DOI: 10.5061/dryad.8sc52
title: Data from: In situ analysis of a silver nanoparticle-precipitating Shewanella biofilm by surface enhanced confocal Raman microscopy

description: Shewanella oneidensis MR-1 is an electroactive bacterium, capable of
 reducing extracellular insoluble electron acceptors, making it important
 for both nutrient cycling in nature and microbial electrochemical
 technologies, such as microbial fuel cells and microbial electrosynthesis.
 When allowed to anaerobically colonize an Ag/AgCl solid interface, S.
 oneidensis has precipitated silver nanoparticles (AgNp), thus providing
 the means for a surface enhanced confocal Raman microscopy (SECRaM)
 investigation of its biofilm. The result is the in-situ chemical mapping
 of the biofilm as it developed over time, where the distribution of
 cytochromes, reduced and oxidized flavins, polysaccharides and phosphate
 in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by
 the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM
 while avoiding the use of a patterned or roughened support or the
 introduction of noble metal salts and reducing agents. This new method
 will allow a spatially and temporally resolved chemical investigation not
 only of Shewanella biofilms at an insoluble electron acceptor, but also of
 other noble metal nanoparticle-precipitating bacteria in laboratory
 cultures or in complex microbial communities in their natural habitats.
description: Proxy component
 spectraThis is a WiTec Project
 file with spectra obtained under the same conditions as for biofilm
 measurements, of pure proxy components with colloidal Ag. From M&M: In
 order to identify the individual SERS spectra of pertinent components of
 the S. oneidensis biofilm, we first performed SECRaM analysis on several
 component proxies mixed with colloidal silver (Sigma Aldrich, Hamburg,
 Germany). The proxy component-colloidal silver mixture was analyzed under
 the same working conditions as the ones applied for biofilm analysis. The
 same excitation wavelength, laser intensity and setup were used, however
 without a Ag/AgCl patch. This was done, separately, for the following
 expected component proxies: horse heart cytochrome c (hhcytc) (Sigma
 Aldrich, Hamburg, Germany) in Phosphate buffer solution (PBS) (Roth,
 Karlsruhe, Germany); riboflavin phosphate (Sigma Aldrich, Hamburg,
 Germany) in PBS; hhcytc in PBS with excess sodium dithionite (Merck,
 Darmstadt, Germany); hhcytc in PBS with excess potassium hexacyanoferrate
 (III) (Sigma Aldrich, Hamburg, Germany); riboflavin phosphate in PBS with
 excess sodium dithionite; riboflavin phosphate in PBS with excess
 potassium hexacyanoferrate; an aqueous solution of sodium alginate (Sigma
 Aldrich, Hamburg, Germany); pure PBS; PBS with sodium dithionite; and PBS
 with potassium hexacyanoferrate. Sodium dithionite and potassium
 hexacyanoferrate, respectively, were used to obtain reduced and oxidized
 cytochrome and flavin species.CRM image scan of 6 day
 old biofilm, cosmic ray correctedWiTec Project file of a
 CRM image scan of the 6 day old Shewanella oneidensis biofilm. From
 M&M: The measurement was performed on a WITec alpha300 confocal Raman
 microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4
 corr air objective with coverslip correction. 20× magnification was used
 in order to keep as many bacteria as possible in the focal plane while
 still resolving individual bacteria. The excitation wavelength was 532 nm,
 with laser power of 3 mW at the focal plane. The Raman detector was a
 newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration
 time was 1 second and lateral resolution 2 pixel/µm.6d CRM2 VidIm14 Scan9
 CRR.WIDCRM image scan of 6 day
 old biofilm, cosmic ray corrected, exported in ASCII
 formatWiTec Project file of a
 CRM image scan of the 6 day old Shewanella oneidensis biofilm. From
 M&M: The measurement was performed on a WITec alpha300 confocal Raman
 microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4
 corr air objective with coverslip correction. 20× magnification was used
 in order to keep as many bacteria as possible in the focal plane while
 still resolving individual bacteria. The excitation wavelength was 532 nm,
 with laser power of 3 mW at the focal plane. The Raman detector was a
 newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration
 time was 1 second and lateral resolution 2 pixel/µm. The file was exported
 in ASCII format.Min_CRM2_6d_ac_z0_VidIm14_ImageScan_009_Spec.Data_1_F_CRR.txtCRM image scan of 9 day old biofilm, cosmic ray correctedWiTec Project file of a CRM image scan of the 9 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm.9d CRM2 VidIm15 Scan2 CRR.WIDCRM image scan of 9 day old biofilm, cosmic ray corrected, exported in ASCII formatWiTec Project file of a CRM image scan of the 9 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm. The file was exported in ASCII format.Min_CRM2_9d_ac_z0_VidIm15_Scan_002_Spec.Data_1_F_CRR.txtCRM image scan of 35 day old biofilm, cosmic ray correctedWiTec Project file of a CRM image scan of the 35 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm.35d CRM2 Scan1 CRR.WIDCRM image scan of 35 day old biofilm, cosmic ray corrected, exported in ASCII formatWiTec Project file of a CRM image scan of the 35 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm. The file was exported in ASCII format.35d_CRM2_Scan1_CRR.txt