Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)

ISME Journal

Volumn 9, Issue 6, 2015, Pages 1306-1318

  Ristova, Petra Pop ^a,b,c   Wenzhöfer, Frank ^a,b,c   Ramette, Alban ^a,b   Felden, Janine ^a,b,c   Boetius, Antje ^a,b,c  

^a ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c UNIVERSITY OF BREMEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANOXIC CONDITIONS; BACTERIUM; COLD SEEP; DEEP-SEA BENTHOS; DEEP-SEA SEDIMENT; MARINE ECOSYSTEM; MICROBIAL COMMUNITY; POREWATER; SEAFLOOR; SPATIAL ANALYSIS;

MEDITERRANEAN SEA; MEDITERRANEAN SEA (EAST);

BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; OTUS;

HYDROCARBON; METHANE; RNA 16S; SEA WATER; SPACER DNA;

BIODIVERSITY; CHEMISTRY; CLASSIFICATION; DELTAPROTEOBACTERIA; ECOSYSTEM; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; GENETICS; MEDITERRANEAN SEA; METABOLISM; MICROBIOLOGY; RIBOSOME; SEDIMENT;

BIODIVERSITY; DELTAPROTEOBACTERIA; DNA, INTERGENIC; ECOSYSTEM; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; GEOLOGIC SEDIMENTS; HYDROCARBONS; MEDITERRANEAN SEA; METHANE; RIBOSOMES; RNA, RIBOSOMAL, 16S; SEAWATER; WATER MICROBIOLOGY;

EID: 84929656645     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2014.217     Document Type: Article

References (75)

1. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, Freestone AL et al. (2011). Navigating the multiple meanings of beta-diversity: a roadmap for the practicing ecologist. Ecol Lett 14: 19-28.
2. Barry JP, Kochevar RE, Baxter CH. (1997). The influence of pore-water chemistry and physiology on the distribution of vesicomyid clams at cold seeps in Monterey Bay: implications for patterns of chemosynthetic community organization. Limnol Oceanogr 42: 318-328.
3. Bienhold C, Boetius A, Ramette A. (2012). The energydiversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISME J 6: 1-9.
4. Bienhold C, Pop Ristova P, Wenzhöfer F, Dittmar T, Boetius A. (2013). How deep-sea wood falls sustain chemosynthetic life. PLoS One 8: e53590.
5. Boetius A, Lochte K. (1996). Effect of organic enrichments on hydrolytic potentials and growth of bacteria in deep-sea sediments. Mar Ecol Prog Ser 140: 239-250.
6. Boetius A, Wenzhöfer F. (2013). Seafloor oxygen consumption fuelled by methane from cold seeps. Nat Geosci 6: 725-734.
7. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A et al. (2004). Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70: 6147-6156.
8. Cordes EE, Cunha MR, Galéron J, Mora C, Olu-Le Roy K, Sibuet M et al. (2010). The influence of geological, geochemical, and biogenic habitat heterogeneity on seep biodiversity. Mar Ecol 31: 51-65.
9. Danovaro R, Company JB, Corinaldesi C, D'Onghia G, Galil B, Gambi C et al. (2010). Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS One 5: e11832.
10. Danovaro R, Gambi C, Dell'Anno A, Corinaldesi C, Fraschetti S, Vanreusel A et al. (2008). Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss. Curr Biol 18: 1-8.
11. de Beer D, Sauter E, Niemann H, Kaul N, Foucher J-P, Witte U et al. (2006). In situ fluxes and zonation of microbial activity in surface sediments of the Håkon Mosby Mud Volcano. Limnol Oceanogr 51: 1315-1331.
12. Dufrêne M, Legendre P. (1997). Species assemblages and indicator species: the need to a flexible asymmetrical approach. Ecol Monogr 67: 345-366.
13. Felden J, Lichtschlag A, Wenzhöfer F, de Beer D, Feseker T, Pop Ristova P et al. (2013). Limitations of microbial hydrocarbon degradation at the Amon mud volcano (Nile deep-sea fan). Biogeosciences 10: 3269-3283.
14. Felden J, Wenzhöfer F, Feseker T, Boetius A. (2010). Transport and consumption of oxygen and methane in different habitats of the Håkon Mosby Mud Volcano (HMMV). Limnol Oceanogr 55: 2366-2380.
15. Frontier S. (1985). Diversity and structure in aquatic ecosystems. Oceanogr Mar Biol 23: 253-312.
16. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL et al. (2008). A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci USA 105: 7774-7778.
17. Glud RN, Stahl H, Berg P, Wenzhöfer F, Oguri K, Kitazato H. (2009). In situ microscale variation in distribution and consumption of O2: A case study from a deep ocean margin sediment (Sagami Bay, Japan). Limnol Oceanogr 54: 1-12.
18. Goffredi SK, Orphan VJ. (2010). Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ Microbiol 12: 344-363.
19. Green J, Bohannan B. (2006). Spatial scaling of microbial biodiversity. Trends Ecol Evol 21: 501-507.
20. Grünke S, Felden J, Lichtschlag A, Girnth A, de Beer D, Wenzhöfer F et al. (2011). Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea). Geobiology 9: 330-348.
21. Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. (2012). Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10: 497-506.
22. He Y, Zhou BJ, Deng GH, Jiang XT, Zhang H, Zhou HW. (2013). Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons. BMC Microbiol 13: 1-8.
23. Heijs SK, Laverman AM, Forney LJ, Hardoim PR, van Elsas JD. (2008). Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol 64: 362-377.
24. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA et al. (2007). Microbial population structures in the deep marine biosphere. Science 318: 97-100.
25. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A et al. (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.
26. Jacob M, Soltwedel T, Boetius A, Ramette A. (2013). Biogeography of Deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic). PLoS One 8: e72779.
27. Jørgensen BB, Boetius A. (2007). Feast and famine - microbial life in the deep-sea bed. Nature 5: 770-781.
28. Kallmeyer J, Ferdelman TG, Weber A, Fossing H, Jørgensen BB. (2004). A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements. Limnol Oceanogr Methods 2: 171-180.
29. Knittel K, Boetius A. (2009). Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63: 311-334.
30. Knittel K, Boetius A, Lemke A, Eilers H, Lochte K, Pfannkuche O et al. (2003). Activity, distribution, and diversity of sulfate reducers and other Bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol J 20: 269-294.
31. Kormas KA, Smith DC, Edgcomb V, Teske A. (2003). Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45: 115-125.
32. Lawton JH. (1999). Are there general laws in ecology? Oikos 84: 177-192.
33. Levin LA. (2005). Ecology of cold seep sediment: interactions of fauna with flow, chemistry and microbes. Oceanogr Mar Biol Annu Rev 43: 1-46.
34. Levin LA, Mendoza GF, Gonzalez JP, Thurber AR, Cordes EE. (2010). Diversity of bathyal macrofauna on the northeastern Pacific margin: the influence of methane seeps and oxygen minimum zones. Mar Ecol 31: 94-110.
35. Levin LA, Sibuet M. (2012). Understanding continental margin biodiversity: a new imperative. Ann Rev Mar Sci 4: 79-112.
36. Levin LL, Ziebis W, Mendoza GF, Growney VA, Tryon MD, Brown KB et al. (2003). Spatial heterogeneity of macrofauna at northern California methane seeps: influence of sulfide concentration and fluid flow. Mar Ecol Prog Ser 265: 123-139.
37. Martiny JBH, Bohannan BJM, Brown J, Colwell R, Fuhrman J, Green J et al. (2006). Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-112.
38. Martiny JBH, Eisen JA, Penn K, Allison SD, Claire Horner-Devine M. (2011). Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci USA 108: 1-5.
39. Menot L, Galeron J, Olu K, Caprais J-C, Crassous P, Khripounoff A et al. (2010). Spatial heterogeneity of macrofaunal communities in and near a giant pockmark area in the deep Gulf of Guinea. Mar Ecol 31: 78-93.
40. Meyer S, Wegener G, Lloyd K, Teske A, Boetius A, Ramette A. (2013). Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin. Front Microbiol 4: 1-11.
41. Oksanen J, Blanchet FG, Roeland K, Legendre P, Minchin PR, O'Hara RB et al. (2011). vegan: Community Ecology Package. R package version 2.0-2. http://CRAN.R-project.org/package=vegan.
42. Olu K, Caprais JC, Galéron J, Causse R, von Cosel R, Budzinski H et al. (2009). Influence of seep emission on the non-symbiont-bearing fauna and vagrant species at an active giant pockmark in the Gulf of Guinea (Congo-Angola margin). Deep-Sea Res Pt II 56: 2380-2393.
43. Omoregie EO, Mastalerz V, de Lange G, Straub KL, Kappler A, Røy H et al. (2008). Biogeochemistry and community composition of iron- and sulfur-precipitating microbial mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean). Appl Environ Microbiol 74: 3198-3215.
44. Omoregie EO, Niemann H, Mastalerz V, de Lange G, Stadnitskaia A, Mascle J et al. (2009). Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea. Mar Geol 261: 114-127.
45. 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.
46. Orphan VJ, Hinrichs K, Ussler W III, Paull CK, Taylor LT, Sylva SP et al. (2001). comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67: 1922-1934.
47. Pachiadaki MG, Lykousis V, Stefanou EG, Kormas KA. (2010). Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol Ecol 72: 429-444.
48. Papke R, Ramsing NB, Bateson MM, Ward DM. (2003). Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5: 650-659.
49. Polymenakou PN, Bertilsson S, Tselepides A, Stephanou EG. (2005). Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16 S ribosomal DNA clone libraries. Microb Ecol 50: 447-462.
50. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P et al. (2007). Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16: 867-880.
51. Pop Ristova P, Wenzhöfer F, Ramette A, Zabel M, Fischer D, Kasten S et al. (2012). Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160m water depth). Biogeosciences 9: 5031-5048.
52. Pop Ristova P, Wenzhöfer F, Ramette A, Fleden J, Boetius A. (2014). Biogeochemical investigation of cold seep sediments in the Eastern Mediterranean Sea. doi:10.1594/PANGAEA.830241. http://wiki.pangaea.de/wiki/Citation.
53. Pradillon F, Schmidt A, Peplies J, Dubilier N. (2007). Species identification of marine invertebrate early stages by whole-larvae in situ hybridisation of 18S ribosomal RNA. Mar Ecol Prog Ser 333: 103-116.
54. Pradillon F, Zbinden M, Mullineaux LS, Gaill F. (2005). Colonisation of newly-opened habitat by a pioneer species, Alvinella pompejana (Polychaeta: Alvinellidae), at East Pacific Rise vent sites. Mar Ecol Prog Ser 302: 147-157.
55. Quaiser A, Zivanovic Y, Moreira D, López-García P. (2011). Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara. ISME J 5: 285-304.
56. Ramette A. (2007). Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62: 142-160.
57. Ramette A. (2009). Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol 75: 2495-2505.
58. Ramette A, Tiedje JM. (2007). Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci USA 104: 2761-2766.
59. Ramirez-Llodra E, Tyler Pa, Baker MC, Bergstad OA, Clark MR, Escobar E et al. (2011). Man and the last great wilderness: human impact on the deep sea. PLoS One 6: e22588.
60. Ritt B, Pierre C, Gauthier O, Wenzhöfer F, Boetius A, Sarrazin J. (2011). Diversity and distribution of cold-seep fauna associated with different geological and environmental settings at mud volcanoes and pockmarks of the Nile Deep-Sea Fan. Mar Biol 158: 1187-1210.
61. Roberts DW. (2013). labdsv: Ordination and Multivariate Analysis for Ecology. R package version 1.6-1. http://CRAN.R-project.org/package=labdsv.
62. Rosenzweig ML. (1995). Species Diversity in Space and Time. Cambridge University Press: Cambridge, UK.
63. Ruff SE, Arnds J, Knittel K, Amann R, Wegener G, Ramette A et al. (2013). Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand). PLoS One 8: e72627.
64. Sahling H, Rickert D, Lee RW, Linke P, Suess E. (2002). Macrofaunal community structure and sulfide flux at gas hydrate deposits from the Cascadia convergent margin, NE Pacific. Mar Ecol Prog Ser 231: 121-138.
65. Schauer R, Bienhold C, Ramette A, Harder J. (2010). Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4: 159-170.
66. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
67. Seeberg-Elverfeldt J, Schlüter M, Feseker T, Koelling M. (2005). Rhizon sampling of porewaters near the sediment-water interface of aquatic systems. Limnol Oceanogr Methods 3: 361-371.
68. Sibuet M, Olu K. (1998). Biogeography, biodiversity and fluid dependence of deep-sea cold-seep communities at active and passive margins. Deep-Sea Res Pt II 45: 517-567.
69. Treude T, Smith CR, Wenzhöfer F, Carney E, Bernardino AF, Hannides AK et al. (2009). Biogeochemistry of a deep-sea whale fall: sulfate reduction, sulfide efflux and methanogenesis. Mar Ecol Prog Ser 382: 1-21.
70. Tyler PA, Young CM. (1999). Reproduction and dispersal at vents and cold seeps. J Mar Biol Assoc UK 79: 193-208.
71. van Dover C, Smith C, Ardron J, Arnaud S, Beaudoin Y. (2011). Environmental management of deep-sea chemosynthetic ecosystems: justification of and considerations for a spatially-based approach. ISA Technical Study No. 9. International Seabed Authority, Kingston, Jamaica, 2011, 90pp. http://www.isa.org.jm/files/documents/EN/Pubs/TS9/index.html#/.
72. van Gaever S, Galéron J, Sibuet M, Vanreusel A. (2009). Deep-sea habitat heterogeneity influence on meiofaunal communities in the Gulf of Guinea. Deep-Sea Res Pt II 56: 2259-2269.
73. Whitaker RJ, Grogan DW, Taylor JW. (2003). Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
74. Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-DevineMC, Huse SM, Welch DBM et al. (2011). Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One 6: e24570.
75. Zinger L, Boetius A, Ramette A. (2014). Bacterial taxa-area and distance-decay relationships in marine environments. Mol Ecol 23: 954-964.