Shifts in the Microbial Community Composition of Gulf Coast Beaches Following Beach Oiling

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Newton, Ryan J ^a   Huse, Susan M ^b   Morrison, Hilary G ^b   Peake, Colin S ^a   Sogin, Mitchell L ^b   McLellan, Sandra L ^a  

^a UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^b MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; HYDROCARBON; RIBOSOME RNA; SEA WATER;

ALCANIVORAX; ALTEROMONAS; ARTICLE; BACTERIAL GENE; BACTERIUM; BACTERIUM IDENTIFICATION; COMMUNITY DYNAMICS; COMMUNITY STRUCTURE; CONTROLLED STUDY; ENVIRONMENTAL IMPACT ASSESSMENT; GENE ISOLATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GULF OF MEXICO; MARINOBACTER; MICROBIAL COMMUNITY; NONHUMAN; OIL SPILL; POPULATION ABUNDANCE; SAND; SEASHORE; SPECIES COMPOSITION; SYNECOLOGY; UNITED STATES; WINOGRADSKYELLA; ZEAXANTHINIBACTER;

BATHING BEACHES; ECOSYSTEM; FLAVOBACTERIACEAE; GAMMAPROTEOBACTERIA; GRAM-NEGATIVE AEROBIC RODS AND COCCI; GULF OF MEXICO; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; HYDROCARBONS; MICROBIAL CONSORTIA; PETROLEUM POLLUTION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 84883765148     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0074265     Document Type: Article

References (49)

1. Huettel M, Rusch A, (2000) Transport and degradation of phytoplankton in permeable sediment. Limnol Oceanogr 45: 534-549. doi:10.4319/lo.2000.45.3.0534.
2. Mills HJ, Hunter E, Humphrys M, Kerkhof L, McGuinness L, et al. (2008) Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico. Appl Environ Microbiol 74: 4440-4453. doi:10.1128/AEM.02692-07. PubMed: 18487394.
3. USEPA (2004) Report to Congress: Impacts and Control of CSOs and SSOs. District of Columbia: Washington Office of Water.
4. USEPA (2011) EPA's BEACH Report 2010 Swimming Season. pp. 1-4. Washington, D.C.
5. Gobet A, Böer SI, Huse SM, van Beusekom JE, Quince C, et al. (2012) Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6: 542-553. doi:10.1038/ismej.2011.132. PubMed: 21975598.
6. Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, et al,. (2011) Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico. Beach: Sands Impacted by the Deepwater Horizon Oil Spill. Appl Environ Microbiol 77: 7962-7974.
7. Hunter EM, Mills HJ, Kostka JE, (2006) Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl Environ Microbiol 72: 5689-5701. doi:10.1128/AEM.03007-05. PubMed: 16957183.
8. Sørensen KB, Glazer B, Hannides A, Gaidos E, (2007) Spatial structure of the microbial community in sandy carbonate sediment. Mar Ecol Prog Ser 346: 61-74. doi:10.3354/meps06996.
9. Böer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, Ramette A, (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3: 780-791. doi:10.1038/ismej.2009.29. PubMed: 19340087.
10. Hewson I, Fuhrman JA, (2006) Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities. Mar Ecol Prog Ser 306: 79-86. doi:10.3354/meps306079.
11. Polymenakou PN, Bertilsson S, Tselepides A, Stephanou EG, (2005) Links between geographic location, environmental factors, and microbial community composition in sediments of the Eastern Mediterranean Sea. Microb Ecol 49: 367-378. doi:10.1007/s00248-004-0274-5. PubMed: 16003476.
12. Lehr B, Sky B, Possolo A, (2010) Oil Budget Calculator Deepwater Horizon U, [!(surname)!], eds.
13. Hayworth JS, Clement TP, Valentine JF, (2011) Deepwater Horizon oil spill impacts on Alabama beaches. Hydrol Earth Syst Sci 15: 3639-3649. doi:10.5194/hess-15-3639-2011.
14. Harayama S, Kasai Y, Hara A, (2004) Microbial communities in oil-contaminated seawater. Curr Opin Biotechnol 15: 205-214. doi:10.1016/j.copbio.2004.04.002. PubMed: 15193328.
15. Head IM, Jones DM, Röling WFM, (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4: 173-182. doi:10.1038/nrmicro1348. PubMed: 16489346.
16. Yakimov MM, Timmis KN, Golyshin PN, (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18: 257-266. doi:10.1016/j.copbio.2007.04.006. PubMed: 17493798.
17. Coulon F, McKew BA, Osborn AM, McGenity TJ, Timmis KN, (2007) Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters. Environ Microbiol 9: 177-186. doi:10.1111/j.1462-2920.2006.01126.x. PubMed: 17227422.
18. Alonso-Gutiérrez J, Figueras A, Albaigés J, Jiménez N, Viñas M, et al. (2009) Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill. Appl Environ Microbiol 75: 3407-3418. doi:10.1128/AEM.01776-08. PubMed: 19376924.
19. Newton RJ, VandeWalle JL, Borchardt MA, Gorelick MH, McLellan SL, (2011) Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor. Appl Environ Microbiol 77: 6972-6981. doi:10.1128/AEM.05480-11. PubMed: 21803887.
20. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196. doi:10.1093/nar/gkm864. PubMed: 17947321.
21. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143. doi:10.1186/gb-2007-8-7-r143. PubMed: 17659080.
22. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. doi:10.1093/bioinformatics/btr381. PubMed: 21700674.
23. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML, (2008) Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLOS Genet 4(11):: e1000255. doi:10.1371/journal.pgen.1000255. PubMed: 19023400.
24. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi:10.1093/bioinformatics/btq461. PubMed: 20709691.
25. Magurran AE, (2004) Measuring Biological Diversity. Malden, MA, USA: Blackwell Publishing House Science Ltd.
26. Oksanen J, Blanchet GF, Kindt R, Legendre P, Minchin PR, et al. (2011) vegan: Community Ecology Package. R Package Version 2: 0-2. http://CRAN.R-project.org/package=vegan.
27. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
28. Chao A, Chazdon RL, Colwell RK, Shen TJ, (2006) Abundance-Based Similarity Indices and Their Estimation When There Are Unseen Species in Samples. Biometrics 62: 361-371. doi:10.1111/j.1541-0420.2005.00489.x. PubMed: 16918900.
29. Clarke KR, (1993) Nonparametric Multivariate Analyses of Changes in Community Structure. Aust J Ecol 18: 117-143. doi:10.1111/j.1442-9993.1993.tb00438.x.
30. Clarke KR, Gorley RN, (2006) PRIMER v6: User Manual/Tutorial. UK: Plymouth.
31. Urakawa H, Yoshida T, Nishimura M, Ohwada K, (2000) Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Environ Microbiol 2: 542-554. doi:10.1046/j.1462-2920.2000.00137.x. PubMed: 11233162.
32. Boone PA, (1973) Depositional systems of the Alabama, Mississippi, and western Florida coastal zone. Gulf Coast Assoc Geol Soc Trans 23: 226-277.
33. Llobet-Brossa E, Rosselló-Mora R, Amann R, (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64: 2691-2696. PubMed: 9647850.
34. Bühring SI, Elvert M, Witte U, (2005) The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization. Environ Microbiol 7: 281-293. doi:10.1111/j.1462-2920.2004.00710.x. PubMed: 15658995.
35. Biers EJ, Sun SL, Howard EC, (2009) Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome. Appl Environ Microbiol 75: 2221-2229. doi:10.1128/AEM.02118-08. PubMed: 19201952.
36. Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, et al. (2011) Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLOS ONE 6(9):: e24570. doi:10.1371/journal.pone.0024570. PubMed: 21931760.
37. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLOS Biol 5(3):: e77. doi:10.1371/journal/pbio.0050077. PubMed: 17355176.
38. Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S, (2011) A Guide to the Natural History of Freshwater Lake Bacteria. Microbiol Mol Biol Rev 75: 14-49. doi:10.1128/MMBR.00028-10. PubMed: 21372319.
39. White PS, Pickett STA, (1985) The Ecology of Natural Disturbance and Patch Dynamics. Orlando, FL, USA: Academic Press. pp. pp. 3-13.
40. Carpenter SR, Brock WA, (2006) Rising variance: a leading indicator of ecological transition. Ecol Lett 9: 308-315. PubMed: 16958897.
41. Carpenter SR, Cole JJ, Pace ML, Batt R, Brock WA, et al. (2011) Early Warnings of Regime Shifts: A Whole-Ecosystem Experiment. Science 332: 1079-1082. doi:10.1126/science.1203672. PubMed: 21527677.
42. Hewson I, Vargo GA, Fuhrman JA, (2003) Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: Effects of virus infection, containment, and nutrient enrichment. Microb Ecol 46: 322-336. doi:10.1007/s00248-002-1067-3. PubMed: 14502411.
43. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S, (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A 103: 13104-13109. doi:10.1073/pnas.0602399103. PubMed: 16938845.
44. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139. doi:10.1111/j.1462-2920.2009.02017.x. PubMed: 19659500.
45. Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, et al. (2012) Defining seasonal marine microbial community dynamics. ISME J 6: 298-308. doi:10.1038/ismej.2011.107. PubMed: 21850055.
46. Giovannoni SJ, Vergin KL, (2012) Seasonality in Ocean Microbial Communities. Science 335: 671-676. doi:10.1126/science.1198078. PubMed: 22323811.
47. Hanski I, (1982) Dynamics of regional distribution: the core and satellite species hypothesis. Oikos 38: 210-221. doi:10.2307/3544021.
48. Gibson DJ, Ely JS, Collins SL, (1999) The core-satellite species hypothesis provides a theoretical basis for Grime's classification of dominant, subordinate, and transient species. J Ecol 87: 1064-1067. doi:10.1046/j.1365-2745.1999.00424.x.
49. Shade A, Handelsman J, (2012) Beyond the Venn diagram: the hunt for a core microbiome. Environ Microbiol 14: 4-12. doi:10.1111/j.1462-2920.2011.02585.x. PubMed: 22004523.