Article Figures & Data
Figures
- Fig 1
Isometric drawings of the Mary Rose hull and stempost. (A) The intact Mary Rose hull recovered from the seabed in 1982 is drawn in relation to the stempost raised in 2005, which provided crucial information about the shape of the ship's bow. The missing areas and proposed silhouette of the hull are represented by dashed lines. (B) Detailed isometric drawing of the stempost and adjoining apron timber with dimensions and locations of iron bolts, raised from the seabed in 2005 at a latitude and longitude of 49°52.2628′N, 006°26.5928′W. C, location of the stempost sample (MRT04A) used in this study. Drawings courtesy of the Mary Rose Trust.
- Fig 2
The Mary Rose stempost sample used in this study, with pH values indicated. The areas of wood measuring pH 1.7 are correlated with proximity to the bolt hole that historically contained an iron bolt and yellow sulfur salt deposits on the surface of the wood. Originally, extensive yellow deposits surrounding and internal to the bolt hole existed; however, these were removed and used as initial inocula in enrichment cultures. A, location of wood and sulfur deposits used as inocula for MRT04A Fe and S cycling enrichment culture SM18.
- Fig 3
Neighbor-joining phylogenetic tree of 16S rRNA gene sequences from the stempost sample clone library with related taxa. Evolutionary distances were computed using the maximum composite likelihood method with 1,000 bootstraps, and all positions containing gaps and missing data were eliminated. A total of 92 nucleotide sequences, including 18 stempost clone library sequences representing operational taxonomic units (OTUs), were included in the analysis. The rate variation of all sequences was modeled with a gamma distribution. Substitution pattern and rates were estimated under the general time reversible model (+G) shape parameter of 0.2754. The mean evolutionary rates among sites estimated for 5 discrete categories were 0.00, 0.04, 0.23, 0.86, and 3.88 substitutions per site, and there were a total of 881 positions in the final data set. An automatically generated neighbor-joining tree was used as the initial tree for estimating maximum-likelihood values; the maximum log likelihood for this computation was −27160.733. The tree is rooted by Rhodothermus marinus.
- Fig 4
Neighbor-joining phylogenetic tree of 16S rRNA gene sequences from the enrichment SM18 coculture clone library with related taxa. Evolutionary distances were computed using the maximum composite likelihood method with 1,000 bootstraps. A total of 95 sequences were included in the analyses. The rate variation of all sequences was modeled with a gamma distribution. Substitution pattern and rates were estimated under the general time reversible model (+G) shape parameter of 0.3903 The mean evolutionary rates among sites estimated for 5 discrete categories were 0.00, 0.04, 0.24, 0.88, and 3.84 substitutions per site, and there were a total of 1,079 positions in the final data set. An automatically generated neighbor-joining tree was used as the initial tree for estimating maximum-likelihood values; the maximum log likelihood for this computation was −8165.931. The tree is rooted by gammaproteobacteria outgroup taxa E. coli and A. ferrooxidans.
- Fig 5
Iron oxidation by Alicyclobacillus MRT18 grown in a series of NaCl concentrations, 2 to 20% (wt/vol). Ferrous iron concentrations are depicted by solid lines (left-hand vertical axis), and ferric iron concentrations are depicted by dashed lines (right-hand axis). Measurements were taken from the culture supernatant and therefore do not include the extensive Fe3+ deposits on the sides and bottom of the conical flasks. Media contained 1.25 g/liter (NH4)2SO4, 0.5 g/liter MgSO4 · 7H2O, 0.025% tryptone soya broth (wt/vol), 10 mM galactose, and 25 mM Fe(II)SO4. Concentrations of ferrous iron were measured using the ferrozine colorimetric assay (28), and concentrations of ferric iron were measured with a turbidimetric assay (36). Absorbance was measured using an Ultrospec 2000 UV/Visible spectrophotometer (Pharmacia Biotech). NaCl percent trials were performed in triplicate, and each assay measurement was also taken in triplicate. The average values are presented. A control series of each NaCl concentration contained sterile media with ferrous iron but no Alicyclobacillus. Values for all NaCl percent control series were combined to provide a single control series.
Additional Files
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Clone library 16S rRNA gene sequences from Mary Rose stem post wood and iron and sulfur enrichment culture SM18 (Table S1).
PDF, 65K
- Supplemental file 2 -
Microbial diversity analysis of A. Mary Rose stem post wood sample containing a historic source of iron (A) and of Fe- and S-cycling acidophilic enrichment co-culture SM18 (pH 3.0) initiated from the stem post material containing growth substrates elemental sulfur, K2S4O6, and Fe(II)SO4 (B) (Figure S1); decrease of pH in bacterial co-culture SM18 containing Alicyclobacillus MRT18 and Acidiphilium sp. (Figure S2).
PDF, 56K
- Supplemental file 1 -
