NanoSIMS depth profiles of biomineralized cells of Acidovorax sp. ST3 grown under denitrifying and As(III) & Fe(II)-oxidizing conditions, using both the O- & Cs+ beams

Data for
Figures 3 and S6 in paper:

"Elucidating
Heterogeneous Iron Biomineralization Patterns in a Denitrifying
As(III)-Oxidizing Bacterium: Implications for Arsenic Immobilization"

Single Acidovorax sp. ST3
cells (7 days incubation) were selected for depth profiling. Both Cs+
and O- were used as primary ions and the selected areas were not
implanted prior to starting the analysis (to preserve and keep the biomineral
coating on the cells intact). Image raster sizes were 3-7 µm width. Spatial resolution
was achieved by using D1=4 or 5 (beam size=120-100 nm). Pixel sizes were 128 x 128 or 256 x 256, and
dwell time varied from 5,000-20,000 µs px-1. 50-170 planes were
collected, and the scanning was stopped when the 12C14N or
56Fe+ signal disappeared.

The data was processed using the L’image
software (Larry Nittler, Carnegie Institution of Washington) and the plugin
OpenMIMS for ImageJ (www.nrims.harvard.edu).

3D reconstructions of the depth
profiles were generated using the Thermo Scientific™ Avizo™ Software 9.7.0.
Stack data of the negative secondary ions 12C-, 56Fe16O-
and 75As- , and the positive secondary ions 23Na+,
56Fe+, and 75As+, were first
extracted in ImageJ and saved as “.raw” format files, which were loaded into
Avizo™. The Z depth was compressed to 15-20 %. The 12C-
and 23Na+ signals were smoothed over 2-3 pixels. The
commands “generate surface” and “show surface” were used sequentially, and the
“transparent” display with a transparency of 80 % was selected. 56Fe+
and 56Fe16O- signals were smoothed to 2 pixels
and displayed as “shaded”. The 75As+/- ion counts were
smoothed to 1 pixel.

Four depth profile files are presented, including the .im raw nanoSIMS files, extracted 75As+/-, 56Fe16O-/56Fe+, 12C/23Na counts as .raw format (ready to load into AVIZO), and complementary image and videos of the 3D reconstructions for each depth profile (jpg and mpg formats).