Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system

FEMS Microbiology Ecology

Volumn 83, Issue 2, 2013, Pages 324-339

  Anderson, Rika E ^a   Beltrán, Mónica Torres ^b   Hallam, Steven J ^b   Baross, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Hydrothermal plume; Hydrothermal vent; SUP05

Indexed keywords

RNA 16S; SEA WATER;

BACTERIUM; BIOGEOCHEMISTRY; GENE EXPRESSION; HYDROTHERMAL PLUME; HYDROTHERMAL VENT; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; NICHE PARTITIONING; POLYMERASE CHAIN REACTION; SEAWATER;

ARCHAEON; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; ECOSYSTEM; GENETICS; HYDROTHERMAL VENT; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ARCHAEA; BACTERIA; BIODIVERSITY; ECOSYSTEM; HYDROTHERMAL VENTS; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEAWATER;

JUAN DE FUCA RIDGE; PACIFIC OCEAN;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 84871967040     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01478.x     Document Type: Article

References (65)

1. Alldredge AL & Cohen Y (1987) Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235: 689-691.
2. Anderson RE, Brazelton WJ & Baross JA (2011) Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol Ecol 77: 120-133.
3. Bourbonnais A, Juniper SK, Butterfield DA et al. (2012) Activity and abundance of denitrifying bacteria in the subsurface biosphere of diffuse hydrothermal vents of the Juan de Fuca Ridge. Biogeosciences 9: 4177-4223.
4. Brown MV, Schwalbach MS, Hewson I & Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7: 1466-1479.
5. Burnham KP & Overton WS (1978) Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika 65: 623-633.
6. Burnham KP & Overton WS (1979) Robust estimation of population size when capture probabilities vary among animals. Ecology 60: 927-936.
7. Butterfield DA, Jonasson IR, Massoth GJ, Feely RA, Roe KK, Embley RE, Holden JF, McDuff RE, Lilley MD & Delaney JR (1997) Seafloor eruptions and evolution of hydrothermal fluid chemistry. Philos Trans R Soc Lond A 355: 369-386.
8. Butterfield DA, Roe KK, Lilley MD, Huber JA, Baross JA, Embley RW & Massoth GJ (2004) Mixing, reaction and microbial activity in the sub-seafloor revealed by temporal and spatial variation in diffuse flow vents at Axial Volcano. The Subseafloor Biosphere at Mid-Ocean Ridges (Wilcock WSD, DeLong EF, Kelley DS, Baross JA & Cary SC, eds), pp. 269-290. American Geophysical Union, Washington, DC.
9. Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, Revsbech NP & Ulloa O (2010) A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330: 1375-1378.
10. Cavanaugh CM (1983) Symbiotic chemoautotrophic bacteria in marine invertebrates from sulphide-rich habitats. Nature 302: 58-61.
11. Chao A (1987) Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43: 783-791.
12. Chao A, Chazdon RL, Colwell RK & Shen T-J (2005) A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol Lett 8: 148-159.
13. Clarke KR & Gorley RN (2006) PRIMER v6: User Manual/Tutorial. Primer-E Ltd, Plymouth.
14. Collins RE & Rocap G (2007) REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Res 35: W58-W62.
15. Colwell RK, Mao CX & Chang J (2004) Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85: 2717-2727.
16. Corliss JB, Dymond J, Gordon LI et al. (1979) Submarine thermal sprirngs on the Galapagos Rift. Science 203: 1073-1083.
17. De Angelis MA, Lilley MD, Olson EJ & Baross JA (1993) Methane oxidation in deep-sea hydrothermal plumes of the Endeavour Segment of the Juan de Fuca Ridge. Deep Sea Res Part 1 Oceanogr Res Pap 40: 1169-1186.
18. DeLong EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 89: 5685-5689.
19. DeSantis TZ, Hugenholtz N, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P & Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069.
20. Dick GJ & Tebo BM (2010) Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Environ Microbiol 12: 1334-1347.
21. Edwards U, Rogall T, Blöcker H, Emde M & Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17: 7843-7853.
22. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
23. German CR, Bowen A, Coleman ML et al. (2010) Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise. P Natl Acad Sci USA 107: 14020-14025.
24. Grote J, Jost G, Labrenz M, Herndl GJ & Jurgens K (2008) Epsilonproteobacteria represent the major portion of chemoautotrophic bacteria in sulfidic waters of pelagic redoxclines of the Baltic and Black Seas. Appl Environ Microbiol 74: 7546-7551.
25. Grote J, Schott T, Bruckner CG, Glöckner FO, Jost G, Teeling H, Labrenz M & Jürgens K (2012) Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. P Natl Acad Sci USA 109: 506-510.
26. Heltshe J & Forrester NE (1983) Estimating species richness using the jackknife procedure. Biometrics 39: 1-11.
27. Hewson I & Fuhrman JA (2006) Improved strategy for comparing microbial assemblage fingerprints. Microb Ecol 51: 147-153.
28. Huber JA, Butterfield DA & Baross JA (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microbiol 68: 1585-1594.
29. Huber JA, Butterfield DA & Baross JA (2003) Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol 43: 393-409.
30. Huber JA, Butterfield DA & Baross JA (2006) Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean. J Geophys Res 111: G04016.
31. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA & Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
32. Johnson KS, Beehler CL, Sakamoto-Arnold CM & Childress JJ (1986) In situ measurements of chemical distributions in a deep-sea hydrothermal vent field. Science 231: 1139-1141.
33. Kadko DCC, Rosenberg NDD, Lupton JEE, Collier RWW & Lilley MDD (1990) Chemical reaction rates and entrainment within the Endeavour Ridge hydrothermal plume. Earth Planet Sci Lett 99: 315-335.
34. Karl DM & Tilbrook BD (1994) Production and transport of methane in oceanic particulate organic matter. Nature 368: 732-734.
35. Karl DM, Knauer GA, Martin JH & Ward BB (1984) Bacterial chemolithotrophy in the ocean is associated with sinking particles. Nature 309: 54-56.
36. Labrenz M, Jost G & Jurgens K (2007) Distribution of abundant prokaryotic organisms in the water column of the central Baltic Sea with an oxic-anoxic interface. Aquat Microb Ecol 46: 177-190.
37. Lam P, Cowen JP, Popp BN & Jones RD (2008) Microbial ammonia oxidation and enhanced nitrogen cycling in the Endeavour hydrothermal plume. Geochim Cosmochim Acta 72: 2268-2286.
38. Lavik G, Stührmann T, Brüchert V et al. (2008) Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457: 581-584.
39. Lin XJ, Scranton MI, Chistoserdov AY, Varela R & Taylor GT (2008) Spatiotemporal dynamics of bacterial populations in the anoxic Cariaco Basin. Limnol Oceanogr 53: 37-51.
40. Lloyd KG, Macgregor BJ & Teske A (2010) Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition. FEMS Microbiol Ecol 72: 143-151.
41. Ludwig W, Strunk R, Westram R et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
42. Lupton JE, Delaney JR, Johnson HP & Tivey MK (1985) Entrainment and vertical transport of deep-ocean water by buoyant hydrothermal plumes. Nature 316: 621-623.
43. McCollom TM (2000) Geochemical constraints on primary productivity in submarine hydrothermal vent plumes. Deep Sea Res Part 1 Oceanogr Res Pap 47: 85-101.
44. McCollom TM & Shock EL (1997) Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta 61: 4375-4391.
45. Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K & Sako Y (2005) Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 7: 1619-1632.
46. Newton ILG, Woyke T, Auchtung TA et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315: 998-1000.
47. Opatkiewicz AD, Butterfield DA & Baross JA (2009) Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities. FEMS Microbiol Ecol 70: 81-92.
48. Orcutt BN, Sylvan JB, Knab NJ & Edwards KJ (2011) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75: 361-422.
49. Osborne CA, Rees GN, Bernstein Y & Janssen PH (2006) New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72: 1270.
50. Polz MF & Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
51. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
52. Shanks AL & Reeder ML (1993) Reducing microzones and sulfide production in marine snow. Mar Ecol Prog Ser 96: 43-47.
53. Smith EP & van Belle G (1984) Nonparametric estimation of species richness. Biometrics 40: 119-129.
54. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM & Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". P Natl Acad Sci USA 103: 12115-12120.
55. Stackebrandt E & Liesack W (1993) Nucleic acids and classification. Handbook of New Bacterial Systematics (Goodfellow M & O'Donnell AG, eds), pp. 152-189. Academic Press, London, UK.
56. Sunamura M, Higashi Y, Miyako C, Ishibashi J-I & Maruyama A (2004) Two Bacteria phylotypes are predominant in the Suiyo Seamount hydrothermal plume. Appl Environ Microbiol 70: 1190-1198.
57. Swan BK, Martinez-Garcia M, Preston CM et al. (2011) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333: 1296-1300.
58. Sylvan JB, Pyenson BC, Rouxel O, German CR & Edwards KJ (2012) Time-series analysis of two hydrothermal plumes at 9°50′N East Pacific Rise reveals distinct, heterogeneous bacterial populations. Geobiology 10: 178-192.
59. Tamura K & Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
60. Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
61. Thompson JR, Marcelina LA & Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by "reconditioning PCR". Nucl Acids Res 30: 2083-2088.
62. Walsh DA & Hallam SJ (2011) Bacerial community structure and dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Handbook of Molecular Microbiology II: Metagenomics in Different Habitats (de Bruijn FJ, ed), pp. 253-267. John Wiley and Sons, Inc., Hoboken, NJ, USA.
63. Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD & Hallam SJ (2009) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326: 578.
64. Woebken D, Fuchs BM, Kuypers MMM & Amann R (2007) Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl Environ Microbiol 73: 4648-4657.
65. Zaikova E, Walsh DA, Stilwell CP, Mohn WW, Tortell PD & Hallam SJ (2010) Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ Microbiol 12: 172-191.