Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 May 18:14:1167083.
doi: 10.3389/fmicb.2023.1167083. eCollection 2023.

Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt

Samah Mohamed Rizk  1 , Mahmoud Magdy  1 , Filomena De Leo  2 , Olaf Werner  3 , Mohamed Abdel-Salam Rashed  1 , Rosa M Ros  3 , Clara Urzì  2
Affiliations

Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt

Samah Mohamed Rizk et al. Front Microbiol. .

Abstract

A large percentage of the world's tangible cultural heritage is made from stone; thus, it deteriorates due to physical, chemical, and/or biological factors. The current study explored the microbial community inhabiting two prehistoric sites with high cultural value in the Memphis necropolis of Egypt (Djoser and Lahun Pyramids) using amplicon-based metabarcoding and culture-dependent isolation methods. Samples were examined by epifluorescent microscopy for biological signs before environmental DNA extraction and in vitro cultivation. The metabarcoding analysis identified 644 bacterial species (452 genera) using the 16S rRNA and 204 fungal species (146 genera) using ITS. In comparison with the isolation approach, an additional 28 bacterial species (13 genera) and 34 fungal species (20 genera) were identified. A total of 19 bacterial and 16 fungal species were exclusively culture-dependent, while 92 bacterial and 122 fungal species were culture-independent. The most abundant stone-inhabiting bacteria in the current study were Blastococcus aggregatus, Blastococcus saxobsidens, and Blastococcus sp., among others. The most abundant rock-inhabiting fungi were Knufia karalitana and Pseudotaeniolina globosa, besides abundant unknown Sporormiaceae species. Based on previous reports, microorganisms associated with biodeterioration were detected on color-altered sites at both pyramids. These microorganisms are potentially dangerous as physical and chemical deterioration factors and require proper conservation plans from a microbiological perspective.

Keywords: biodeterioration; cultural heritage; microbial genomics; microbial isolation; rock-inhabiting fungi; stone-inhabiting bacteria; tangible monuments.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Sampling site information in Djoser pyramid (DP) and Lahun pyramid (LP). (A,B): photographs of DP and LP, respectively, (by Samah Mohamed Rizk). (C,D): schematic drawing of DP and LP complexes, respectively, showing the sampling sites by numbers (Table 1). (E,F): sampling sites photographs showing their location in the pyramid and the sampling spot (by Samah Mohamed Rizk).
Figure 2
Figure 2
16S rRNA-based metabarcoding profiling of Djoser and Lahun pyramids. (A) Bacterial community composition bar-plot based on the identified OTUs for DP and LP in the metabarcoding samples. The percentage of community abundance at the class level is shown. (B) Circos plot for the comparative bacterial community composition based on the identified OTUs for both DP (MetaDP; red) and LP (MetaLP; blue) in the metabarcoding samples. The percentage of community abundance at the family level is shown for each pyramid. NC = not classified. (C) Bacterial community heatmap for the top 20 of the most abundant genera. The relative abundance ratio is shown for the two pyramids (DP and LP) using a colour scale given on the left of the figure. The family is indicated by colour mark for each genus. The top represented genera are clustered and marked by the red dot. NC = not classified.
Figure 3
Figure 3
ITS-based metabarcoding profiling of Djoser and Lahun pyramids. (A) Fungal community composition bar-plot based on the identified OTUs for DP and LP in the metabarcoding samples. The percentage of community abundance on the class level is shown. (B) Circos plot for the comparative fungal community composition based on the identified OTUs for both DP (MetaDP; red) and LP (MetaLP; blue) in the metabarcoding samples. The percentage of community abundance at the family level is shown for each pyramid. NC = not classified. (C) Fungal community heatmap for the top 20 of the most abundant genera. The relative abundance ratio is shown for the two pyramids (DP and LP) using a color scale given on the left of the figure. The family is indicated by color for each genus. The top represented genera are clustered and marked by a red dot. NC = not classified.
Figure 4
Figure 4
Unrooted phylogenetic tree based on the taxonomic ranking retrieved from the NCBI database (https://www.ncbi.nlm.nih.gov/taxonomy) for the bacterial (A) and fungal (B) species isolated from the Djoser pyramid (DP) and Lahun pyramid (LP). The abundance percentage of each order and class is demonstrated as a pie chart between both pyramids at each node. (Note: order Capnodiales node includes Mycosphaerellales and Cladosporiales species).
Figure 5
Figure 5
Venn Diagram illustrate a comparative listing of the culturable and culturable microbial species detected from both Djoser and Lahun Pyramids.
See this image and copyright information in PMC

References

    1. Abdulla H., May E., Bahgat M., Dewedar A. (2008). Characterisation of actinomycetes isolated from ancient stone and their potential for deterioration. Pol. J. Microbiol. 57, 213–220. PMID: - PubMed
    1. Afifi H., Geweely N. (2011). Comparative study on fungal deterioration and ozone conservation of El-Anfoushi and Al-Shatby archeological tombs-Alexandria-Egypt. J. Am. Sci. 7, 776–784.
    1. Allsopp D., Seal K. J., Gaylarde C. C. (2004). Introduction to Biodeterioration. 2nd Edn London, UK: CRC Press Chem Tec Publishing.
    1. Atlas R. M. (2005). Handbook of Media for Environmental Microbiology. 2nd Edn, Taylor & Francis, Boca Raton, Florida: CRC Press.
    1. Batista-Silva W., Heinemann B., Rugen N., Nunes-Nesi A., Araújo W. L., Braun H., et al. . (2019). The role of amino acid metabolism during abiotic stress release. Plant Cell Environ. 42, 1630–1644. doi: 10.1111/pce.13518 - DOI - PubMed

LinkOut - more resources