The microbial biodiversity at the archeological site of Tel Megiddo (Israel)

Abstract

Introduction: The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes.

Methods: We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically.

Results: We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former.

Discussion: We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.

Keywords: MetaSUB; Monumentome; Urban microbiome; acid-producing bacteria (APB); biocorrosion; microbiome; monuments; pathogens.

Figure 1

Map of the southern Levant and the site of Megiddo.

Figure 2

Distribution of taxa prevalence in different areas of Tel Megiddo. The number and percentage of taxa classified into phyla in different areas are shown. 428 bacterial taxa occur in all areas (100%), representing the core microbiome. 583 bacterial taxa occur in only one area, thus being unique to a specific part of Tel Megiddo.

Figure 3

Microbial diversity in different areas and materials at the phylum level. The taxonomic composition of the taxa varied between samples found in different areas (A) and surface materials (B). “Other” refers to all other phyla with lower RSA than the displayed phylum. Subfigures show the RSA (%) (A,B) of the top eight most abundant phyla and the Shannon index of the microbial communities (C). Significance was assessed using the Wilcoxon signed-rank test with the p-value marked in the plots as 0–0.001***, 0.001–0.01**, 0.01–0.05* or NS (non-significant difference), and principal component analyses based on Bray-Curtis distances of the microbial communities in different sites (D) PERMANOVA test (r = 0.38 ± 0.03, p = 0.04 ± 0.04) Convex hull function was used to draw the clusters.

Figure 4

Venn diagram showing the taxa overlap among Tel Megiddos’ public and restricted sites, MetaSUB, and the Monumentome projects. The small yellow and blue bubbles represent extensions of intersections in other parts of the plot.

Figure 5

Geographic variations in the average abundance of the top 25 most common species-level taxa in Tel Megiddo observed across monuments in 12 cities. (A) The average RSA of these taxa in each city. (B) The average RSA of each taxon is normalized to account for variations between cities. Normalized abundance values are depicted on a scale from 0 (very dark blue) to 1 (bright blue), with the latter indicating higher taxon abundance in comparison to other cities.