Bacterial Community Composition and Diversity in Methane Charged Sediments Revealed by Multitag Pyrosequencing

Geomicrobiology Journal

Volumn 29, Issue 4, 2012, Pages 340-351

  Hamdan, Leila J ^a   Sikaroodi, Masoumeh ^b   Gillevet, Patrick M ^b  

^a NAVAL RESEARCH LABORATORY   (United States)

^b GEORGE MASON UNIVERSITY   (United States)

Author keywords

AOM; bacteria; Chilean margin; methane; multi tag; pyrosequencing; sulfate

Indexed keywords

CLONE; COMMUNITY COMPOSITION; GEOMICROBIOLOGY; METHANE; METHANOGENESIS; RNA; SEDIMENT CHEMISTRY; SPECIES DIVERSITY; SULFATE-REDUCING BACTERIUM; TAXONOMY;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; DELTAPROTEOBACTERIA;

EID: 84857311162     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490451.2011.559305     Document Type: Article

References (48)

1. Adrian, L. 2009. ERC-group microflex: microbiology of Dehalococcoides-like Chloroflexi. Rev Environ Sci Biotechnol, 8: 225-229.
2. Biddle, J F, House, C H and Brenchley, J E. 2005. Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology, 3: 287-295.
3. Blazejak, A, Erseus, C, Amann, R and Dubilier, N. 2005. Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru margin. Appl Environ Microbiol, 71: 1553-1561.
4. Blazejak, A and Schippers, A. 2010. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol, 72: 198-207.
5. Boetius, A, Ravenschlag, K, Schubert, C J, Rickert, D, Widdel, F, Gleseke, A, Amann, R, Jørgensen, B B, Witte, U and Pfannkuche, O. 2000. A marine microbial consortium apparently mediating anaerobic oxidation methane. Nature, 407: 623-626.
6. Brazelton, W J, Sogin, M L and Baross, J A. 2010. Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms. Environ Microbiol Repts, 2: 236-242.
7. Campbell, B J and Cary, S C. 2001. Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana. Appl Environ Microbiol, 67: 110-117.
8. Coffin, R, Pohlman, J, Gardner, J, Downer, R, Wood, W, Hamdan, L, Walker, S, Plummer, R, Gettrust, J and Diaz, J. 2007. Methane hydrate exploration on the mid Chilean coast: A geochemical and geophysical survey. J Petrol Sci Eng, 56: 32-41.
9. Espinosa, L F, Pantoja, S, Pinto, L A and Rullkotter, J. 2009. Water column distribution of phospholipid-derived fatty acids of marine microorganisms in the Humboldt Current system off northern Chile. Deep-Sea Research Part Ii-Top Stud Oceanogr, 56: 1039-1048.
10. Gallardo, VA. 1977. Large benthic microbial communities in sulphide biota under Peru-Chile subsurface countercurrent. Nature, 268: 331-332.
11. Ghannoum, M A, Jurevic, R J, Mukherjee, P K, Cui, F, Sikaroodi, M, Naqvi, A and Gillevet, P M. 2010. Characterization of the oral fungal microbiome (Mycobiome) in healthy individuals. PLoS Pathog, 6: e1000713
12. Girguis, P R, Cozen, A E and DeLong, E F. 2005. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Appl Environ Microbiol, 71: 3725-3733.
13. Grant, A and Ogilvie, L A. 2004. Name that microbe: rapid identification of taxa responsible for individual fragments in fingerprints of microbial community structure. Mol Ecol. Notes, 4: 133-136.
14. Hamdan, L J, Gillevet, P M, Sikaroodi, M, Pohlman, J W, Plummer, R E and Coffin, R B. 2008. Geomicrobial characterization of gas hydrate-bearing sediments along the mid-Chilean margin. FEMS Microbiol Ecol, 65: 15-30.
15. Hamdan, L J, Gillevet, P M, Pohlman, J W, Sikaroodi, M, Greinert, J and Coffin, R B. 2011. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand. FEMS Microbiology Ecology, 77: 518-532.
16. Harrison, B K, Zhang, H, Berelson, W and Orphan, V J. 2009. Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microbiol, 75: 1487-1499.
17. Heck, K L, Vanbelle, G and Simberloff, D. 1975. Explicit calculation of rarefaction diversity measurement and determination of sufficient sample size. Ecology, 56: 1459-1461.
18. Heijs, S, Haese, R, van der Wielen, P, Forney, L and van Elsas, J. 2007. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb Ecol, 53: 384-398.
19. Huber, J A, Johnson, H P, Butterfield, D A and Baross, J A. 2006. Microbial life in ridge flank crustal fluids. Environ Microbiol, 8: 88-99.
20. Huber, J A, Mark Welch, D, Morrison, H G, Huse, S M, Neal, P R, Butterfield, D A and Sogin, M L. 2007. Microbial population structures in the deep marine biosphere. Science, 318: 97-100.
21. Hudson, ME. 2008. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Notes, 8: 3-17.
22. Huse, S M, Dethlefsen, L, Huber, J A, Welch, D M, Relman, D A and Sogin, M L. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLOS Genetics,: 4
23. Inagaki, F, Nunoura, T, Nakagawa, S, Teske, A, Lever, M, Lauer, A, Suzuki, M, Takai, K, Delwiche, M and Colwell, F S. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin. Proc Natl Acad Sci USA, 103: 2815-2820.
24. Kemp, P F and Aller, J Y. 2004. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol, 47: 161-177.
25. Knittel, K, Lösekann, T, Boetius, A, Amann, R and Kort, R. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol, 71: 467-479.
26. Kowalchuk, G A, Speksnijder, AGCL, Zhang, K, Goodman, R M and van Veen, J A. 2007. Finding the needles in the metagenome haystack. Microb Ecol, 53: 475-485.
27. Lanoil, B D, Sassen, R, La Duc, M T, Sweet, S T and Nealson, K H. 2001. Bacteria and archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microbiol, 67: 5143-5153.
28. Lozupone, C, Hamady, M and Knight, R. 2006. UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics, 7: 371
29. Lozupone, C and Knight, R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol, 71: 8228-8235.
30. Margulies, M, Egholm, M, Altman, W E, Attiya, S, Bader, J S, Bemben, L A, Berka, J, Braverman, M S, Chen, Y J and Chen, Z. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437: 376-380.
31. Masquelier, S and Vaulot, D. 2008. Distribution of micro-organisms along a transect in the South-East Pacific Ocean (BIOSOPE cruise) using epifluorescence microscopy. Biogeosciences, 5: 311-321.
32. Mills, D K, Fitzgerald, K, Litchfield, C D and Gillevet, P M. 2003. A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. J Microbiol Meth, 54: 57-74.
33. Nauhaus, K, Albrecht, M, Elvert, M, Boetius, A and Widdel, F. 2007. In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol, 9: 187-196.
34. Orcutt, B, Boetius, A, Elvert, M, Samarkin, V and Joye, S B. 2005. Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta, 69: 4267-4281.
35. Orphan, V J, Hinrichs, K U, Ussler, W, Paull, C K, Taylor, L T, Sylva, S P, Hayes, J M and Delong, E F. 2001. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol, 67: 1922-1934.
36. Parameswaran, P, Jalili, R, Tao, L, Shokralla, S, Gharizadeh, B, Ronaghi, M and Fire, A Z. 2007. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucl Acids Res, 35: e130
37. Parkes, R J, Webster, G, Cragg, B A, Weightman, A J, Newberry, C J, Ferdelman, T G, Kallmeyer, J, Jørgensen, B B, Aiello, I W and Fry, J C. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature, 436: 390-394.
38. Pernthaler, A, Dekas, A E, Brown, C T, Goffredi, S K, Embaye, T and Orphan, V J. 2008. Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci, 105: 7052-7057.
39. Reed, A, Lutz, R and Vetriani, C. 2006. Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles, 10: 199-211.
40. Sekiguchi, Y. 2006. Yet-to-be cultured microorganisms relevant to methane fermentation processes. Microbes Environ, 21: 1-15.
41. Smith, S W, Overbeek, R, Woese, C R, Gilbert, W and Gillevet, P M. 1994. The Genetic Data Environment (GDE): An expandable graphic interface for manipulating molecular information. CABIOS, 10: 671-675.
42. Sogin, M L, Morrison, H G, Huber, J A, Welch, D M, Huse, S M, Neal, P R, Arrieta, J M and Herndl, G J. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA, 103: 12115-12120.
43. Taylor, D L, Booth, M G, McFarland, J W, Herriott, I C, Lennon, N J, Nusbaum, C and Marr, T G. 2008. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Mol Ecol Resour, 8: 742-752.
44. Valentine, DL. 2002. Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: A review. Antonie Van Leeuwenhoek Int J Gen Molec Microbiol, 81: 271-282.
45. Valentine, D L and Reeburgh, W S. 2000. New perspectives on anaerobic methane oxidation. Environ Microbiol, 2: 477-484.
46. Webster, G, Parkes, R J, Fry, J C and Weightman, A J. 2004. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol, 70: 5708-5713.
47. Whiticar, MJ. 1999. Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem Geol, 161: 291-314.
48. Williams, M M, Domingo, J WS, Meckes, M C, Kelty, C A and Rochon, H S. 2004. Phylogenetic diversity of drinking water bacteria in a distribution system simulator. J Appl Microbiol, 96: 954-964.