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Microbial Community of an 11th Century Manuscript by Both Culture-Dependent and -Independent Approaches

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Abstract

In this study, the microbial community (Bacteria, Archaea, and Fungi) of a historical manuscript was investigated by microscopic observation (field emission scanning electron microscopy), culture-dependent methods, and sequencing of amplicons on the Illumina MiSeq platform. Microbial isolates were also assayed for production of hydrolytic enzymes (cellulase, amylase, and protease). Observation of gold-coated paper samples in high-vacuum mode revealed bacterial cells, conidia, and fungal mycelium among the fibers. Eleven bacterial strains, including species of Bacillus, Streptomyces, Corynebacterium, and four fungal strains, including species of Aspergillus and Alternaria, were isolated by culture-dependent methods and identified by 16S rRNA and ITS sequencing, by comparison with the EzBioCloud and MycoBank databases, respectively. Illumina MiSeq sequencing revealed the presence of 20 bacterial genera, including Pseudomonas, Bacillus, Citrococcus, Promicromonospora, Carnobacterium, Arthrobacter, Salinibacterium, and Streptomyces. According to the number of reads, Pseudomonas (58%) was the most abundant genus and P. stutzeri (55.2%) was the most abundant bacterial species. Sequencing results of fungal amplicons indicated 62 genera, including Penicillium, Aspergillus, Alternaria, Mucor, and Chaetomium. Penicillium (58.89%) and Aspergillus (33.02%) were the most abundant genera. P. polonicum (55.45%) and A. ruber (22.55%) were the most abundant species of the fungal community. The results of searching for archaea in the microbial community of the manuscript by culture-dependent and high-throughput amplicon sequencing were negative. The enzymatic activity of microbial isolates indicated a potential risk of biodeterioration. It seems that using a combination of culture-dependent and high-throughput sequencing methods has a significant advantage over using them individually.

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REFERENCES

  1. Area, M.C. and Cheradame, H., Paper aging and degradation: recent findings and research methods, BioResources, 2011, vol. 6, pp. 5307–5337. https://doi.org/10.15376/biores.6.4.5307-5337

    Article  CAS  Google Scholar 

  2. Bastian, F., Alabouvette, C., Jurado, V., and Saiz-Jimenez, C., Impact of biocide treatments on the bacterial communities of the Lascaux Cave, Naturwissenschaften, 2009, vol. 96, pp. 863–868. https://doi.org/10.1007/s00114-009-0540-y

    Article  CAS  PubMed  Google Scholar 

  3. Bicchieri, M., Biocca, P., Colaizzi, P., and Pinzari, F., Microscopic observations of paper and parchment: the archaeology of small objects, Herit. Sci., 2019, vol. 7, no. 1, pp. 1–12. [accessed 2021 Mar 9]. https://doi.org/10.1186/s40494-019-0291-9

  4. Duan, Y., Wu, F., Wang, W., He, D., Gu, J.D., Feng, H., Chen, T., Liu, G., and An, L., The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China, PLoS One, 2017, vol. 12, no. 7.https://doi.org/10.1371/JOURNAL.PONE.0179718

  5. Gutarowska, B. (Ed.), A Modern Approach to Biodeterioration Assessment and Disinfection of Historical Book, Lodz Univ. Technol., 2016 [accessed 2021 Mar 5]. https://docplayer.net/50335305-Modern-approach-for-biodeterioration-assessment-and-disinfection-of-historical-book-collections.html.

  6. Harkawy, A., Górny, R.L., Ogierman, L., Wlazło, A., Ławniczek-wałczyk, A., and Niesler, A., Bioaerosol assessment in naturally ventilated historical library building with restricted personnel access, Ann. Agric. Environ. Med., 2011, vol. 18, no. 2, pp. 323–329. [accessed 2021 Mar 5]. http://www.aaem.pl/Bioaerosol-assessment-in-naturally-ventilated-historical-library-building-with-restricted,71708,0,2.html.

    PubMed  Google Scholar 

  7. Heyrman, J., Logan, N.A., Rodríguez-Díaz, M., Scheldeman, P., Lebbe, L., Swings, J., Heyndrickx, M., and De Vos, P., Study of mural painting isolates, leading to the transfer of “Bacillus maroccanus” and “Bacillus carotarum” to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to “Bacillus macroides” and description of Bacillus muralis sp. nov., Int. J. Syst. Evol. Microbiol., 2005, vol. 55, no. 1, pp. 119–131. [accessed 2021 Mar 5]. https://www.microbiologyresearch.org/content/journal/ijsem/https://doi.org/10.1099/ijs.0.63221-0.10.1099/ijs.0.63221-0

    Article  CAS  PubMed  Google Scholar 

  8. Jacob, S., Bhagwat, A.M., and Kelkar-mane, V., Bacillus species as an intrinsic controller of fungal deterioration of archival documents, Int. Biodeterior. Biodegrad., 2015, vol. 104, pp. 46–52. https://doi.org/10.1016/j.ibiod.2015.05.001

    Article  CAS  Google Scholar 

  9. Jaén-Luchoro, D., Gonzales-siles, L., Karlsson, R., Svensson-stadler, L., Molin, K., Cardew, S., Jensie-Markopolous, S., Ohlén, M., Inganäs, E., Skovbjerg, S., J. Tindall, B., and Moore, E., Corynebacterium sanguinis sp. nov., a clinical and environmental associated corynebacterium, Syst. Appl. Microbiol., 2020, vol. 43, no. 1. https://doi.org/10.1016/j.syapm.2019.126039

  10. Karakasidou, K., Nikolouli, K., Amoutzias, G.D., Pournou, A., Manassis, C., Tsiamis, G., and Mossialos, D., Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: a case study, Microbiologyopen, 2018, vol. 7. https://doi.org/10.1002/mbo3.596

  11. Karbowska-Berent, J., Górny, R.L., Strzelczyk, A.B., and Wlazło, A., Airborne and dust borne microorganisms in selected Polish libraries and archives, Build. Sci., 2011, vol. 46, pp.1872–1879. https://doi.org/10.1016/j.buildenv.2011.03.007

    Article  Google Scholar 

  12. Kasana, R.C., Salwan, R., Dhar, H., Dutt, S., and Gulati, A., A rapid and easy method for the detection of microbial cellulases on agar plates using Gram’s iodine, Curr. Microbiol., 2008, vol. 57, pp. 503–507. https://doi.org/10.1007/s00284-008-9276-8

    Article  CAS  PubMed  Google Scholar 

  13. Lalucat, J., Bennasar, A., Bosch, R., García-Valdés, E., and Palleroni, N.J., Biology of Pseudomonas stutzeri, Microbiol. Mol. Biol. Rev., 2006, vol. 70, pp. 510–547. https://doi.org/10.1128/mmbr.00047-05

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Liu, Z., Zhang, Y., Zhang, F., Hu, C., Liu, G., and Pan, J., Microbial community analyses of the deteriorated storeroom objects in the Tianjin Museum using culture-independent and culture-dependent approaches, Front. Microbiol., 2018, vol. 9. https://doi.org/10.3389/fmicb.2018.00802

  15. Lupan, I., Ianc, M.B., Kelemen, B.S., Carpa, R., Rosca-Casian, O., Chiriac, M.T., and Popescu, O., New and old microbial communities colonizing a seventeenth-century wooden church, Folia. Microbiol., 2014, vol. 59, pp. 45–51. https://doi.org/10.1007/s12223-013-0265-3

    Article  CAS  Google Scholar 

  16. Mesquita, N., Portugal, A., Videira, S., Rodríguez-Echeverría, S., Bandeira, A.M.L., Santos, M.J.A., and Freitas, H., Fungal diversity in ancient documents. A case study on the Archive of the University of Coimbra, Int. Biodeterior. Biodegrad., 2009, vol. 63, pp. 626–629. https://doi.org/10.1016/j.ibiod.2009.03.010

    Article  CAS  Google Scholar 

  17. Microorganisms in the Deterioration and Preservation of Cultural Heritage, Joseph, E., Ed., Springer Nature, 2021.

    Google Scholar 

  18. Mohammadipanah, F., Montero-Calasanz, M.D.C., Schumann, P., Spröer, C., Rohde, M. and Klenk, H.P., Promicromonospora kermanensis sp. nov., an actinobacterium isolated from soil, Int. J. Syst. Evol. Microbiol., 2017, vol. 67, pp. 262–267. https://doi.org/10.1099/ijsem.0.001613

    Article  CAS  PubMed  Google Scholar 

  19. Nikou, M.M., Ramezani, M., Harirchi, S., Makzoom, S., Amoozegar, M.A., Abolhassan, S., Fazeli, S., Schumann, P., and Ventosa, A., Salinifilum gen. nov., with description of Salinifilum proteinilyticum sp. nov., an extremely halophilic actinomycete isolated from Meighan wetland, Iran, and reclassification of Saccharopolyspora aidingensis as Salinifilum aidingensis comb. nov., Int. J. Syst. Evol. Microbiol., 2017, vol. 67, pp. 4221–4227. https://doi.org/10.1099/ijsem.0.002286

    Article  CAS  Google Scholar 

  20. Oetari, A., Susetyo-Salim, T., Sjamsuridzal, W., Suherman, E.A., Monica, M., Wongso, R., Fitri, R., Nurlaili, D.G., Ayu, D.C., and Teja, T.P., Occurrence of fungi on deteriorated old dluwang manuscripts from Indonesia, Int. Biodeterior. Biodegrad., 2016, vol. 114, pp. 94–103. https://doi.org/10.1016/j.ibiod.2016.05.025

    Article  CAS  Google Scholar 

  21. Otlewska, A., Adamiak, J., and Gutarowska, B., Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects, Acta Biochim. Pol., 2014, vol. 61, pp. 217–225.

    PubMed  Google Scholar 

  22. Pangallo, D., Kraková, L., Chovanová, K., Šimonovičo-vá, A., De Leo, F., and Urzì, C., Analysis and comparison of the microflora isolated from fresco surface and from surrounding air environment through molecular and biodegradative assays, World J. Microbiol. Biotechnol., 2012, vol. 28, pp. 2015–2027. https://doi.org/10.1007/s11274-012-1004-7

    Article  CAS  PubMed  Google Scholar 

  23. Piñar, G., Sterflinger, K., and Ettenauer, J., A combined approach to assess the microbial contamination of the Archimedes palimpsest, Microb. Ecol., 2015, vol. 69, pp. 118–134. https://doi.org/10.1007/s00248-014-0481-7

    Article  PubMed  Google Scholar 

  24. Piñar, G., Sterflinger, K., and Pinzari, F., Unmasking the measles-like parchment discoloration: molecular and microanalytical approach, Environ. Microbiol., 2015, vol. 17, pp. 427–443. https://doi.org/10.1111/1462-2920.12471

    Article  CAS  PubMed  Google Scholar 

  25. Pinheiro, A.C., Macedo, M.F., Jurado, V., Saiz-Jimenez, C., Viegas, C., Brandão, J., and Rosado, L., Mould and yeast identification in archival settings: preliminary results on the use of traditional methods and molecular biology options in Portuguese archives, Int. Biodeterior. Biodegrad., 2011, vol. 65, pp. 619–627. https://doi.org/10.1016/j.ibiod.2011.02.008

    Article  CAS  Google Scholar 

  26. Pinheiro, A.C., Sequeira, S.O, and Macedo, M.F., Fungi in archives, libraries, and museums: a review on paper conservation and human health, Crit. Rev. Microbiol., 2019, vol. 45, pp. 686–700. https://doi.org/10.1080/1040841X.2019.1690420

    Article  CAS  PubMed  Google Scholar 

  27. Principi, P., Villa, F., and Sorlini, C., Molecular studies of microbial community structure on stained pages of Leonardo da Vinci’s Atlantic Codex, Microb. Ecol., 2011, vol. 61, pp. 214–222. https://doi.org/10.1007/s00248-010-9741-3

    Article  PubMed  Google Scholar 

  28. Sakthivel, M., Karthikeyan, N., Jayaveny, R., and Palani, P., Optimization of culture conditions for the production of extracellular cellulase from Corynebacterium lipophiloflavum, J. Ecobiotechnol., 2010, vol. 2, pp. 6–13

    Google Scholar 

  29. Sato, Y., Aoki, M., and Kigawa, R., Microbial deterioration of tsunami-affected paper-based objects: a case study, Int. Biodeterior. Biodegrad., 2014, vol. 88, pp. 142–149. https://doi.org/10.1016/j.ibiod.2013.12.007

    Article  CAS  Google Scholar 

  30. Savković, Ž., Stupar, M., Unković, N., Ivanović, Ž., Blagojević, J., Vukojević, J., and Ljaljević Grbić, M., In vitro biodegradation potential of airborne Aspergilli and Penicillia, Sci. Nat., 2019, vol. 106. PMID: 30734872.https://doi.org/10.1007/s00114-019-1603-330734872

  31. Schabereiter-gurtner, C., Pinar, G., Lubitz, W., and Rolleke, S., An advanced molecular strategy to identify bacterial communities on art objects, J. Microbiol. Me-thods. 2001, vol. 45, pp. 77–87.

    Article  CAS  Google Scholar 

  32. Sequeira, S.O., De Carvalho, H.P., Mesquita, N., Portugal, A., and Macedo, M.F., Fungal stains on paper: is what you see what you get?, Conservar Patrimonio, 2019, vol. 32, pp. 18–27.

    Google Scholar 

  33. Skóra, J., Gutarowska, B., Pielech-Przybylska, K., Stę-pień, Ł., Pietrzak, K., Piotrowska, M., and Pietrowski, P., Assessment of microbiological contamination in the work environments of museums, archives and libraries, Aerobiologia, 2015, vol. 31, pp. 389–401. https://doi.org/10.1007/s10453-015-9372-8

    Article  PubMed  PubMed Central  Google Scholar 

  34. Sterflinger, K. and Piñar, G., Microbial deterioration of cultural heritage and works of art—tilting at windmills?, Ap-pl. Microbiol. Biotechnol., 2013, vol. 97, pp. 9637–9646. https://doi.org/10.1007/s00253-013-5283-1

    Article  CAS  Google Scholar 

  35. Sterflinger, K. and Pinzari, F., The revenge of time: fungal deterioration of cultural heritage with particular reference to books, paper and parchment, Environ. Microbiol., 2012, vol.14, pp. 559–566. https://doi.org/10.1111/j.1462-2920.2011.02584.x

    Article  CAS  PubMed  Google Scholar 

  36. Strlič, M., Kolar, J., Kočar, D., Drnovesek, T., Šelih, V.S., Susič, R., and Pihlar, B., What is the pH of alkaline paper?, e-Preserv. Sci., 2004, no. 1, pp. 35–47.

  37. Suihko, M. and Stackebrandt, E., Identification of aerobic mesophilic bacilli isolated from board and paper products containing recycled fibers, J. Appl. Microbiol., 2003, vol. 94, pp. 25–34.

    Article  CAS  Google Scholar 

  38. Tarsitani, G., Moroni, C., Cappitelli, F., Pasquariello, G., and Maggi, O., Microbiological analysis of surfaces of Leonardo da Vinci’s Atlantic Codex: biodeterioration risk, Int. J. Microbiol., 2014. https://doi.org/10.1155/2014/214364

  39. Tedersoo, L., Sánchez-Ramírez, S., Kõljalg, U., Bahram, M., Döring, M., Schigel, D., May, T., Reyberg, M., and Abarenkov, K., High-level classification of the Fungi and a tool for evolutionary ecological analyses, Fungal Divers., 2018, vol. 90, pp. 135–159. https://doi.org/10.1007/s13225-018-0401-0

    Article  Google Scholar 

  40. Zghair, A., Enzymatic efficacy of some types of Aspergillus fungi isolated from some manuscripts and its effect on some of the physical and chemical properties of the manuscripts. in IOP Conference Series: Materials Science and Engineering, Institute of Physics Publishing, 2019, vol. 571, no. 1, p. 012043.

  41. Zhang, F., Li, L., Sun, M., Hu, C., Zhang, Z., Liu, Z., Shao, H., Xi, G, and Pan J., Fungal community analyses of a pirogue from the Tang Dynasty in the National Maritime Museum of China, Appl. Sci., 2019, vol. 9, no. 19.https://doi.org/10.3390/app9194129

  42. Zhgun, A., Avdanina, D., Shumikhin, K., Simonenko, N., Lyubavskaya, E., Volkov, I., and Ivanov, V., Detection of potential biodeterioration risks for tempera painting in 16th century exhibits from State Tretyakov Gallery, PLoS One, 2020, vol. 15, no. 4, e0230591. [accessed 2021 Mar 5].https://doi.org/10.1371/journal.pone.0230591

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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ACKNOWLEDGMENTS

The authors greatly acknowledge the University of Tehran’s supports, and the facilities provided by NLAI (National Library and Archives of Iran) for this research. Also, we would like to gratitude Dr. Sajjad Sarikhan, the Molecular Bank manager of Iranian Biological Recourse Center (IBRC), and other experts of this center for their valuable scientific support.

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  1. Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran

    N. Raeisnia, E. Arefian & M. A. Amoozegar

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  1. N. Raeisnia
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Correspondence to E. Arefian or M. A. Amoozegar.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Raeisnia, N., Arefian, E. & Amoozegar, M.A. Microbial Community of an 11th Century Manuscript by Both Culture-Dependent and -Independent Approaches. Microbiology 91, 313–323 (2022). https://doi.org/10.1134/S0026261722300117

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