QICS Data: Effect of a controlled sub-seabed release of CO2 in Ardmucknish Bay on microbial activity (2012 - 2014)

Dataset description

The response of the benthic microbial community to a controlled sub-seabed CO2 leak was assessed using quantitative PCR measurements of benthic bacterial, archaeal and cyanobacteria/chloroplast 16S rRNA genes. Similarly, the impact of CO2 release on the abundance of benthic bacterial and archaeal ammonia amoA genes and transcripts, and also to the abundance of nitrite oxidizer (nirS) and anammox hydrazine oxidoreductase (hzo) genes and transcripts. Samples were taken from four zones (epicentre (zone 1); 25m distant (zone 2), 75m distant (zone 3) and 450m distant (zone 4)) during 6 time points (7 days before CO2 exposure, after 14 and 36 days of CO2 release, and 6, 20 and 90 days after the CO2 release had ended). Changes to the active community of microphytobenthos and bacteria were also assessed before, during and after CO2 release using Denaturing Gradient Gel Electrophoresis of cyanobacteria/chloroplast 16S rRNA. Changes to the composition of the active bacterial community was assessed first using Terminal Restriction Fragment Length Polymorphism (T-RFLP) of bacterial 16S rRNA. In depth comparisons of possible changes to the active bacterial community at zone 1 and 4 before, during and immediately after the CO2 release was performed using 16S rRNA 454 pyrosequencing. This dataset was created by Plymouth Marine Laboratory (PML) under the program QICS (Quantifying and monitoring environmental impacts of geological carbon storage) which was funded by the Natural Environment Research Council (NERC), with support from the Scottish Government. The results are contained in three text files. QICS project website: www.bgs.ac.uk/qics/home.html. Tait et al. (2015) Rapid response of the active microbial community to CO2 exposure from a controlled sub-seabed CO2 leak in Ardmucknish Bay (Oban, Scotland). IJGGC DOI: 10.1016/ijggc.2014.11.021. Watanabe et al. (2015) Ammonia oxidation activity of microorganisms in surface sediment to a controlled sub-seabed release of CO2. IJGGC DOI: 10.1016/j.ijggc.2014.11.013.

Further information

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Enquiries

Environmental Science Centre, Nicker Hill, Keyworth
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Associated dataset(s)

NERC Project: QICS - Quantifying and monitoring environmental impacts of geological carbon storage (2010 - 2014)

Dataset details

Author(s) Karen Tait
Principal Investigator(s) Karen Tait
Plymouth Marine Laboratory
Language English
Curator British Geological Survey
Supply media/format .txt; Version:N/A
TIF; Version:N/A
Storage format Not available
Frequency of update not applicable
Start of capture {ts '2010-05-01 00:00:00'} Not known
End of capture {ts '2014-12-01 00:00:00'} December 2014
Online access URL  
Lineage statement Sediment samples were collected 7 days before the CO2 supply was turned on (D-7/8), D13/14 and D35/36 during CO2 release, and after the CO2 release ended on D41/42, D55/56 and D127/128 at each of four zones (zone 1 = at epicentre; zone 2 (25m distant), zone 3 (75m distant), and zone 4 (control, 450m distant). At each zone, five replicate sediment samples were manually collected by divers using five 50 ml syringes with the end cut off. Each syringe was sealed with a rubber bung and transported back to the lab were the top 1 cm was sectioned and frozen at -80 °C. RNA and DNA were extracted from 2 g sediment using the MoBio RNA PowerSoil® Total RNA Isolation Kit with the DNA elution accessory kit according to the manufacturer?s instructions. RNA was reverse transcribed using the QuantiTect Reverse Transcription Kit (Qiagen) with 0.2 μg of RNA and the supplied random primers. An ABI 7000 sequence detection system (Applied Biosystems, Foster City, USA) and QuantiFast SYBR Green PCR Kit (Qiagen) was used for all qPCR measurements. The abundance of bacterial, archaeal and cyanobacterial/chloroplast 16S rRNA (from cDNA) and genes (from DNA) in each sediment sample was determined using quantitative PCR. The method is described in detail in Tait et al. 2015. In addition, for each sediment sample, the abundance of Thaumarchaeal and bacterial amoA transcripts and genes, nitrite reducer (nirS) and hydrazine oxidoreductase (hzo) genes and transcripts was determined. The method is described in detail in Watanabe et al. 2015. The data in the table QICS microbial qPCR data.txt is in the format of Dx (relative to day of injection). D-7/8: 10/11 May 2012 D13/14: 30/31 May 2012 D35/D36: 20/21 June 2012 D41/D42: 27/28 June 2012 D54/D55: 9 July/10 July 2012 D127/D128: 19/20 September 2012 Zones are as described above and data is shown for the 5 replicate cores. Numbers are 16S rRNA/transcript/gene copies per gram sediment. DGGE analysis of cyanobacteria/chloroplast 16S rRNA (cDNA) sequences was performed with the INGENYphorU DGGE system (Ingeny, The Netherlands), as described in detail in Tait et al. 2015 . Replicate cores were combined to give a total of 24 PCR products. The original gel image is QICS cyanobacteria 16S rRNA DGGE image.tif. Gel Compar II software was used to analyse DGGE fingerprinting patterns (Applied Maths, Netherlands) and the data imported into PRIMER vs. 6.1 multivariate analysis software (Clarke and Gorley 2006) for statistical analysis. The data in the table QICS cyanobacteria 16S rRNA DGGE data.txt contains relative abundance of band density for each sample. Data is in the format of Dx as above. Bands are numbered according to their distance migrated down the gel. To compare bacterial communities at each zone and over time, 16S rRNA fragments were amplified and analysed using terminal restriction length polymorphism (T-RFLP) using the protocol of Laverock et al. (2010). 6-FAM labelled PCR products were digested with the restriction enzyme AluI, and the fragment profile for each sample determined by DNA Sequencing Services (Dundee University). Resulting electropherograms were initially analysed using GeneMapper 3.7 software (Applied Biosystems) and subsequently using T-Align (Smith et al., 2005). This data can be found in Blackford et al. (2014) Nature Climate Change DOI: 10.1038/NCLIMATE2381. Relative abundance of TRFs for each sample can be found in QICS bacterial 16S rRNA T-RFLP data.txt. Again, the data is in the format of Dx as above. TRFs are numbered according to their nucleotide length. The relative abundance and composition of 16S rRNA (cDNA) in the five replicate samples collected from zones 1 and zones 4 on D-7/8, D13/14, D35/36 and D41/42 were determined using 16S rRNA tagged pyrosequencing, as described in Tait et al. 2015 . Sequence data has been archived at the European Nucleotide Archive, accession number PRJEB7642.
Supplementary information Blackford et al. (2014) Detection and impacts of leakage from sub-seafloor deep geological carbon dioxide storage. Nature Climate Change DOI: 10.1038/NCLIMATE238. Tait et al. (2015) Rapid response of the active microbial community to CO2 exposure from a controlled sub-seabed CO2 leak in Ardmucknish Bay (Oban, Scotland). IJGGC DOI: 10.1016/ijggc.2014.11.021. Watanabe et al. (2015) Ammonia oxidation activity of microorganisms in surface sediment to a controlled sub-seabed release of CO2. IJGGC DOI: 10.1016/j.ijggc.2014.11.013. QICS project website: www.bgs.ac.uk/qics/home.html.
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Contact details
Department Enquiries
Organisation British Geological Survey
Address Environmental Science Centre, Nicker Hill, Keyworth
City Nottingham
County Nottinghamshire
Country United Kingdom
Postcode NG12 5GG
E-mail enquiries@bgs.ac.uk
Telephone +44 (0)115 936 3143
Fax +44 (0)115 936 3276
Keywords
Topic category code (ISO) geoscientificInformation (information pertaining to earth sciences)
Keywords BACTERIA
CARBON
ENVIRONMENTAL IMPACT
MONITORING
NITROGEN CYCLE
STORAGE
Keyword source BGS Keyphrases
Spatial details
Spatial Reference System Not available
Dataset extent
Coverage (Lat/Long) North boundary : 56.49
East boundary  : -5.42
South boundary : 56.49
West boundary  : -5.42
Metadata
Metadata language English
Metadata last updated 14th December 2016
Metadata standard compliance NERC profile of ISO19115:2003
Copyright and IPR
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.