Rapid response of the active microbial community to CO2 exposure from a controlled sub-seabed CO2 leak in Ardmucknish Bay (Oban, Scotland)

International Journal of Greenhouse Gas Control

Volumn 38, Issue , 2015, Pages 171-181

  Tait, Karen ^a   Stahl, Henrik ^b   Taylor, Pete ^b   Widdicombe, Stephen ^a  

^a PLYMOUTH MARINE LABORATORY   (United Kingdom)

^b Scottish Marine Institute   (United Kingdom)

Author keywords

Bacteria; Carbon capture and storage (CCS); CO2; Microphytobenthos; Sediment

Indexed keywords

BACTERIA; CARBON CAPTURE; GENES; METAL RECOVERY; POLYMERASE CHAIN REACTION; RNA; SEDIMENTS;

BACTERIAL TAXA; CARBON CAPTURE AND STORAGE; MEASUREMENTS OF; MICROBIAL COMMUNITIES; MICROPHYTOBENTHOS; POTENTIALLY TOXIC METALS; QUANTITATIVE PCR; RELATIVE ABUNDANCE;

CARBON DIOXIDE;

EID: 84937939633     PISSN: 17505836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijggc.2014.11.021     Document Type: Article

References (76)

1. S.G. Acinas R. Sarma-Rupavtarm V. Klepac-Ceraj M.F. Polz PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample Appl. Environ. Microbiol. 71 2005 8966 8969
2. L. Alonso-Sáez V. Balague E.L. Sà O. Sanchez J.M. González J. Pinhassi R. Massana J. Pernthaler C. Pedrós-Alió J.M. Gasol Seasonality in bacterial diversity in north-west Mediterranean coastal waters: Assessment through clone libraries, fingerprinting and FISH FEMS Microbiol. Ecol. 60 2007 98 112
3. M. Anderson R.N. Gorley R.K. Clarke Permanova+ for Primer: Guide to Software and Statistical Methods 2008 Plymouth UK
4. Andreotti, R. de León, A.A.P. Dowd, S.E. Guerrero, F.D. Bendele, K.G. Scoles, G.A. 2011 Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing BMC microbiology 11 6
5. 2 Leakage from a Simulated Sub-Seabed Storage Site (submitted) IJGGC CCS in Marine Environment special issue http://dx.doi.org/10.1016/j.ijggc.2014.10.021
6. L. Beaufort I. Probert T. de-Garidel-Thoron E.M. Bendriff D. Ruiz-Pino N. Metzl C. Goyet N. Buchet P. Coupel M. Grelaud B. Rost R.E.M. Rickaby C. de Varges Sensitivity of coccolithophores to carbonate chemistry and ocean acidification Nature 476 2011 80 83
7. J.M. Beman C.E. Chow A.L. King Y. Feng J.A. Fuhrman A. Andersson N.R. Bates B.N. Popp D. Hutchins Global declines in oceanic nitrification rates as a consequence of ocean acidification Proc. Natl. Acad. Sci. U.S.A. 108 2011 208 213
8. M.M. Bengtsson L. Ovreås Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea BMC Microbiol. 10 2010 261
9. J.C. Blackford H. Stahl J.M. Bull B.J.P Bergès M. Cevatoglu A. Lichtschlag et al Detection and impacts of leakage from sub-seafloor deep geological carbon dioxide storage Nat. Clim. Change 2014 http://dx.doi.org/10.1038/NCLIMATE2381
10. D.H. Buckley V. Huangyutitham T.A. Nelson A. Rumberger J.E. Thies Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity Appl. Environ. Microbiol. 72 2006 4522 4531
11. J.G. Caporaso J. Kuczynski J. Stombaugh K. Bittinger F.D. Bushman E.K. Costello et al QIIME allows analysis of high-throughput community sequencing data Nat. Methods 7 2010 335 336
12. Y.J. Chang A.D. Peacock P.E. Long J.R. Stephen J.P. McKinley S.J. Macnaughton A.K.M. Anwar Hussain A.M. Saxton D.C. White Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site Appl. Environ. Microbiol. 67 2001 3149 3160
13. 2-induced ocean acidification interacts to influence the photosynthetic performance of the red tide alga Phaeocystis globosa (Prymnesiophyceae) Hydrobiologia 675 2011 105 117
14. K.R. Clarke M. Ainsworth A method of linking multivariate community structure to environmental variables Mar. Ecol. Prog. Ser. 92 1993 205 219
15. K.R. Clarke R.N. Gorley PRIMER v6: User Manual/Tutorial 2006 PRIMER-E Plymouth, UK
16. M.J.L. Coolen B. Abbas J. van Bleijswijk E.C. Hopmans M.M.M. Kuypers S.G. Wakeman J.S. Sinninge Damstė Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: A basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids Environ. Microbiol. 9 2007 1001 1016
17. A.W. Dale R. Prego Physico-biogeochemical controls on benthic-pelagic coupling of nutrient fluxes and recycling in a coastal upwelling system Mar. Ecol. Prog. Ser. 235 2002 15 28
18. L. Fandino L. Riemann G. Steward F. Azam Population dynamics of Cytophaga-Flavobacteria during marine phytoplankton blooms analyzed by real-time quantitative PCR Aquat. Microb. Ecol. 40 2005 251 257
19. 2, temperature and irradiance on the marine coccolithophore Emiliania huxleyi (Prymnesiophyceae) Eur. J. Phycol. 43 2008 87 98
20. F.X. Fu M.R. Mulholland N.S. Garcia A. Beck P.W. Bernhardt M.E. Warner S.A. Sañudo-Wihelmy D.A. Hutchins Interactions between changing pCO 2 , N 2 fixation, and Fe limitation in the marine unicellular cyanobacterium Crocosphaera Limnol. Oceanogr. 53 2008 2472 2484
21. K. Gao Z. Ruan V.E. Villafane J.P. Gattuso E.W. Helbling Ocean acidification exacerbates the effect of UV radiation on the calcifying phytoplankter Emiliania huxleyi Limnol. Oceanogr. 54 2009 1855 1862
22. G.M. Garrity D.J. Brenner N.R. Krieg J.T. Staley (Eds.) Bergey's Manual of Systematic Bacteriology Volume 2 The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria 2005 Springer, New York, NY
23. T.M. Gihring M. Humphrys H.J. Mills M. Huettel J.E. Kostka Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands Limnol. Oceanogr. 54 2009 1073 1083
24. F.O. Glöckner M. Kube M. Bauer H. Teeling T. Lombardot W. Ludwig et al Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 Proc. Natl. Acad. Sci. U.S.A. 100 2003 8298 8303
25. P.R. Gómez-Pereira B.M. Fuchs C. Alonso M.J. Oliver J.E. van Beusekom R. Amann Distinct flavobacterial communities in contrasting water masses of the north Atlantic Ocean ISME J. 4 2010 472 487
26. O.E. Håvelsrud T.H. Haverkamp T. Kristensen K.S. Jakobsen A.G. Rike Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea BMC Microbiol. 12 2012 203
27. 2 monitoring Energy Procedia 37 2013 4215 4233
28. 2 fixation, photosynthesis, growth rates, and elemental ratios: Implications for past, present, & future ocean biogeochemistry Limnol. Oceanogr 52 2007 1293 1304
29. 2 world Science 320 2008 336 340
30. J.F. Imhoff A. Hiraishi J. Süling Anoxygenic phototrophic purple bacteria Bergey's Manual® of Systematic Bacteriology 2005 Springer US 119 132
31. 2 on deep-sea benthic communities J. Oceanogr. 61 2005 835 843
32. 2 on benthic biota: An in situ benthic chamber experiment in Storfjorden (Norway) Mar. Pollut. Bull. 73 2013 443 451
33. S. Jin J.I. Drever P.J. Colberg Effects of copper on sulfate reduction in bacterial consortia enriched from metal-contaminated and uncontaminated sediments Environ. Toxicol. Chem. 26 2007 225 230
34. 2 gradient in the Mediterranean Sea off Vulcano, Italy Microb. Ecol. 67 2014 819 828
35. 2 Int. J. Greenhouse Gas Control 38 2015 202 209
36. V. Kitidis B. Laverock C.L. McNeil A. Beesley D. Cummings K. Tait A.M. Osborn S. Widdicombe The impact of ocean acidification on sediment nitrification Geophys. Res. Lett. 2011 http://dx.doi.org/10.1029/2011GL049095
37. G. Langer G. Nehrke I. Probert J. Ly P. Ziveri Strain-specific responses of Emiliania huxleyi to changing seawater carbonate chemistry Biogeosci. Discuss. 6 2009 4361 4383
38. B. Laverock J. Gilbert K. Tait A.M. Osborn S. Widdicombe Bioturbation: Impact on the marine nitrogen cycle Biochem. Soc. Trans. 39 2011 315 320
39. B. Laverock V. Kitidis K. Tait J.A. Gilbert A.M. Osborn S. Widdicombe Bioturbation activity determines the response of coastal benthic ammonia oxidising microorganisms to ocean acidification Philos. Trans. R. Soc. London, Ser. B 368 1627 2013 20120441
40. 2 concentrations Environ. Microbiol. 12 2010 1899 1912
41. 2 on the biogeochemistry of shallow marine sediments, their pore waters, and the overlying water column (submitted) Submitted to IJGGC CCS in Marine Environment special issue
42. I. Lidbury V. Johnson J.M. Hall-Spencer C.B. Munn M. Cunliffe Community-level response of coastal microbial biofilms to ocean acidification in a natural carbon dioxide vent ecosystem Mar. Pollut. Bull. 64 2012 1063 1066
43. M.W. Lomas B.M. Hopkinson J.L. Losh D.E. Ryan D.L. Shi Y. Xu F.M.M. Morel Effect of ocean acidification on cyanobacteria in the subtropical north Atlantic Aquat. Microb. Ecol. 66 2012 211 222
44. S.R. Longford N.A. Tujula G.R. Crocetti A.J. Holmes C. Holmstroem S. Kjelleberg et al Comparisons of diversity of bacterial communities associated with three sessile marine eukaryotes Aquat. Microb. Ecol. 48 2007 217 229
45. R.M. Morris K. Longnecker S.J. Giovannoni Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom Environ. Microbiol. 8 2006 1361 1370
46. U. Nübel F. Garcia-Pichel G. Muyzer PCR primers to amplify 16S rRNA genes from cyanobacteria Appl. Environ. Microbiol. 63 1997 3327 3332
47. T. Nunoura Y. Takaki H. Kazama M. Hirai J. Ashi H. Imachi K. Takai Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing Microbes Environ. 4 2012 382 390
48. A.E. Oliver L.K. Newbold A.S. Whiteley C.J. Gast Marine bacterial communities are resistant to elevated carbon dioxide levels Environ. Microbiol. Rep. 2014 http://dx.doi.org/10.1111/1758-2229.12159
49. T. Pollet R.D. Tadonléké J.F. Humbert Spatio-temporal changes in the structure and composition of a less abundant bacterial phylum ( Planctomycetes ) in two peri-alpine lakes Appl. Environ. Microbiol. 77 2011 4811 4821
50. 12C variations in Monterey Bay, California: Evidence of non-diffusive inorganic carbon uptake by phytoplankton in an upwelling environment Deep Sea Res., 1: Oceanogr. Res. Pap. 48 2001 79 94
51. 2 and temperature Plant Cell Environ. 14 1991 779 794
52. J.R. Reinfeilder Carbon concentrating mechanisms in Eukaryotic marine phytoplankton Annu. Rev. Mar. Sci. 3 2011 291 315
53. 2 Nature 407 2000 364 367
54. 2 ocean Nature 450 2007 545 548
55. A.S. Roy S.M. Gibbons H. Schunck S. Owens J.G. Caporaso M. Sperling J.I. Nissimov S. Romac L. Bittner M. Mühling U. Riebesell J. LaRoche J.A. Gilbert Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms Biogeosciences 10 2012 555 566
56. 2 release IJGGC CCS in Marine Environment special issue http://dx.doi.org/10.1016/j.ijggc.2014.10.001
57. E. Pruesse C. Quast K. Knittel B.M. Fuchs W. Ludwig J. Peplies F.O. Glöckner SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Nucleic Acids Res. 35 2007 7188 7196
58. T.R. Sandrin R.M. Maier Impact of metals on the biodegradation of organic pollutants Environ. Health Perspect. 111 2003 1093 1101
59. C.J. Smith D.B. Nedwell L.F. Dong A.M. Osborn Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples Environ. Microbiol. 8 2006 804 815
60. 2 and phosphate availability on domoic acid production and physiology of the marine harmful bloom diatom Pseudo-nitzschia multi-series Limnol. Oceanogr. 56 2011 829 840
61. M.T. Suzuki L.T. Taylor E.F. Delong Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays Appl. Environ. Microbiol. 66 2000 4605 4614
62. K. Tait B. Laverock J. Shaw P.J. Somerfield S. Widdicombe Minor impact of ocean acidification to the structure of the active microbial community in an Arctic sediment Environ. Microbiol. Rep. 5 2013 851 860
63. J.D. Taylor R. Ellis M. Milazzo J.M. Hall-Spencer M. Cunliffe Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient FEMS Microbiol. Ecol. 89 2014 670 678
64. 2 release experiment for quantifying and monitoring potential ecosystem impacts from geological carbon storage (submitted) Submitted to IJGGC CCS in Marine Environment special issue http://dx.doi.org/10.1016/j.ijggc.2014.09.007
65. Taylor, P. Lichtschlag, A. Toberman, M. Sayer, M.D.J. Reynolds, A. Sato, T. Stahl, H. Sediment pH microprofiles, during and after a novel carbon dioxide release experiment: Impact, recovery and volume of carbon dioxide remaining within the interstitial water Submitted to IJGGC CCS in Marine Environment Special Issue http://dx.doi.org/10.1016/j.ijggc.2014.09.006
66. H. Teeling B.M. Fuchs D. Becher C. Klockow A. Gardebrecht C.M. Bennke et al Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom Science 336 2012 608 611
67. 2 sensitivity of Southern Ocean phytoplankton Geophys. Res. Lett. 35 2008 L04605 http://dx.doi.org/10.1029/2007GL032583
68. 2 on carbon acquisition and intracellular assimilation in four marine diatoms J. Exp. Mar. Biol. Ecol. 376 2009 26 36
69. K.L. Vergin E. Urbach J.L. Stein E.F. DeLong B.D. Lanoil S.J. Giovannoni Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales Appl. Environ. Microbiol. 64 1998 3075 3078
70. Watanabe, Y. Tait, K. Gregory, S. Hayashi H. Shimamoto, A. Taylor, P. Stahl, H. Green, K. Yoshinaga, I. Suwa Y. Kita, J. Ammonia oxidation activity of microorganisms in surface sediment to a controlled sub-seabed release of CO2 (submitted) Submitted to IJGGC CCS in Marine Environment Special Issue http://dx.doi.org/10.1016/j.ijggc.2014.11.013
71. 2-induced seawater acidification on the burrowing activity of Nereis virens and sediment nutrient flux Mar. Ecol. Prog. Ser. 341 2007 111 122
72. 2 induced seawater acidification on sediment diversity and nutrient flux Mar. Ecol. Prog. Ser. 379 2009 59 75
73. 2 on animal mediated ecosystem function: The modification of sediment nutrient fluxes by burrowing urchins Mar. Pollut. Bull. 73 2013 416 427
74. Widdicombe, S. McNeill, C.L. Stahl, H. Taylor, P. Queirós, A.M. Nunes, J. Tait, K. Impact of sub-seabed CO2 leakage on macrobenthic community structure and diversity (submitted) Submitted to IJGGC CCS in Marine Environment special issue
75. T.J. Williams D. Wilkins E. Long F. Evans M.Z. DeMaere M.J. Raftery R. Cavicchioli The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics Environ. Microbiol. 15 2013 1302 1317
76. 2 and low-pH extremes ISME J. 7 2012 555 567