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 and Science

Introduction 5


Introduction 7



Heritage Monuments and Materials 13

































































4,000

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0 120 180 300 1350 1530 1740 2790 3015 3180 4230 4440 4620 5670

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D. vulgaris D. desulfuricans












Molecular Methods for Heritage Artefacts and Monuments 99








































































Historic Ships and their Preservation 181








































































































Endnote 295


Endnote 297


Endnote 299

SUBJECT INDEX

Acidithiobacillus ferrooxidans 118, 209, 213Acidity 184, 204, 238, 242, 243, 252Acidobacteria 148, 166, 167, 169, 170, 173Acidobacterial sequences 167, 169, 170Acidobacterium 169, 171, 172Acids 15, 76, 126, 205, 209, 217, 246, 248, 250,

252, 254, 255, 257humic 101, 112, 115, 116sulfuric 76, 77

Actinobacteria 48, 161, 162, 164, 167, 213Algae 12, 13, 19, 20, 39, 41, 42, 51, 53, 143,

144Altamira Cave 103, 104, 166, 167, 169–173Alterations 11, 12, 14–16, 30–32, 51, 63, 76, 77,

80, 86, 87Amplifications 101, 102, 118, 151, 158, 168Angkor Wat 19–21, 26, 31, 32, 34Anodes 258, 260, 261, 263, 269, 273, 276Archaeological

sites 15, 24, 25, 155, 158, 160, 180, 190, 198,199, 201, 202

of Milet 22wood 115, 151, 154, 155, 185, 240

waterlogged 109, 141, 151, 153, 201Archaeology 3, 15, 129, 140, 179, 200, 202, 279,

289, 293Arsenic 130, 132Arthrobacter 48, 49, 59, 157Autofluorescence 120, 121, 124, 147

Bacillus 48, 49, 216BACPOLES (EU Project) Final report 201, 202Bacteria

biocalcifying 78, 80, 81, 84iron-oxidising 118, 121, 205, 209, 213iron-reducing 121, 169, 208nitrate-reducing 80, 84sulfate-reducing 18, 23, 80, 182, 212, 213wood-degrading 151wood-inhabiting 152, 155

Bacterial cell fractions 65, 68, 73Bacteroidetes 161, 162, 167, 212Baltic Sea 181, 189, 200Barrier, anti-graffiti 52–54Beams

electron 129stored 129, 211, 213

Beetles, death watch 228, 229BIOBRUSH (EU Project) 76, 78, 79, 92Biocidal treatments 11, 17, 19, 20, 24Biocides 14, 17, 51, 52, 56, 57, 168, 269, 271,

273, 276, 277commercial 52, 57, 59

BIODAM (EU Project) 56, 60Biodegradation 25, 43, 92, 93, 155, 201Biodeterioration 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, 105Biofilms 11, 12, 14, 39, 40, 51, 59, 60, 120,

147, 158, 159, 162, 163, 165, 209, 278, 294

epilithic biofilms 162–164Biofouling 12, 44, 78, 79, 92, 165Biomass 40, 41, 43, 163, 164Biomineralization 62, 73, 74BIOREINFORCE (EU Project) 65, 73Bioremediation 4, 62, 65, 76, 78, 80, 83,

84, 86, 87BisBAL 52, 55–57, 59, 60Blastobacter 152Blocking agent 116, 120, 121, 124, 125Burgzand Noord (BZN) 182, 187–189, 201, 202Burial 15, 181, 200, 204

environment 192, 198site 212

Calcium 37, 68, 135, 168, 245, 246, 249, 250, 252

carbonate 62, 63, 134sulfate (see also gypsum) 134, 135, 245

Calceine 68, 70, 71Calcite 63, 65, 70–73, 78, 82 Cambodia 12, 18, 19, 31Canvas 203, 236, 237, 239, 242Carbogel 84, 85, 87–91Carrier 84, 87, 89, 91, 115, 116Cathode 258, 260, 270, 273Caves 4, 103, 167, 170, 173, 294cDNA (complementary or copy DNA) 118, 211Cellulose 115, 135, 136, 151, 152, 154, 238,

239, 241, 246Chimeras 102, 159Chlorella 42, 43

Subject Index 301

Chloride 18, 252, 258–260, 265, 266, 273, 281ions 258–261, 265, 266, 273, 276, 277

electrolytic removal of 261, 276, 277sodium 261, 266, 273, 276, 277

Chlorophyll 40, 56Chroma values 55Classification 30, 32–34, 166

scheme 29, 31, 32systems 29, 30unsupervised 30, 32, 33, 35user-defined 34, 37

Clay 190, 191Clone(s) 100, 102, 118, 152–154, 162, 168, 211

libraries 116, 117Cloth 196, 237, 238Colonisation 13, 39, 41, 45, 51, 53, 91, 104, 192Colour 29, 30, 55–57, 59, 63, 70, 132, 296Conservation 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, 211plan 280, 289practice 16, 24, 25, 30, 78, 79procedures 17, 266products 52, 54, 59, 63strategies 11, 12, 98treatments 12, 16, 17, 22, 24, 30, 31, 52, 53,

77, 80, 198, 242work 22, 228, 276

Consolidation 17, 65Contamination 12, 13, 15, 20, 21, 132Corrosion 18, 76, 139, 140, 246, 258, 259, 261,

266, 273, 277, 279–284, 286–289control 279, 280, 282, 283, 288processes 15, 246, 258, 279, 280, 283products 137, 140, 258–260, 273, 280, 281,

283, 286–288Crusts 11, 22, 23, 45, 46, 48, 78, 80, 85, 90, 134,

135, 258black 29, 76, 77, 135

Crystals, crystalline structures 62, 63, 77, 86, 91Cultural

artefacts 11–13, 16, 24, 109, 157, 164assets 97, 98, 105, 166heritage 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, 200Culture collections 80, 81, 84, 90Cutty Sark 213, 265–267, 269, 277Cyanobacteria 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

Darsser Cog 189, 202Decay 30, 37, 109, 194, 221, 222, 226–228, 232Deck 231, 266

lower gun 231, 233Degradation 25, 27, 37, 121, 151, 155, 181, 182,

185, 195, 258, 259, 266, 275–277bacterial 109, 110, 181

Dehydration 145, 283, 284Delivery systems 79, 84, 87, 89, 90Density 57, 185–187, 190, 196, 202, 261

current 261, 273, 276, 277Desiccation 280, 282Desulfobacterium 213DGGE (denaturing gradient gel electrophoresis)

100, 104, 116, 117, 156Diffraction patterns 133–135Dissolved oxygen 181, 195, 198, 199, 260Diversity 102, 108, 116, 120, 151, 163, 166, 167,

169, 170, 173, 213, 217, 293, 294acidobacterial 167, 170, 173bacterial 108, 115, 151, 155, 170microbial 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, 157fragments 99, 101, 102, 105, 166, 169microarrays 105

Douglas fir 226, 227, 229–231, 234Dry dock 234, 262, 265, 266, 280

EDDHMA 247–249, 254, 255EDTA (ethylenediaminetetraacetic acid) 113,

122, 145, 246, 247Efficacy 23, 24, 56, 59, 84, 192, 198Efficiency 64, 70–73, 115, 261, 269Electrolysis 257, 259–261, 264–266, 269, 272,

273, 275–277Electrolyte 258, 259, 261, 266, 269, 273, 279–281Electrolytic treatment 259–261, 263, 265, 266,

273, 276, 277Environmental

conditions 12, 15, 17, 23, 24, 63, 87, 103,108, 109, 156, 159, 163, 194, 258

signals 120, 217site analysis 11

Environments controlled 238, 242, 281hypogean 148, 149oxic 208, 209

EPS (extracellular polysaccharide or extracellularpolymeric substances) 13, 51, 52

ERDAS Imagine© (image analysis software) 33–36Erosion 109, 133, 181, 182, 184, 187, 189, 191,

194bacteria 116, 117

302 Subject Index

Excavation 3, 5, 7, 11, 15–17, 152, 180, 182,187, 189, 190, 194, 198

site 17, 18Extraction 64, 110–113, 249, 250, 252–255

Fabric 27, 237, 238, 241, 242FeOOH 281–283, 285–288Ferrous chloride 281–284, 287, 288

hydrate, stable 283, 286Fibres 135, 136, 237, 238, 242Field trials 52, 59, 60, 81, 84, 86, 87, 89,

91, 195Fingerprinting techniques 100

FISH (fluorescent in-situ hydridisation) 104,108, 120–125, 143–145, 156

technique 120, 144, 147, 149Flagship 3, 7, 219, 223, 236Fluorochromes 143Formamide 100, 122, 123, 145Foundation piles 201, 202Framework, common spatial 29, 32, 37Fungi 17, 19, 21, 39, 40, 44–46, 52, 59, 103,

118, 143, 144, 156, 157, 181, 185, 192, 296

Gamma-Proteobacteria 212, 213Geobacter 154GIS 27–34, 36, 37Glass 11, 15, 45, 46, 48, 49, 120, 198, 294

stained 46, 48surfaces 45

Gloeocapsa 42Gotland sandstone 80, 91GRADOC 31, 38Growth media 81, 86Gypsum 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

Historicmonuments 40, 42, 156, 157sites 12, 18, 24, 280

HMS Victory 219, 220, 222–225, 229–235, 243,293

Trafalgar sail 236–238, 242, 243Hull 3–5, 118, 186, 189, 194, 204, 211–213,

216, 219–223, 225, 226, 229, 245, 246,261, 266, 280, 281

planking 226, 227, 229timbers 204, 205, 209

Humidity 14–17, 55, 77, 259, 281, 284, 287, 288

Hybridisation buffers 122, 123Hydrocerussite 137, 138

Image analysis 32, 71, 73, 147Iron 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, 152archaeological 130, 282chloride-infested 281composites 258compounds 245, 246, 250, 251, 254, 255, 276

extraction of 245, 250, 253, 256concentrations of 245, 246, 249content, estimated total 251, 252conversion of 286–288corrosion of 140, 181, 279–285cycles 205, 208frames 266hull 280, 281oxidation of 139, 208, 284, 287oxide 207, 259, 286powder 281, 283, 285, 287, 288ship 289sulfides 118, 182, 204, 245, 246, 253wood/ 273tubercules, build-up of 269, 271-reducing bacteria 121, 266

Ironwork 266, 267Isoamyl alcohol 111

James Matthews 181, 194, 195, 197, 200–202Japanese paper 84, 90

Keel 219, 220, 222, 233, 266Knees 222, 228–231

Leucobacter 48, 49Libraries 12, 118, 212, 213Lichens 12, 19, 20, 45, 51, 156Ligand 247, 251, 254Lignin 151, 154, 182, 204, 239, 252, 254, 255Limestone 42, 60, 64, 65, 80–82, 86, 164Linen 238, 239, 241, 242

aged 239, 240fibres 237, 239sailcloth 240–243

Locharbriggs stone 57–59

Malachite 137–139Maps 27, 28, 30, 132, 151, 182, 269Marble 23, 24, 39, 60, 65, 87, 88, 91, 135, 144

surface 23, 24Marine

environments 37, 181, 185, 198, 199, 213,217, 260, 277

sediments 62, 172, 181, 204, 206, 212, 213Mary Rose 3–7, 114, 118, 139, 182, 204, 205,

209, 211–213, 216, 238, 243, 277, 293

Subject Index 303

Matera Cathedral 80, 81, 86, 89Materials

archaeological 5, 198, 199bolting 258, 266–268composite 62, 130inorganic 62, 269, 276, 277

Mats 192, 194, 196, 278microbial 23

Mayan buildings 40Mesh, synthetic 194Metals 11, 17, 18, 26, 133, 136, 181, 182, 197,

198, 203, 204, 229, 249, 258–260, 269,273, 276, 277, 294

Methylobacterium 216Microbial

biofilms 12, 13, 19, 20, 24communities 20, 25, 45, 97–100, 103, 105,

116, 143, 147, 149, 156, 157, 173, 269,294, 295

community analysis 157consortia 12–14contamination 13, 14, 16, 17, 80, 273populations 143, 145, 210

Microbially Influenced Corrosion 50, 165Microbiological methods

culture-independent 99, 156traditional 91, 92, 156

Microelectrodes 198, 199Microorganisms 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, 166heterotrophic 59metabolism of 99molecular surveys of 102, 103water-borne 15

Milan Cathedral 86–88Milet 22, 24Molecular techniques 97, 99, 108, 112, 143, 205

amplification 168, 169primers 113, 116, 157, 168, 169, 212probes 120, 121, 123, 124, 132, 138, 143–145,

147, 148, 239Monitoring 17, 19, 22, 27, 89, 104, 105, 182,

186, 187, 189, 198, 199, 201programme 196, 197wooden 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, 113Mural paintings conservation 38Museums 5, 6, 16, 200, 201, 203, 233, 234, 259,

299

NIR (Near Infrared) 240, 242Nets 187–191, 194, 202

polypropylene 189–191

Nickel 130, 132, 165Nitrates 13, 76–78, 80, 86, 87, 89, 92, 207, 252Nostoc 42, 43NRB, (nitrate-reducing bacteria) 80, 83, 84, 87,

89, 91Nucleic acids 99, 110, 112, 115, 116, 147, 159Nucleotides 119, 166, 168, 170, 214, 215Nydam 17, 18, 151, 152

Oak 108, 110, 114, 117, 124, 192, 198, 220,221, 226–231, 234

Obernkirchen stones 57–59Organic materials 11, 144, 181, 182, 190, 192,

195, 198, 239, 273Oxygen 11, 13, 15, 17, 98, 181, 184, 196, 199,

205–207, 213, 246, 258, 260, 261, 279

Paintings 15, 76, 103, 167, 169, 173, 296PCR (Polymerase Chain Reaction) 99, 101, 108,

114–119, 151, 166amplifications 97, 101, 102, 153inhibitors 101, 115standard 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 23Phylogenetic

analyses 99, 118, 153, 159, 168–170, 173, 211Pine, pitch 226, 227, 230, 231, 234Planktosphaeria 42Pleurococcus 42PLFA (phospholipid fatty acid) 40, 157, 164

profiles 159, 163Polders 187, 202Polyethylene 90

glycol (see also PEG) 114, 115, 209, 246, 255Polysaccharides 112, 115Pores 65, 71, 72, 156, 239Porosity 11, 13, 24, 56, 63, 65, 68, 70, 80, 87, 91Precipitation 62, 63, 115, 245Preservation 5, 7, 15–17, 24, 77, 137, 166, 167,

195, 233, 237, 242, 266state of 185, 186, 194, 217

Preventol A8 56–60Primers (see molecular) Probes (see molecular) Proteobacteria 118, 153Pyrite 118, 205–207, 209

rDNA (DNA coding for rRNA) 46, 47, 108, 153,168, 169

Reburial 182, 185–187, 198, 199, 202, 203projects 185, 195, 199–201trenches 198, 199

Red alizarine 70, 71Redox 11, 184, 186, 194, 195, 198, 199Relative humidity 31, 55, 163, 240, 241,

280–289low 280, 283, 287programme 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 113extraction of 113, 114sample 113, 114, 119

digested 114rRNA 108, 118, 148, 166, 167, 169, 216

gene sequences 99, 169, 170genes 99, 143, 151, 166, 168–170, 173

Rubrobacter 162

Sail 236–239, 242, 243Sailcloth 236, 237Salinibacter 162, 164Salts 15, 37, 78–80, 91, 115, 164, 205, 245, 255,

261, 281Sand 5, 25, 165, 185, 187, 190, 195Sandbags 186, 187, 189–191, 195, 196Sandstone 18, 39, 42, 52, 56, 59, 60Sandy soil 171, 172Scaffolding nets 189, 191, 194, 202Scour 181, 182, 192, 196Scytonema 40, 42, 43Seabed response 195–197Seawater 181, 205, 281Sediment 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, 168Shade cloth 196, 197

mat 196, 197Ship 6, 139, 179, 182, 187, 189, 190, 204, 205,

222, 225–227, 233, 261, 262, 265, 266,269, 276, 277, 280, 281

screw-driven 280timbers 114, 115, 118, 216wooden 222

Shipwreck sites 179, 181, 182, 195, 199registered historic 180

SRB 80, 84, 87, 90, 91, 266ss Great Britain Trust 280, 288, 289SSCP (single strand conformation polymorphism)

profiles 158, 159, 161Stone(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, 93materials 64, 65, 70, 73, 80, 83, 86monumental 64, 71, 73

natural 13, 18, 19, 63, 80porosity 64, 71, 72protectives, microbially-resistant 22surfaces 20, 54, 59, 60, 63, 68, 70, 73, 79,

81, 84Sulfate 18, 76, 78, 80, 83, 86, 87, 90, 91, 181,

182, 205, 206, 209, 210, 245, 252, 253Sulfides 182, 198, 199, 206, 209, 210, 245Sulfur 5, 110, 126, 139, 204–206, 209, 213, 217,

249, 252, 253, 255compounds 204, 245, 253, 255

reduced 204cycle 205–207reduced forms of 245, 253

Sulfuric acid 182, 204, 209, 245, 246Surfaces 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, 164heritage 51, 52, 59, 60inner 13, 139, 159, 163metal 258, 277test 56, 59unpainted 41, 43

Synchrotronradiation 128–130, 140, 141, 276sources 128–130, 139

Synechococcus 42, 43Synechocystis 42, 43

Teak 226–232, 234, 266Temples 18, 22, 158Teredo 181, 185, 200Terracotta warriors 16, 17Terram 190, 192, 194, 195Textiles 11, 16, 18, 135, 198, 239, 242,

243, 294Thiobacillus 118, 213, 216, 217Thiosulfate pathways 208–210Timbers 5, 118, 181, 187, 194, 195, 204, 205,

213, 216, 217, 219, 220, 222, 228,231–234, 266, 268, 269, 276

buried softwood 109exposed 5, 192, 194, 195rotten 228

Trentepohlia 42T-RFLP (terminal restriction fragment length

polymorphism) 116, 151Tricyclazole 55–57, 59

Underwaterheritage sites 179maritime heritage sites 180sites 187, 200

post-excavation 186UV (ultraviolet) light 70, 71, 119Uxmal 40, 41, 158, 160

304 Subject Index

Subject Index 305

Vasa 114, 118, 120, 121, 124, 126, 139, 182,204, 209, 217, 245, 249, 252, 255, 256

wood 245, 246, 254, 255Victory (see HMS Victory)

Wadden Sea 181, 182, 184, 187, 189–191, 201Wall 30, 32, 39, 41, 159, 296

wood cell 185, 204Water 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, 91capillary absorption 53, 54, 59column 181, 184, 187, 194, 196content 239level 22, 23, 269porosity 65, 68uptake 70, 91

Water-repellent 52–54, 63Weathering 27, 30, 54, 55, 92, 135, 140

forms 27, 30–33William Salthouse 192, 193Wood 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, 273deterioration 121, 125matrix 246, 251, 254

preventing bacterial decay of 201, 202samples 111–115, 245, 249, 254

dried 111environmental 111, 113eroded 120mashed oak 121, 124pine 181

in situ 185surfaces 245, 249, 253waterlogged 108, 109, 110, 120, 185, 254, 255

archaeological 151, 154density of 185pine 245

Woodenpoles 190shipwrecks 181warships 222, 224, 233

Wreck 179, 182, 187, 189, 192, 194, 196–198,200–202, 212

site 4, 5, 185, 186, 189, 194, 197, 246Wrought iron 266, 268, 269, 271, 273, 274, 276,

277, 288

X-rays 128, 138–140XRD (X-ray diffraction) 133, 135, 281, 283

Yarns 237, 238, 242Yucatan 158, 160, 165

Documents

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