READ ME

This text describes the data presented in the paper: Microbial fuel cells with highly active aerobic biocathodes 

========================
Introductory information
========================

Files included in the data deposit (include a short description of what data are contained): 

Figure 1 - CA and CV data for the -0.1 V AS inoc. half-cells. Average CA current with time (A), CV at 61 days in air (B) and with addition of azide at the end of the half-cell operational period (C).
Figure 2 - CV data in air and N2 for the half-cells; -0.1 V AS inococulum, -0.1 V half-cell effluent inoculum, +0.2 V half-cell effluent inoculum
Figure 3 (file 1) - CV data from which oxidation and reduction peak values were extracted for the -0.1 V half-cell effluent inoculum half-cell.
Figure 3 (file 2) - Peak values used to plot Figure 3 (-0.1 V half-cell effluent inoculum) 
Figure 4 (file 1) - FASTQ file produced from the raw ion torrent BAM file. Contains all raw sequence data with quality scores.
Figure 4 (file 2) - Mapping file for FASTQ file (with barcodes)
Figure 4 (file 3) - BIOM file converted to TXT file used to plot stacked bar chart data in Figure 4A) and the data for Table S1 (BIOM file produced from FASTQ file using QIIME)
Figure 4 (file 4) - Data used to give PCoA plots (produced from FASTQ file using QIIME) 
Figure 5 - MFC polarisation curve data for three different cathodes (Bicathode, plain carbon felt cathode and platinized cathode) 
Figure S3 - Equivalent CV to those depicted in Figure 1B and 1C for the duplicate -0.1 V AS inococulum half-cell.
Figure S4 - Equivelent CV to those depicted in Figure 2A, 2B and 2C for the duplicate half-cells;  -0.1 V AS inoculum, -0.1 V half-cell effluent inococulum, +0.2 V half-cell effluent inococulum.
Figure S5 (file 1) - TRE file used to construct the phylogenetic tree (processed from FASTQ file using QIIME)
Figure S5 (file 2) - FNA file built from representative sequences from this study (processed from FASTQ file using QIIME) and sequences from Genbank. Used to produce the TRE file.
Figure S5 (file 3) - TXT file used to produce the phylogenetic tree annotations
Table 3 - CA data used to determine average CA currents in Table 3

Key words used to describe the data:
Activated Sludge (AS)
Microbial fuel cell (MFC)
Half-cell
Chronoamperometry (CA)
Cyclic voltammatry (CV)
FASTQ file
TRE file
BIOM file
Principal Coordinates Analysis (PCoA)
Stacked bar chart
Phylogenetic tree
Quantative Insights Into Molecular Ecology (QIIME)

========================== 
Methodological information
==========================
What the data is, how and why it was collected or created, and how it was processed:
CA data collected to monitor aerobic biocathode growth and compare aerobic biocathode performances at different applied potential. Raw CA data were processed by normalising to electrode area (dividing by 12.16 cm2).
CV data collected to determine aerobic biocathode performance and information relating to electron transfer mechanism. CV were recorded under different conditions and at different scan rate. Raw CV data were processed by normalising to electrode area (dividing by 12.16 cm2).
MFC polarisation curve data were collected to assess MFC performance with an aerobic biocathode and other chemical cathodes. From raw cell voltage data, power and current outputs were calculated and normalised to cathode electrode area (division by 12.16 cm2).
16S rRNA sequence data recovered from the aerobic biocathode electrodes were used to determine community composition. The FASTQ file containing this sequence data was processed using QIIME.   

Instruments, hardware and software used:
Single channel potentiostats (Sycopel, UK) were used to poise the half-cell potentials and collect CA data.
An Autolab PGSTAT302 potentiostat (Metrohm, Switzerland) was used to produce the CV data.
NOVA (Metrohm, Autolab) was used for peak analysis of CV data (where applicable).
Cell voltage, anode and cathode potentials were recorded using a National Instruments data logger.
An Ion Torrent Personal Genome Machine (Life technologies, USA) was used to sequence the purified amplicon library, producing a BAM file (which was converted into a FASTQ file)
Quantative Insights Into Molecular Ecology (QIIME) software was used to process all sequence data in the FASTQ file produced from the ion torrent sequencing run

Date(s) of data collection: 
CA and CV data collected from 16/05/2013 to 27/02/2014
Community analysis data collected on 03/06/2014  

Geographic coverage of data:
Data is for lab-based bioelectrochemical systems, which were operated in lab C318, Merz court (CEAM), Newcastle University.

Data validation (how was the data checked, proofed and cleaned):
Electrochemical data was collected directly from the potentiostats and is normalised to cathode electrode area in most instances (12.16 cm2). 
Sequences from the FASTQ file were aligned to the Greengenes template sequence database using the PyNast algorithm in QIIME. Chimeric sequences were removed using the ChimeraSlayer algorithm in QIIME.

=========================
Data-specific information
=========================
Definitions of names, labels, acronyms or specialist terminology uses for variables, records and their values: 
Activated Sludge (AS) - The biological sludge formed from the activated sludge process in which wastewater containing organics is aerated using pumps
Microbial fuel cell (MFC) - An electrochemical device using bacteria at the anode which oxidises organic substrates, producing electricity 
Half-cell - A 3-electrode electrochemical cell comprising a working electrode (WE), counter electrode (CE) and reference electrode (RE).
Chronoamperometry (CA) - An electrochemical method in which the WE potential is fixed and the current measured with time. 
Cyclic voltammatry (CV) - An electrochemical method in which the WE potential is scanned at a fixed rate in both a positive and negative direction whilst measuring the current.
FASTQ file - A file containing both biological sequence data with corresponsing quality scores. 
TRE file - Newick formatted tree file containing the phylogenetic tree data. Distances are represented using parantheses and commas.
Stacked bar chart - Bar chart graphical representation of % sequence abundance according to taxonomic classification.

Explanation of weighting and grossing variables:
Raw current and power outputs normalised to cathode electrode area in most instances (12.16 cm2). 

=======
Contact
=======
Please contact rdm@ncl.ac.uk for further information