Viruses, Bacteria, Archaea, Protists, and Fungi

  • Elizabeth J. Reitz
  • Myra Shackley
Chapter
Part of the Manuals in Archaeological Method, Theory and Technique book series (MATT)

Abstract

Viruses, bacteria, archaea, protists, and fungi make up much of the biological world. Many of these are very small organisms known as microorganisms. Some are not organisms at all (e.g., viruses); others are not microscopic, though the parts recovered from archaeological sites may be small. Microorganisms are widespread and form the basis of food chains, contribute to nutrient cycling, and enhance soil fertility vital to the health of ecosystems. Some are restricted to specific habitats and are highly sensitive to changes in climates, water quality, and ecosystem processes. These provide direct and indirect information about environmental histories in aquatic and terrestrial landscapes of anthropogenic and non-anthropogenic origin. Some microorganisms have symbiotic or parasitic relationships with people or other organisms. Others are implicated in the deterioration of Paleolithic art at the Lascaux (Dordogne, France) and Altamira (Cantabria, Spain) caves, important World Heritage Sites (Saiz-Jimenez et al. 2011). Numerous species live in and on us, colonizing specific parts of the body and known collectively as a microbiome. Pennisi (2010) reports that 9 out of 10 cells in our bodies are members of this microbiome and that our own gastrointestinal system contains as many as 1,000 species.

Keywords

Clay Mold Calcite Aspergillus Calcium Carbonate 

References

  1. Ashbee, P. (1957). The Great Barrow at Bishop’s Waltham, Hampshire. Proceedings of the Prehistoric Society, 23, 137–166.Google Scholar
  2. Aufderheide, A. C., Salo, W., Madden, M., Streitz, J., Buikstra, J., Guhl, F., et al. (2004). A 9,000-year record of Chagas’ disease. Proceedings of the National Academy of Sciences of the USA, 101, 2034–2039.CrossRefGoogle Scholar
  3. Barber, K., & Langdon, P. (2001). Peat stratigraphy and climate change. In D. R. Brothwell & A. M. Pollard (Eds.), Handbook of archaeological sciences (pp. 155–166). Chichester, UK: Wiley.Google Scholar
  4. Barnes, E. (2005). Diseases and human evolution. Albuquerque: University of New Mexico Press.Google Scholar
  5. Bathurst, R. R., Zori, D., & Byock, J. (2010). Diatoms as bioindicators of site use: Locating turf structures from the Viking Age. Journal of Archaeological Science, 37, 2920–2938.CrossRefGoogle Scholar
  6. Battarbee, R. W. (1986). Diatom analysis. In B. E. Berglund (Ed.), Handbook of Holocene palaeoecology and palaeohydrology (pp. 527–570). Chichester, UK: Wiley.Google Scholar
  7. Bendrey, R., Taylor, G. M., Bouwman, A. S., & Cassidy, J. P. (2008). Suspected bacterial disease in two archaeological horse skeletons from southern England: Palaeopathological and biomolecular studies. Journal of Archaeological Science, 35, 1581–1590.CrossRefGoogle Scholar
  8. Bianucci, R., Rahalison, L., Peluso, A., Massa, E. R., Ferroglio, E., Signoli, M., et al. (2009). Plague immunodetection in remains of religious exhumed from burial sites in central France. Journal of Archaeological Science, 36, 616–621.CrossRefGoogle Scholar
  9. Branch, N., Canti, M., Clark, P., & Turney, C. (2005). Environmental archaeology: Theoretical and practical approaches. London: Hodder Arnold.Google Scholar
  10. Brodie, H. J. (1978). Fungi, delight of curiosity. Toronto: University of Toronto Press.Google Scholar
  11. Brusca, R. C., & Brusca, G. J. (2003). Invertebrates (2nd ed.). Sunderland, USA: Sinauer Associates.Google Scholar
  12. Buckley, H. R., & Tayles, N. G. (2003). The functional cost of tertiary yaws (Treponema pertenue) in a prehistoric Pacific island skeletal sample. Journal of Archaeological Science, 30, 1301–1314.CrossRefGoogle Scholar
  13. Campbell, N. A., Reece, J. B., Urry, L. A., Cain, S. A., Wasserman, S. A., Minorsky, P. V., et al. (2008). Biology (8th ed.). San Francisco, CA: Pearson Benjamin Cummings.Google Scholar
  14. Carlile, M. J., Watkinson, S. C., & Gooday, G. W. (2001). The fungi (2nd ed.). San Diego, CA: Academic.Google Scholar
  15. Caseldine, C., & Gearey, B. (2005). A multiproxy approach to reconstructing surface wetness changes and prehistoric bog bursts in a raised mire system at Derryville Bog, Co. Tipperary, Ireland. The Holocene, 15, 585–601.CrossRefGoogle Scholar
  16. Clark, J. G. D. (1954). Excavations at Star Carr, an early Mesolithic site at Seamer near Scarborough, Yorkshire. Cambridge, UK: Cambridge University Press.Google Scholar
  17. Cronberg, G. (1986). Blue-green algae, green algae and chrysophyceae in sediments. In B. E. Berglund (Ed.), Handbook of Holocene palaeoecology and palaeohydrology (pp. 507–526). Chichester, UK: Wiley.Google Scholar
  18. Crosby, A. W. (1986). Ecological imperialism: The biological expansion of Europe, 900–1900. Cambridge, UK: Cambridge University Press.Google Scholar
  19. Dillehay, T. D., Ramírez, C., Pino, M., Collins, M. B., Rossen, J., & Pino-Navarro, J. D. (2008). Monte Verde: Seaweed, food, medicine, and the peopling of South America. Science, 320, 784–789.CrossRefGoogle Scholar
  20. Dimbleby, G. W. (1978). Plants and archaeology. London: Baker.Google Scholar
  21. Faegri, K., Kaland, P. E., & Krzywinski, K. (1989). Textbook of pollen analysis (4th ed.). Chichester, UK: Wiley.Google Scholar
  22. Gaines, S. M., Eglinton, G., & Rullkötter, J. (2009). Echoes of life: What fossil molecules reveal about earth history. Oxford, UK: Oxford University Press.Google Scholar
  23. Gearey, B. R., & Caseldine, C. J. (2006). Archaeological applications of testate amoebae analysis: A case study from Derryville, Co. Tipperary, Ireland. Journal of Archaeological Science, 33, 49–55.CrossRefGoogle Scholar
  24. Gill, J. L., Williams, J. W., Jackson, S. T., Lininger, K. B., & Robinson, G. S. (2009). Pleistocene megafaunal collapse, novel plant communities, and enhanced fire regimes in North America. Science, 326, 1100–1103.CrossRefGoogle Scholar
  25. Gregory, P. H. (1961). The microbiology of the atmosphere. London: Hill.Google Scholar
  26. Grieve, M. (1971). A modern herbal (originally 1931). New York: Dover Publications.Google Scholar
  27. Guilizzoni, P., Lami, A., Marchetto, A., Jones, V., Manca, M., & Bettinetti, R. (2002). Palaeoproductivity and environmental changes during the Holocene in central Italy as recorded in two crater lakes (Albano and Nemi). Quaternary International, 88, 57–68.CrossRefGoogle Scholar
  28. Haslam, M. (2006). Potential misidentification of in situ archaeological tool-residues: Starch and conidia. Journal of Archaeological Science, 33, 114–121.CrossRefGoogle Scholar
  29. Hasle, G. R., & Syvertsen, E. E. (1996). Marine diatoms. In C. R. Tomas (Ed.), Identifying marine diatoms and dinoflagellates (pp. 5–385). San Diego, CA: Academic.CrossRefGoogle Scholar
  30. Heimdal, B. R. (1993). Modern coccolithophorids. In C. R. Tomas (Ed.), Marine phytoplankton: A guide to naked flagellates and coccolithophorids (pp. 147–247). San Diego, CA: Academic.Google Scholar
  31. Hunt, C. O., Gilbertson, D. D., & Rushworth, G. (2007). Modern humans in Sarawak, Malaysian Borneo, during oxygen isotope stage 3: Paleoenvironmental evidence from the Great Cave of Niah. Journal of Archaeological Science, 34, 1953–1969.CrossRefGoogle Scholar
  32. Innes, J. B., & Blackford, J. J. (2003). The ecology of Late Mesolithic woodland disturbances: Modal testing with fungal spore assemblage data. Journal of Archaeological Science, 30, 185–194.CrossRefGoogle Scholar
  33. Juggins, S., & Cameron, N. (1999). Diatoms and archaeology. In E. F. Stoermer & J. P. Smol (Eds.), The diatoms: Applications for the environmental and earth sciences (pp. 389–401). Cambridge, UK: Cambridge University Press.Google Scholar
  34. Kolman, C. J., Centurion-Lara, A., Lukehart, S. A., Owsley, D. W., & Tuross, N. (1999). Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen. Journal of Infectious Diseases, 180, 2060–2063.CrossRefGoogle Scholar
  35. Krogh, D. (2009). Biology: A guide to the natural world (4th ed.). San Francisco, CA: Pearson, Benjamin Cummings.Google Scholar
  36. Larsen, C. S. (1997). Bioarchaeology: Interpreting behavior from the human skeleton. Cambridge, UK: Cambridge University Press.CrossRefGoogle Scholar
  37. Linford, N., Linford, P., & Platzman, E. (2005). Dating environmental change using magnetic bacteria in archaeological soils from the upper Thames Valley, UK. Journal of Archaeological Science, 32, 1037–1043.CrossRefGoogle Scholar
  38. Marguerie, D., & Hunot, J.-Y. (2007). Charcoal analysis and dendrology: Data from archaeological sites in North-Western France. Journal of Archaeological Science, 34, 1417–1433.CrossRefGoogle Scholar
  39. Matiskainen, H., & Alhonen, P. (1984). Diatoms as indicators of provenance in Finnish sub-Neolithic pottery. Journal of Archaeological Science, 11, 147–157.CrossRefGoogle Scholar
  40. McNeill, W. H. (1976). Plagues and peoples. Oxford, UK: Basil Blackwell.Google Scholar
  41. Mitchell, P. D., Stern, E., & Tepper, Y. (2008). Dysentery in the crusader kingdom of Jerusalem: An ELISA analysis of two Medieval latrines in the city of Acre (Israel). Journal of Archaeo­logical Science, 35, 1849–1853.CrossRefGoogle Scholar
  42. Money, N. P. (2007). The triumph of the fungi. New York: Oxford University Press.Google Scholar
  43. Moodley, Y., Linz, B., Yamaoka, Y., Windsor, H. M., Breurec, S., Wu, J.-Y., et al. (2009). The peopling of the Pacific from a bacterial perspective. Science, 323, 527–530.CrossRefGoogle Scholar
  44. Moskal-del Hoyo, M., Wachowiak, M., & Blanchette, R. A. (2010). Preservation of fungi in archaeological charcoal. Journal of Archaeological Science, 37, 2106–2116.CrossRefGoogle Scholar
  45. Mudie, P. J., Marret, F., Aksu, A. E., Hiscott, R. N., & Gillespie, H. (2007). Palynological evidence for climatic change, anthropogenic activity and outflow of Black Sea water during the late Pleistocene and Holocene: Centennial- to decadal-scale records from the Black and Marmara Seas. Quaternary International, 167–168, 73–90.CrossRefGoogle Scholar
  46. Odum, E. P., & Barrett, G. W. (2005). Fundamentals of ecology (5th ed.). Belmont, CA: Thomson Brooks/Cole.Google Scholar
  47. Okumura, M. M. M., & Eggers, S. (2005). The people of Jabuticabeira II: Reconstruction of the way of life in a Brazilian shellmound. HOMO-Journal of Comparative Human Biology, 55, 263–281.CrossRefGoogle Scholar
  48. Ortner, D. J. (2001). Disease ecology. In D. R. Brothwell & A. M. Pollard (Eds.), Handbook of archaeological sciences (pp. 225–235). Chichester, UK: Wiley.Google Scholar
  49. Padden, A. N., John, P., Collins, M. D., Hutson, R., & Hall, A. R. (2000). Indigo-reducing Clostridium isatidis isolated from a variety of sources, including a 10th-century Viking dye vat. Journal of Archaeological Science, 27, 953–956.CrossRefGoogle Scholar
  50. Pennisi, E. (2010). Body’s hardworking microbes get some overdue respect. Science, 330, 1619.CrossRefGoogle Scholar
  51. Preus, H. R., Marvik, O. J., Selvig, K. A., & Bennike, P. (2011). Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains. Journal of Archaeological Science, 38, 1827–1831.CrossRefGoogle Scholar
  52. Reinhard, K. J. (2008). Pathoecology of two Ancestral Pueblo villages. In E. J. Reitz, C. M. Scarry, & S. J. Scudder (Eds.), Case studies in environmental archaeology (2nd ed., pp. 191–209). London: Springer.CrossRefGoogle Scholar
  53. Robbins, G., Tripathy, V. M., Misra, V. N., Mohanty, R. K., Shinde, V. S., Gray, K. M., et al. (2009). Ancient skeletal evidence for leprosy in India (2000 B.C.). PLoS One, 4, E5669.CrossRefGoogle Scholar
  54. Rolfe, R. T., & Rolfe, F. W. (1974). The romance of the fungus world. New York: Dover Publications.Google Scholar
  55. Rollo, F., Luciani, S., Marota, I., Olivieri, C., & Ermini, L. (2007). Persistence and decay of the intestinal microbiota’s DNA in glacier mummies from the Alps. Journal of Archaeological Science, 34, 1294–1305.CrossRefGoogle Scholar
  56. Rosendahl, D., Ulm, S., & Weisler, M. I. (2007). Using foraminifera to distinguish between natural and cultural shell deposits in coastal eastern Australia. Journal of Archaeological Science, 34, 1584–1593.CrossRefGoogle Scholar
  57. Rubini, M., & Zaio, P. (2009). Lepromatous leprosy in an early mediaeval cemetery in Central Italy (Morrione, Campochiaro, Molise, 6th-8th century AD). Journal of Archaeological Science, 36, 2771–2779.CrossRefGoogle Scholar
  58. Ryan, W. B. F., Major, C. O., Lericolais, G., & Goldstein, S. L. (2003). Catastrophic flooding of the Black Sea. Annual Review of Earth and Planetary Sciences, 31, 525–554.CrossRefGoogle Scholar
  59. Saiz-Jimenez, C., Cuezva, S., Jurado, V., Fernandz-Cortes, A., Porca, E., Benavente, D., et al. (2011). Paleolithic art in peril: Policy and science collide at Altamira Cave. Science, 334, 42–43.CrossRefGoogle Scholar
  60. Seaward, M. R. D., Cross, T., & Unsworth, B. A. (1976). Viable bacterial spores recovered from an archaeological excavation. Nature, 261, 407–408.CrossRefGoogle Scholar
  61. Seaward, M. R. D., & Williams, D. (1976). An interpretation of mosses found in recent archaeological excavations. Journal of Archaeological Science, 3, 173–177.CrossRefGoogle Scholar
  62. Sen Gupta, B. K. (Ed.). (1999). Modern foraminifera. London: Kluwer Academic.Google Scholar
  63. Shackley, M. (1981). Environmental archaeology (1st ed.). London: George Allen & Unwin.Google Scholar
  64. Steidinger, K. A., & Tangen, K. (1996). Dinoflagellates. In C. R. Tomas (Ed.), Identifying marine diatoms and dinoflagellates (pp. 387–584). San Diego, CA: Academic.CrossRefGoogle Scholar
  65. Stoermer, E. F., & Smol, J. P. (1999a). Applications and uses of diatoms: Prologue. In E. F. Stoermer & J. P. Smol (Eds.), The diatoms: Applications for the environmental and earth sciences (pp. 3–8). Cambridge, UK: Cambridge University Press.Google Scholar
  66. Stoermer, E. F., & Smol, J. P. (Eds.). (1999b). The diatoms: Applications for the environmental and earth sciences. Cambridge, UK: Cambridge University Press.Google Scholar
  67. Sveinbjarnardóttir, G., Erlendsson, E., Vickers, K., McGovern, T. H., Milek, K. B., Edwards, K. J., et al. (2007). The palaeoecology of a high status Icelandic farm. Environmental Archaeology, 12, 187–206.CrossRefGoogle Scholar
  68. Tasker, A., Wilkinson, I. P., Fulford, M. G., & Williams, M. (2011). Provenance of chalk tesserae from Bading Roman Villa, Isle of Wight, UK. Proceedings of the Geologist’s Association, 122, 933–937.Google Scholar
  69. Taylor, G. M., Widdison, S., Brown, I. N., & Young, D. (2000). A Mediaeval case of lepromatous leprosy from 13-14th century Orkney, Scotland. Journal of Archaeological Science, 27, 1133–1138.CrossRefGoogle Scholar
  70. Thain, M., & Hickman, M. (2004). The Penguin dictionary of biology (11th ed.). London: Penguin Books.Google Scholar
  71. Throndsen, J. (1993). The planktonic marine flagellates. In C. R. Tomas (Ed.), Marine phytoplankton: A guide to naked flagellates and coccolithophorids (pp. 7–145). San Diego, CA: Academic.Google Scholar
  72. Tomas, C. R. (1993). Introduction. In C. R. Tomas (Ed.), Marine phytoplankton: A guide to naked flagellates and coccolithophorids (pp. 1–5). San Diego, CA: Academic.Google Scholar
  73. Traverse, A. (2008). Paleopalynology (2nd ed.). Dordrecht, The Netherlands: Springer.Google Scholar
  74. Trombold, C. D., & Israde-Alcantara, I. (2005). Paleoenvironment and plant cultivation on terraces at La Quemada, Zacatecas, Mexico: The pollen, phytolith, and diatom evidence. Journal of Archaeological Science, 32, 341–353.CrossRefGoogle Scholar
  75. van Geel, B., Buurman, J., Brinkkemper, O., Schelvis, J., Aptroot, A., van Reenen, G., et al. (2003). Environmental reconstruction of a Roman period settlement site in Uitgeest (The Netherlands) with special reference to coprophilous fungi. Journal of Archaeological Science, 30, 873–883.CrossRefGoogle Scholar
  76. von Hunnius, T. E., Yang, D., Eng, B., Waye, J. S., & Saunders, S. R. (2007). Digging deeper into the limits of ancient DNA research on syphilis. Journal of Archaeological Science, 34, 2091–2100.CrossRefGoogle Scholar
  77. Waldron, T. (2009). Paleopathology. Cambridge, UK: Cambridge University Press.Google Scholar
  78. Watling, R. (1975). Prehistoric puff-balls. Bulletin of the British Mycological Society, 9, 112–114.Google Scholar
  79. Watling, R., & Seaward, M. R. D. (1976). Some observations on puff-balls from British archaeological sites. Journal of Archaeological Science, 3, 165–172.CrossRefGoogle Scholar
  80. Wilkinson, I. P., Williams, M., Young, J. R., Cook, S. R., Fulford, M. G., & Lott, G. K. (2008). The application of microfossils in assessing the provenance of chalk used in the manufacture of Roman mosaics, at Silchester. Journal of Archaeological Science, 35, 2415–2422.CrossRefGoogle Scholar
  81. Zhu, C., & Yu, S.-Y. (2007). Lichenometric contraints on the age of the Huashan Grottoes, east China. Journal of Archaeological Science, 34, 2064–2070.CrossRefGoogle Scholar
  82. Zink, A., Haas, C. J., Reischl, U., Szeimies, U., & Nerlich, A. G. (2001). Molecular analysis of skeletal tuberculosis in an ancient Egyptian population. Journal of Medical Microbiology, 50, 355–366.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Elizabeth J. Reitz
    • 1
  • Myra Shackley
    • 2
  1. 1.Georgia Museum of Natural HistoryUniversity of GeorgiaAthensUSA
  2. 2.Nottingham Business SchoolNottingham Trent UniversityNottinghamUK

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