime Materials (Special Publications)

vi Preface Preface vii viii Preface Preface ix xii Contents Contents xiii 4 Heritage Microbiology an...

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vi

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Contents

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Heritage Microbiology and Science

Introduction

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Heritage Monuments and Materials

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D. vulgaris

300 1350 1530 1740 2790 3015 3180 4230 4440 4620 5670

D. desulfuricans

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SUBJECT INDEX

Acidithiobacillus ferrooxidans 118, 209, 213 Acidity 184, 204, 238, 242, 243, 252 Acidobacteria 148, 166, 167, 169, 170, 173 Acidobacterial sequences 167, 169, 170 Acidobacterium 169, 171, 172 Acids 15, 76, 126, 205, 209, 217, 246, 248, 250, 252, 254, 255, 257 humic 101, 112, 115, 116 sulfuric 76, 77 Actinobacteria 48, 161, 162, 164, 167, 213 Algae 12, 13, 19, 20, 39, 41, 42, 51, 53, 143, 144 Altamira Cave 103, 104, 166, 167, 169–173 Alterations 11, 12, 14–16, 30–32, 51, 63, 76, 77, 80, 86, 87 Amplifications 101, 102, 118, 151, 158, 168 Angkor Wat 19–21, 26, 31, 32, 34 Anodes 258, 260, 261, 263, 269, 273, 276 Archaeological sites 15, 24, 25, 155, 158, 160, 180, 190, 198, 199, 201, 202 of Milet 22 wood 115, 151, 154, 155, 185, 240 waterlogged 109, 141, 151, 153, 201 Archaeology 3, 15, 129, 140, 179, 200, 202, 279, 289, 293 Arsenic 130, 132 Arthrobacter 48, 49, 59, 157 Autofluorescence 120, 121, 124, 147

Beetles, death watch 228, 229 BIOBRUSH (EU Project) 76, 78, 79, 92 Biocidal treatments 11, 17, 19, 20, 24 Biocides 14, 17, 51, 52, 56, 57, 168, 269, 271, 273, 276, 277 commercial 52, 57, 59 BIODAM (EU Project) 56, 60 Biodegradation 25, 43, 92, 93, 155, 201 Biodeterioration 11, 13–16, 18, 26, 39, 44, 60, 61, 65, 74, 79, 97–99, 104, 105, 143–145, 155, 165, 166 processes 12–16, 19, 24, 79, 104, 105 Biofilms 11, 12, 14, 39, 40, 51, 59, 60, 120, 147, 158, 159, 162, 163, 165, 209, 278, 294 epilithic biofilms 162–164 Biofouling 12, 44, 78, 79, 92, 165 Biomass 40, 41, 43, 163, 164 Biomineralization 62, 73, 74 BIOREINFORCE (EU Project) 65, 73 Bioremediation 4, 62, 65, 76, 78, 80, 83, 84, 86, 87 BisBAL 52, 55–57, 59, 60 Blastobacter 152 Blocking agent 116, 120, 121, 124, 125 Burgzand Noord (BZN) 182, 187–189, 201, 202 Burial 15, 181, 200, 204 environment 192, 198 site 212

Bacillus 48, 49, 216 BACPOLES (EU Project) Final report 201, 202 Bacteria biocalcifying 78, 80, 81, 84 iron-oxidising 118, 121, 205, 209, 213 iron-reducing 121, 169, 208 nitrate-reducing 80, 84 sulfate-reducing 18, 23, 80, 182, 212, 213 wood-degrading 151 wood-inhabiting 152, 155 Bacterial cell fractions 65, 68, 73 Bacteroidetes 161, 162, 167, 212 Baltic Sea 181, 189, 200 Barrier, anti-graffiti 52–54 Beams electron 129 stored 129, 211, 213

Calcium 37, 68, 135, 168, 245, 246, 249, 250, 252 carbonate 62, 63, 134 sulfate (see also gypsum) 134, 135, 245 Calceine 68, 70, 71 Calcite 63, 65, 70–73, 78, 82 Cambodia 12, 18, 19, 31 Canvas 203, 236, 237, 239, 242 Carbogel 84, 85, 87–91 Carrier 84, 87, 89, 91, 115, 116 Cathode 258, 260, 270, 273 Caves 4, 103, 167, 170, 173, 294 cDNA (complementary or copy DNA) 118, 211 Cellulose 115, 135, 136, 151, 152, 154, 238, 239, 241, 246 Chimeras 102, 159 Chlorella 42, 43

Subject Index Chloride 18, 252, 258–260, 265, 266, 273, 281 ions 258–261, 265, 266, 273, 276, 277 electrolytic removal of 261, 276, 277 sodium 261, 266, 273, 276, 277 Chlorophyll 40, 56 Chroma values 55 Classification 30, 32–34, 166 scheme 29, 31, 32 systems 29, 30 unsupervised 30, 32, 33, 35 user-defined 34, 37 Clay 190, 191 Clone(s) 100, 102, 118, 152–154, 162, 168, 211 libraries 116, 117 Cloth 196, 237, 238 Colonisation 13, 39, 41, 45, 51, 53, 91, 104, 192 Colour 29, 30, 55–57, 59, 63, 70, 132, 296 Conservation 5–7, 19, 24–26, 31, 37, 60–63, 65, 74, 92, 93, 125, 126, 173, 174, 242–244, 259, 260, 276–278, 293, 294 fluid 209, 211 plan 280, 289 practice 16, 24, 25, 30, 78, 79 procedures 17, 266 products 52, 54, 59, 63 strategies 11, 12, 98 treatments 12, 16, 17, 22, 24, 30, 31, 52, 53, 77, 80, 198, 242 work 22, 228, 276 Consolidation 17, 65 Contamination 12, 13, 15, 20, 21, 132 Corrosion 18, 76, 139, 140, 246, 258, 259, 261, 266, 273, 277, 279–284, 286–289 control 279, 280, 282, 283, 288 processes 15, 246, 258, 279, 280, 283 products 137, 140, 258–260, 273, 280, 281, 283, 286–288 Crusts 11, 22, 23, 45, 46, 48, 78, 80, 85, 90, 134, 135, 258 black 29, 76, 77, 135 Crystals, crystalline structures 62, 63, 77, 86, 91 Cultural artefacts 11–13, 16, 24, 109, 157, 164 assets 97, 98, 105, 166 heritage 14, 25, 62, 74, 75, 79, 97, 98, 101, 103, 105, 106, 126, 127, 129, 149, 166, 174, 175, 179, 180 sites 117, 181, 199, 200 Culture collections 80, 81, 84, 90 Cutty Sark 213, 265–267, 269, 277 Cyanobacteria 12, 17, 19, 20, 23, 39–42, 51, 143, 144, 149, 156, 161–164, 167, 173 Damage 23, 30, 31, 79, 91, 110, 136, 222, 223, 227, 228, 237–239, 246, 266, 276 microbially-influenced material 24

301 Darsser Cog 189, 202 Decay 30, 37, 109, 194, 221, 222, 226–228, 232 Deck 231, 266 lower gun 231, 233 Degradation 25, 27, 37, 121, 151, 155, 181, 182, 185, 195, 258, 259, 266, 275–277 bacterial 109, 110, 181 Dehydration 145, 283, 284 Delivery systems 79, 84, 87, 89, 90 Density 57, 185–187, 190, 196, 202, 261 current 261, 273, 276, 277 Desiccation 280, 282 Desulfobacterium 213 DGGE (denaturing gradient gel electrophoresis) 100, 104, 116, 117, 156 Diffraction patterns 133–135 Dissolved oxygen 181, 195, 198, 199, 260 Diversity 102, 108, 116, 120, 151, 163, 166, 167, 169, 170, 173, 213, 217, 293, 294 acidobacterial 167, 170, 173 bacterial 108, 115, 151, 155, 170 microbial 99, 108, 118, 151, 154 DNA (deoxyribonucleic acid) 5, 97, 99–105, 108, 110–112, 114–119, 153, 158, 167, 168, 210, 298 environmental 116, 118, 157 fragments 99, 101, 102, 105, 166, 169 microarrays 105 Douglas fir 226, 227, 229–231, 234 Dry dock 234, 262, 265, 266, 280 EDDHMA 247–249, 254, 255 EDTA (ethylenediaminetetraacetic acid) 113, 122, 145, 246, 247 Efficacy 23, 24, 56, 59, 84, 192, 198 Efficiency 64, 70–73, 115, 261, 269 Electrolysis 257, 259–261, 264–266, 269, 272, 273, 275–277 Electrolyte 258, 259, 261, 266, 269, 273, 279–281 Electrolytic treatment 259–261, 263, 265, 266, 273, 276, 277 Environmental conditions 12, 15, 17, 23, 24, 63, 87, 103, 108, 109, 156, 159, 163, 194, 258 signals 120, 217 site analysis 11 Environments controlled 238, 242, 281 hypogean 148, 149 oxic 208, 209 EPS (extracellular polysaccharide or extracellular polymeric substances) 13, 51, 52 ERDAS Imagine© (image analysis software) 33–36 Erosion 109, 133, 181, 182, 184, 187, 189, 191, 194 bacteria 116, 117

302 Excavation 3, 5, 7, 11, 15–17, 152, 180, 182, 187, 189, 190, 194, 198 site 17, 18 Extraction 64, 110–113, 249, 250, 252–255 Fabric 27, 237, 238, 241, 242 FeOOH 281–283, 285–288 Ferrous chloride 281–284, 287, 288 hydrate, stable 283, 286 Fibres 135, 136, 237, 238, 242 Field trials 52, 59, 60, 81, 84, 86, 87, 89, 91, 195 Fingerprinting techniques 100 FISH (fluorescent in-situ hydridisation) 104, 108, 120–125, 143–145, 156 technique 120, 144, 147, 149 Flagship 3, 7, 219, 223, 236 Fluorochromes 143 Formamide 100, 122, 123, 145 Foundation piles 201, 202 Framework, common spatial 29, 32, 37 Fungi 17, 19, 21, 39, 40, 44–46, 52, 59, 103, 118, 143, 144, 156, 157, 181, 185, 192, 296 Gamma-Proteobacteria 212, 213 Geobacter 154 GIS 27–34, 36, 37 Glass 11, 15, 45, 46, 48, 49, 120, 198, 294 stained 46, 48 surfaces 45 Gloeocapsa 42 Gotland sandstone 80, 91 GRADOC 31, 38 Growth media 81, 86 Gypsum 77, 85, 134, 135, 205, 245 Heritage 3, 7, 31, 38, 50, 79, 106, 149, 200, 202, 293 materials 4, 5, 7, 60, 79, 125, 130, 278, 294, 295, 299 Historic monuments 40, 42, 156, 157 sites 12, 18, 24, 280 HMS Victory 219, 220, 222–225, 229–235, 243, 293 Trafalgar sail 236–238, 242, 243 Hull 3–5, 118, 186, 189, 194, 204, 211–213, 216, 219–223, 225, 226, 229, 245, 246, 261, 266, 280, 281 planking 226, 227, 229 timbers 204, 205, 209 Humidity 14–17, 55, 77, 259, 281, 284, 287, 288 Hybridisation buffers 122, 123 Hydrocerussite 137, 138

Subject Index Image analysis 32, 71, 73, 147 Iron 12, 84, 118, 130, 132, 133, 182, 198, 213, 245–252, 254, 255, 257, 258, 269–271, 279, 281–284, 286–289 Age 130, 151, 152 archaeological 130, 282 chloride-infested 281 composites 258 compounds 245, 246, 250, 251, 254, 255, 276 extraction of 245, 250, 253, 256 concentrations of 245, 246, 249 content, estimated total 251, 252 conversion of 286–288 corrosion of 140, 181, 279–285 cycles 205, 208 frames 266 hull 280, 281 oxidation of 139, 208, 284, 287 oxide 207, 259, 286 powder 281, 283, 285, 287, 288 ship 289 sulfides 118, 182, 204, 245, 246, 253 wood/ 273 tubercules, build-up of 269, 271 -reducing bacteria 121, 266 Ironwork 266, 267 Isoamyl alcohol 111 James Matthews 181, 194, 195, 197, 200–202 Japanese paper 84, 90 Keel 219, 220, 222, 233, 266 Knees 222, 228–231 Leucobacter 48, 49 Libraries 12, 118, 212, 213 Lichens 12, 19, 20, 45, 51, 156 Ligand 247, 251, 254 Lignin 151, 154, 182, 204, 239, 252, 254, 255 Limestone 42, 60, 64, 65, 80–82, 86, 164 Linen 238, 239, 241, 242 aged 239, 240 fibres 237, 239 sailcloth 240–243 Locharbriggs stone 57–59 Malachite 137–139 Maps 27, 28, 30, 132, 151, 182, 269 Marble 23, 24, 39, 60, 65, 87, 88, 91, 135, 144 surface 23, 24 Marine environments 37, 181, 185, 198, 199, 213, 217, 260, 277 sediments 62, 172, 181, 204, 206, 212, 213 Mary Rose 3–7, 114, 118, 139, 182, 204, 205, 209, 211–213, 216, 238, 243, 277, 293

Subject Index Matera Cathedral 80, 81, 86, 89 Materials archaeological 5, 198, 199 bolting 258, 266–268 composite 62, 130 inorganic 62, 269, 276, 277 Mats 192, 194, 196, 278 microbial 23 Mayan buildings 40 Mesh, synthetic 194 Metals 11, 17, 18, 26, 133, 136, 181, 182, 197, 198, 203, 204, 229, 249, 258–260, 269, 273, 276, 277, 294 Methylobacterium 216 Microbial biofilms 12, 13, 19, 20, 24 communities 20, 25, 45, 97–100, 103, 105, 116, 143, 147, 149, 156, 157, 173, 269, 294, 295 community analysis 157 consortia 12–14 contamination 13, 14, 16, 17, 80, 273 populations 143, 145, 210 Microbially Influenced Corrosion 50, 165 Microbiological methods culture-independent 99, 156 traditional 91, 92, 156 Microelectrodes 198, 199 Microorganisms 11–16, 23, 39, 40, 45, 78–80, 86, 97–100, 102–106, 143, 144, 147, 148, 155–158, 166, 169, 170, 269, 294–296 detection of 98, 99, 104, 105, 166 heterotrophic 59 metabolism of 99 molecular surveys of 102, 103 water-borne 15 Milan Cathedral 86–88 Milet 22, 24 Molecular techniques 97, 99, 108, 112, 143, 205 amplification 168, 169 primers 113, 116, 157, 168, 169, 212 probes 120, 121, 123, 124, 132, 138, 143–145, 147, 148, 239 Monitoring 17, 19, 22, 27, 89, 104, 105, 182, 186, 187, 189, 198, 199, 201 programme 196, 197 wooden shipwrecks 201 Monuments 16, 22, 60, 73, 78, 80, 86, 97, 101, 102, 105, 156, 158, 162–164, 295 Mortar 4, 6, 22, 51, 74, 84, 85, 89, 91, 113 Mural paintings conservation 38 Museums 5, 6, 16, 200, 201, 203, 233, 234, 259, 299 NIR (Near Infrared) 240, 242 Nets 187–191, 194, 202 polypropylene 189–191

303 Nickel 130, 132, 165 Nitrates 13, 76–78, 80, 86, 87, 89, 92, 207, 252 Nostoc 42, 43 NRB, (nitrate-reducing bacteria) 80, 83, 84, 87, 89, 91 Nucleic acids 99, 110, 112, 115, 116, 147, 159 Nucleotides 119, 166, 168, 170, 214, 215 Nydam 17, 18, 151, 152 Oak 108, 110, 114, 117, 124, 192, 198, 220, 221, 226–231, 234 Obernkirchen stones 57–59 Organic materials 11, 144, 181, 182, 190, 192, 195, 198, 239, 273 Oxygen 11, 13, 15, 17, 98, 181, 184, 196, 199, 205–207, 213, 246, 258, 260, 261, 279 Paintings 15, 76, 103, 167, 169, 173, 296 PCR (Polymerase Chain Reaction) 99, 101, 108, 114–119, 151, 166 amplifications 97, 101, 102, 153 inhibitors 101, 115 standard 101, 102 PEG (polyethylene glycol) 111, 114, 115, 209, 246, 250, 252, 253, 255 pH 11, 14, 51, 83, 84, 121, 122, 124, 145, 184–186, 194, 195, 198, 199, 209, 210, 247–250, 252, 261, 276, 277 Photosynthetic algae 23 Phylogenetic analyses 99, 118, 153, 159, 168–170, 173, 211 Pine, pitch 226, 227, 230, 231, 234 Planktosphaeria 42 Pleurococcus 42 PLFA (phospholipid fatty acid) 40, 157, 164 profiles 159, 163 Polders 187, 202 Polyethylene 90 glycol (see also PEG) 114, 115, 209, 246, 255 Polysaccharides 112, 115 Pores 65, 71, 72, 156, 239 Porosity 11, 13, 24, 56, 63, 65, 68, 70, 80, 87, 91 Precipitation 62, 63, 115, 245 Preservation 5, 7, 15–17, 24, 77, 137, 166, 167, 195, 233, 237, 242, 266 state of 185, 186, 194, 217 Preventol A8 56–60 Primers (see molecular) Probes (see molecular) Proteobacteria 118, 153 Pyrite 118, 205–207, 209 rDNA (DNA coding for rRNA) 46, 47, 108, 153, 168, 169 Reburial 182, 185–187, 198, 199, 202, 203 projects 185, 195, 199–201 trenches 198, 199

304 Red alizarine 70, 71 Redox 11, 184, 186, 194, 195, 198, 199 Relative humidity 31, 55, 163, 240, 241, 280–289 low 280, 283, 287 programme 288 Restoration 19, 24, 25, 45, 46, 79, 219, 225, 226, 231, 235 RNA (ribonucleic acid) 97, 103, 104, 108, 110, 112, 114–119, 210, 211 clean-up 113 extraction of 113, 114 sample 113, 114, 119 digested 114 rRNA 108, 118, 148, 166, 167, 169, 216 gene sequences 99, 169, 170 genes 99, 143, 151, 166, 168–170, 173 Rubrobacter 162 Sail 236–239, 242, 243 Sailcloth 236, 237 Salinibacter 162, 164 Salts 15, 37, 78–80, 91, 115, 164, 205, 245, 255, 261, 281 Sand 5, 25, 165, 185, 187, 190, 195 Sandbags 186, 187, 189–191, 195, 196 Sandstone 18, 39, 42, 52, 56, 59, 60 Sandy soil 171, 172 Scaffolding nets 189, 191, 194, 202 Scour 181, 182, 192, 196 Scytonema 40, 42, 43 Seabed response 195–197 Seawater 181, 205, 281 Sediment 18, 74, 110, 112, 181, 182, 184, 186, 187, 189–192, 194–196, 198, 199, 206, 211–213, 216, 217 Sequencing 100, 105, 118, 153, 155, 158, 168 Shade cloth 196, 197 mat 196, 197 Ship 6, 139, 179, 182, 187, 189, 190, 204, 205, 222, 225–227, 233, 261, 262, 265, 266, 269, 276, 277, 280, 281 screw-driven 280 timbers 114, 115, 118, 216 wooden 222 Shipwreck sites 179, 181, 182, 195, 199 registered historic 180 SRB 80, 84, 87, 90, 91, 266 ss Great Britain Trust 280, 288, 289 SSCP (single strand conformation polymorphism) profiles 158, 159, 161 Stone(s) 19, 20, 26, 39, 52–54, 56, 57, 59, 63, 65, 70, 76–80, 84–87, 89–91, 134, 156, 165 conservation of 25, 26, 37, 74, 92, 93 materials 64, 65, 70, 73, 80, 83, 86 monumental 64, 71, 73

Subject Index natural 13, 18, 19, 63, 80 porosity 64, 71, 72 protectives, microbially-resistant 22 surfaces 20, 54, 59, 60, 63, 68, 70, 73, 79, 81, 84 Sulfate 18, 76, 78, 80, 83, 86, 87, 90, 91, 181, 182, 205, 206, 209, 210, 245, 252, 253 Sulfides 182, 198, 199, 206, 209, 210, 245 Sulfur 5, 110, 126, 139, 204–206, 209, 213, 217, 249, 252, 253, 255 compounds 204, 245, 253, 255 reduced 204 cycle 205–207 reduced forms of 245, 253 Sulfuric acid 182, 204, 209, 245, 246 Surfaces 20, 23, 29, 30, 39, 41, 51–54, 56, 134–138, 147, 148, 158, 209, 210, 238, 239, 245, 246, 252–255, 259 external 39, 72, 160, 162, 164 heritage 51, 52, 59, 60 inner 13, 139, 159, 163 metal 258, 277 test 56, 59 unpainted 41, 43 Synchrotron radiation 128–130, 140, 141, 276 sources 128–130, 139 Synechococcus 42, 43 Synechocystis 42, 43 Teak 226–232, 234, 266 Temples 18, 22, 158 Teredo 181, 185, 200 Terracotta warriors 16, 17 Terram 190, 192, 194, 195 Textiles 11, 16, 18, 135, 198, 239, 242, 243, 294 Thiobacillus 118, 213, 216, 217 Thiosulfate pathways 208–210 Timbers 5, 118, 181, 187, 194, 195, 204, 205, 213, 216, 217, 219, 220, 222, 228, 231–234, 266, 268, 269, 276 buried softwood 109 exposed 5, 192, 194, 195 rotten 228 Trentepohlia 42 T-RFLP (terminal restriction fragment length polymorphism) 116, 151 Tricyclazole 55–57, 59 Underwater heritage sites 179 maritime heritage sites 180 sites 187, 200 post-excavation 186 UV (ultraviolet) light 70, 71, 119 Uxmal 40, 41, 158, 160

Subject Index Vasa 114, 118, 120, 121, 124, 126, 139, 182, 204, 209, 217, 245, 249, 252, 255, 256 wood 245, 246, 254, 255 Victory (see HMS Victory) Wadden Sea 181, 182, 184, 187, 189–191, 201 Wall 30, 32, 39, 41, 159, 296 wood cell 185, 204 Water 11, 13–15, 23, 39, 56, 64, 68, 76, 77, 208, 209, 239–241, 245, 246, 252–254, 266, 279–281, 285, 286 absorption 54, 70, 72, 91 capillary absorption 53, 54, 59 column 181, 184, 187, 194, 196 content 239 level 22, 23, 269 porosity 65, 68 uptake 70, 91 Water-repellent 52–54, 63 Weathering 27, 30, 54, 55, 92, 135, 140 forms 27, 30–33 William Salthouse 192, 193 Wood 11, 17, 18, 108–117, 121, 125, 154, 155, 181, 186, 197, 198, 204, 205, 217, 218, 245, 246, 249–256, 269, 270, 276, 277 core samples of 266, 273 deterioration 121, 125 matrix 246, 251, 254

305 preventing bacterial decay of 201, 202 samples 111–115, 245, 249, 254 dried 111 environmental 111, 113 eroded 120 mashed oak 121, 124 pine 181 in situ 185 surfaces 245, 249, 253 waterlogged 108, 109, 110, 120, 185, 254, 255 archaeological 151, 154 density of 185 pine 245 Wooden poles 190 shipwrecks 181 warships 222, 224, 233 Wreck 179, 182, 187, 189, 192, 194, 196–198, 200–202, 212 site 4, 5, 185, 186, 189, 194, 197, 246 Wrought iron 266, 268, 269, 271, 273, 274, 276, 277, 288 X-rays 128, 138–140 XRD (X-ray diffraction) 133, 135, 281, 283 Yarns 237, 238, 242 Yucatan 158, 160, 165

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Heritage Microbiology and Science: Microbes, Monuments and Maritime Materials (Special Publications)

Conservation Science: Heritage Materials

Recent Advances in Actinide Science (Special Publications)

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Lipids in Health and Nutrition (Special Publications)

Materials science and engineering

Miles, Mutants and Microbes

Combining and Reporting Analytical Results (Special Publications)

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Maritime Delimitation (Publications on Ocean Development, 53)

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Microbes: Applications and Effects

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Composite Materials: Science and Applications

Contemporary Boron Chemistry (Special Publications)

Composite Materials: Science and Applications

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Nanoporous Materials: Science and Engineering

Ceramic Materials: Science and Engineering

Particle Size Analysis (Special Publications)

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