Date (Creation)

2013-01-31

Citation identifier

http://data.bgs.ac.uk/id/dataHolding/13607162

Point of contact

Organisation name	Individual name	Electronic mail address	Role
University of Manchester	Dr Helen Downie	not available	Point of contact
University of Manchester	Prof Jonathan Lloyd	not available	Point of contact

Maintenance and update frequency

notApplicable

GEMET - INSPIRE themes, version 1.0

• Geology

BGS Thesaurus of Geosciences

• NGDC Deposited Data

• Microbiological processes

• Simulation

• Microscopy

• Chemical analysis

dataCentre

• NGDC Deposited Data

Keywords

• NERC_DDC

Access constraints

Other restrictions

Other constraints

no limitations

Other constraints

The dataset is made freely available for access, e.g. via the Internet. Either no third party data / information is contained in the dataset or BGS has secured written permission from the owner(s) of any third party data / information contained in the dataset to make the dataset freely accessible.

Use constraints

Other restrictions

Other constraints

The copyright of materials derived from the British Geological Survey's work is vested in the Natural Environment Research Council [NERC]. No part of this work may be reproduced or transmitted in any form or by any means, or stored in a retrieval system of any nature, without the prior permission of the copyright holder, via the BGS Intellectual Property Rights Manager. Use by customers of information provided by the BGS, is at the customer's own risk. In view of the disparate sources of information at BGS's disposal, including such material donated to BGS, that BGS accepts in good faith as being accurate, the Natural Environment Research Council (NERC) gives no warranty, expressed or implied, as to the quality or accuracy of the information supplied, or to the information's suitability for any use. NERC/BGS accepts no liability whatever in respect of loss, damage, injury or other occurence however caused.

Other constraints

Available under the Open Government Licence subject to the following acknowledgement accompanying the reproduced NERC materials "Contains NERC materials ©NERC [year]"

Language

English

Topic category

• Geoscientific information

Begin date

2014-03

End date

2016-06

Distribution format

Name	Version

OnLine resource

Protocol	Linkage	Name
	http://onlinelibrary.wiley.com/doi/10.1002/ppsc.201600073/full

OnLine resource

Protocol	Linkage	Name
	http://www.bgs.ac.uk/services/ngdc/accessions/index.html#item75389

Hierarchy level

Non geographic dataset

Other

non geographic dataset

Statement

Preparation of thin film experiment bottles A spin coating technique was used to produce surfaces with thin films of Fe(III) mineral. A solution of 0.15 M Fe gel and methanol at a v:v ratio of 3:1 was added to microscope slide cover glasses fixed to the base of a salad spinner. They were spun vigorously for 15 seconds and allowed to air dry at room temperature and were then were cut into 1 cm2 pieces using a diamond-tipped scriber. The final mass of Fe(III) on the slides was 0.08 ± 0.007 µM (n=6) and the coatings were found to be saturating but variable in thickness. Mineral-coated cover slides were added to serum bottles and placed vertically in slide holders prior to inoculation. Anaerobic modified minimal medium with 25 mM acetate as the electron donor and no electron acceptor was added to the bottles to cover the films. Fluorescence microscopy Cover glasses were removed from serum bottles, under a stream of argon gas in a box, and placed mineral side up onto microscope slides inside a window of PAP, which had been drawn on with liquid blocker pen. A solution of 150 µl of anaerobic 30 mM NaHCO3 buffer and fluorescent probes was added to the mineral film, the excess removed, and a cover slide was placed on top and the edges sealed to the slide using nail varnish. The probes were DAPI, SYTO9 and Redox Sensor Green (all from Invitrogen) used at final concentrations of 25 µg l-1, 20 µM and 1 µM in 30 mM NaHCO3, respectively. To visualise Fe(II), we synthesised the highly selective turn-on fluorescent probe RhoNox-1 and used it at a final concentration of 5 µM in 30 mM NaHCO3. The slides were imaged using a Zeiss Axio Scope A1 microscope with CCD monochrome camera and EC PLAN 100 × 1.3 oil lens. Confocal laser scanning microscopy was performed using a Leica SP5 inverted tandem head microscope and HCX PL APO lambda blue 63× 1.40 oil lens. The excitation and emission wavelengths were as follows; DAPI: Ex. 350 nm, Em. 420 – 480 nm; SYTO9: Ex. 488 nm, Em. 495 – 550 nm; Redox Sensor Green: Ex. 488 nm, Em. 500 – 540 nm; RhoNox-1: Ex. 543 nm, Em. 560 – 600 nm. Multiple channels were recorded sequentially with 2 × line averaging. Atomic force microscopy After 12 days of incubation in the experiment bottles, slides were removed from the serum bottles and mounted directly onto the Veeco NanoScope V. Samples were scanned in tapping mode and data was analysed using WSxM 5.0 software. Image analysis Image analysis was performed using the software imageJ [55]. Cells were counted by measuring the area of representative individual G. sulfurreducens cells (n=29) in segmented images. In other images the total area of bacteria fluorescence was divided by the mean area of 1 cell to estimate the total number of cells in an image [56] of a known area. The first step of comparing the location of G. sulfurreducens cells with the intensity RhoNox-1 fluorescence (and therefore Fe(II) concentration) and the location of thick regions of mineral coating was to segment the cells, patches of Fe(II) and thick regions of mineral from the background in respective channels of the same image. These were saved as regions of interest (ROIs) and the RhoNox-1 fluorescence intensity for each ROI was measured and categorised into areas which corresponded with a cell, a thick piece of mineral, with one of these or without either. Statistical analyses were performed using OriginPro 8.5. Extracellular appendages were measured from 10 CLSM images using the straight line tool in image J; pili extending beyond the field of view were not included and a total of 80 features were measured.

Metadata

File identifier

50e27c44-74ea-4ac1-e054-002128a47908 XML

Metadata language

English

Hierarchy level

Non geographic dataset

Hierarchy level name

non geographic dataset

Date stamp

2024-12-06

Metadata standard name

UK GEMINI

Metadata standard version

2.3

Metadata author

Organisation name	Individual name	Electronic mail address	Role
British Geological Survey		enquiries@bgs.ac.uk	Point of contact

Dataset URI

http://data.bgs.ac.uk/id/dataHolding/13607162