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. 2024 Feb 6;12(2):338.
doi: 10.3390/microorganisms12020338.

A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis

Bessem Chouaia  1 , Jessica Dittmer  2   3
Affiliations

A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis

Bessem Chouaia et al. Microorganisms. .

Abstract

Some bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment.

Keywords: Bacillus stercoris; ancient bacteria; surfactin.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The genome of Bacillus stercoris strain Mal05. (A) Circular genome plot of B. stercoris Mal05. The four outer-most circles represent forward CDS, reverse CDS, ribosomal RNAs, and tRNAs. The inner circles represent the conserved genes in B. stercoris strain BS21 and B. subtilis strain 168. The shading indicates the degree of sequence similarity compared to B. stercoris Mal05. (B) Comparison of functional COG categories between B. stercoris Mal05, B. stercoris strain BS21, and B. subtilis strain 168.
Figure 2
Figure 2
Phylogeny of the Bacillus subtilis group. Left panel: maximum-likelihood tree based on the concatenated amino acid sequence alignment of 954 single-copy orthologous genes from 19 reference genomes representing the different species and subspecies of the B. subtilis group with B. cereus as the outgroup. Only bootstrap values below 100 are indicated. Right panel: a matrix of the Average Nucleotide Identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the different genomes is shown next to the tree. The color scale ranges from dark red (low-similarity values) to dark blue (high-similarity values).
Figure 3
Figure 3
Phylogeny of B. stercoris. Maximum-likelihood tree based on 2623 single-copy orthologous genes present in eight high-quality B. stercoris genomes with B. subtilis subsp. subtilis as the outgroup. Only bootstrap values below 100 are indicated. The completeness of the fengycin and surfactin biosynthesis operons in each genome is indicated on the right: dark colors = complete, pale colors = incomplete.
Figure 4
Figure 4
Synteny and evolution of the surfactin biosynthesis genes. (A) Synteny of the genomic region surrounding the surfactin biosynthesis genes. The five genes involved in surfactin biosynthesis are colored in dark red. Pink indicates genes involved in other biosynthetic processes, green indicates genes involved in regulation, and blue indicates genes involved in transport. Grey indicates genes involved in other processes. (B) Sites under selection for each gene. Blue indicates genes under purifying selection, red indicates sites under diversifying selection. Colored shading delimits the different functional domains in each gene. The x-axis reports the position of each site (i.e., codon) while the y-axis reports the log10 of the dN/dS ratio.
Figure 5
Figure 5
Synteny and evolution of the fengycin biosynthesis genes. (A) Synteny of the genomic region surrounding the fengycin biosynthesis genes. The five genes involved in fengycin biosynthesis are colored in dark red. Pink indicates genes involved in other biosynthetic processes, green indicates genes involved in regulation, and blue indicates genes involved in transport. Grey indicates genes involved in other processes. (B) Sites under selection for each gene. Blue indicates genes under purifying selection, red indicates sites under diversifying selection. Colored shading delimits the different functional domains in each gene. The x-axis reports the position of each site (i.e., codon) while the y-axis reports the log10 of the dN/dS ratio.
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References

    1. Errington J. Regulation of Endospore Formation in Bacillus subtilis. Nat. Rev. Microbiol. 2003;1:117–126. doi: 10.1038/nrmicro750. - DOI - PubMed
    1. Cano R., Borucki M. Revival and Identification of Bacterial Spores in 25- to 40-Million-Year-Old Dominican Amber. Science. 1995;268:1060–1064. doi: 10.1126/science.7538699. - DOI - PubMed
    1. Vreeland R.H., Rosenzweig W.D., Powers D.W. Isolation of a 250 Million-Year-Old Halotolerant Bacterium from a Primary Salt Crystal. Nature. 2000;407:897–900. doi: 10.1038/35038060. - DOI - PubMed
    1. Arriola L.A., Cooper A., Weyrich L.S. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front. Ecol. Evol. 2020;8:40. doi: 10.3389/fevo.2020.00040. - DOI
    1. Johnson S.S., Hebsgaard M.B., Christensen T.R., Mastepanov M., Nielsen R., Munch K., Brand T., Thomas M., Gilbert P., Zuber M.T., et al. Ancient Bacteria Show Evidence of DNA Repair. Proc. Natl. Acad. Sci. USA. 2007;104:14401–14405. doi: 10.1073/pnas.0706787104. - DOI - PMC - PubMed

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