Stratification of archaeal communities in shallow sediments of the Pearl River Estuary, Southern China

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 99, Issue 4, 2011, Pages 739-751

  Jiang, Lijing ^a   Zheng, Yanping ^a   Chen, Jinquan ^b,c   Xiao, Xiang ^b,c   Wang, Fengping ^b,c  

^a Key Laboratory of Marine Genetic Resources of Fujian Province   (China)

^b Shanghai Jiao Tong University   (China)

^c Shanghai Jiao Tong University   (China)

Author keywords

Methyl coenzyme M reductase; Miscellaneous crenarchaeotal group; Pearl River estuarine sediments

Indexed keywords

BACTERIAL PROTEIN; PROTEIN MCRA; RNA 16S; UNCLASSIFIED DRUG;

ARTICLE; CHINA; CONTROLLED STUDY; GENE LIBRARY; METHANOMICROBIALES; METHANOTROPH; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL IDENTIFICATION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SEDIMENT; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

AQUATIC ORGANISMS; ARCHAEA; BIODIVERSITY; CHINA; DNA RESTRICTION ENZYMES; DNA, ARCHAEAL; GENETIC VARIATION; GEOLOGIC SEDIMENTS; METHANE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVERS; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

ARCHAEA; METHANOMICROBIALES;

EID: 79958220480     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-011-9548-3     Document Type: Article

References (56)

1. Alperin MJ, Reeburg WS, Whiticar MJ (1988) Carbon and hydrogen isotope fractionation resulting from anaerobic methane oxidation. Global Biogeochem Cycles 2:279-288
2. Bange HW, Bartell UH, Rapsomanikis S, Andreae MO (1994) Methane in the Baltic and North Seas and a reassessment of the marine emissions of methane. Global Biogeochem Cycles 8:465-480
3. Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sorensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP (2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846-3851 (Pubitemid 43376643)
4. Bottcher ME, Hespensheide B, Llobet-Brossa E, Bearsdley C, Larsen O, Schramm A, Wieland A, Böttcher G, Berninger UG, Amann R (2000) The biogeochemistry, stable isotope geochemistry, and microbial community structures of a temperate intertidal mudflat: an integrated study. Cont Shelf Res 20:1749-1769
5. Cai W, Dai M, Wang Y, Zhai W, Huang T, Chen S, Zhang F, Chen Z, Wang Z (2004) The biogeochemistry of inorganic carbon and nutrients in the Pearl River estuary and the adjacent Northern South China Sea. Cont Shelf Res 24:1301-1319 (Pubitemid 38893849)
6. Cicerone RJ, Oremland RS (1988) Biogeochemical aspects of atmospheric methane. Global Biogeochem Cycles 1:61-86
7. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689
8. Earl J, Hall G, Pickup RW, Ritchie DA, Edwards C (2003) Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences. Microb Ecol 46:270-278 (Pubitemid 37298779)
9. Erkel C, Kube M, Reinhardt R, Liesack W (2006) Genome of Rice Cluster I archaea-the key methane producers in the rice rhizosphere. Science 313:370-372
10. Friborg T, Christensen TR, Sogaard H (1997) Rapid response of greenhouse gas emission to early spring thaw in a subarctic mire as shown by micrometeorological techniques. Geophys Res Lett 24:3061-3064 (Pubitemid 127686536)
11. Granberg G, Mikkela C, Sundh I, Svensson BH, Nilsson M (1997) Sources of spatial variation in methane emission from mires in northern Sweden: a mechanistic approach in statistical modeling. Global Biogeochem Cycles 11:135-150
12. Hales BA, Edwards C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668-675 (Pubitemid 26047434)
13. Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:5483-5491 (Pubitemid 37150773)
14. Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457-1462 (Pubitemid 39167664)
15. Harrison BK, Zhang HS, Berelson W, Orpan VJ (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
16. Huang XP, Huang LM, Yue WZ (2003) The characteristics of nutrients and eutrophication in the Pearl River estuary, South China. Mar Pollut Bull 47:30-36 (Pubitemid 36627617)
17. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K et al (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Ohkotsk. Appl Environ Microbiol 69:7224-7235 (Pubitemid 38585373)
18. 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
19. Jiang LJ, Zheng YP, Peng XT, Zhou HY, Zhang CL, Xiao X, Wang FP (2009) Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol 70:249-262
20. Kasai Y, Takahata Y, Hoaki T, Watanabe K (2005) Physiological and molecular characterization of a microbial community established in unsaturated, petroleum-contaminated soil. Environ Microbiol 7:806-818 (Pubitemid 40697639)
21. Kim B-S, Oh H-M, Kang H, Chun J (2005) Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J Microbiol 43:144-151 (Pubitemid 40720616)
22. Knittel K, Losekann T, Boetius A, Kort R, Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71:467-479 (Pubitemid 40116303)
23. Koch M, Rudolph C, Moissl C, Huber R (2006) A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water. FEMS Microbiol Ecol 57:55-66 (Pubitemid 43876439)
24. Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an auto-trophic ammonia-oxidizing marine archaeon. Nature 437: 543-546 (Pubitemid 41613550)
25. Kormas KA, Meziti A, Dahlmann A, De Lange G, Lykousis V (2005) Molecular fingerprinting of methanogens in eastern Mediterranean Sea mud volcanoes. Geochim Cosmochim Acta 69:A77-a77
26. Krebs CJ (1989) Ecological methodology. Harper and Row, New York
27. Kruger M, Meyerdierks A, Glockner FO, Amann R, Widdel F, Kube M, Reinhardt R, Kahnt R, Bocher R, Thauer RK, Shima S (2003) A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426: 878-881 (Pubitemid 38056878)
28. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
29. Losekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl Environ Microbiol 73:3348-3362
30. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371 (Pubitemid 38854737)
31. Lueders T, Chin KJ, Conrad R, Friedrich M (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3:194-204 (Pubitemid 33136743)
32. Meyerdierks A, Kube M, Kostadinov I, Teeling H, Gloc̈kner FO, Reinhardt R, Amann R (2010) Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 12:422-439
33. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlanticand Pacific bacterioplankton communities. Limnol Oceanogr 40:148-158
34. Nauhaus K, Albrecht M, Elvert M, Boetius A, Widdel F (2007) In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol 9:187-196
35. Niemann H, Losekann T, de Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ, Schluter M, Klages M, Foucher JP, Boetius A (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443:854-858
36. Nunoura T, Oida H, Miyazaki J, Miyashita A, Imachi H, Takai K (2008) Quantification of mcrA by fluorescent PCR in methanogenic and anaerobic methanotrophic microbial communities. FEMS Microbiol Ecol 64:240-247 (Pubitemid 351533418)
37. Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484-487 (Pubitemid 32679074)
38. Parkes RJ, Cragg BA, Banning N, Brock F, Webster G, Fry JC, Hornibrook E, Pancost RD, Kelly S, Knab N (2007) Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerrak, Denmark). Environ Microbiol 9:1146-1161 (Pubitemid 46697271)
39. Poremba K, Tillmann U, Hesse KJ (1999) Tidal impact on planktonic primary and bacterial production in the German Wadden Sea. Helgoland Marine Res 53:19-27 (Pubitemid 129698621)
40. 4 emission from Coastal wetlands of South India. Environ Manage 27:547-557
41. Ramesh R, Purvaja R, Parashar DC, Gupta PK, Mitra AP (1997) Anthropogenic forcing on methane emission from the polluted wetlands (Adyar River) of Madras City, India. Ambio 26:369-374 (Pubitemid 27439786)
42. Reed D, Fujita Y, Delwiche M, Blackwelder D, Sheridan P, Uchida T (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68:3759-3770 (Pubitemid 34836683)
43. Shalini A, Ramesh R, Purvaja R, Barnes J (2006) Spatial and temporal distribution of methane in an extensive shallow estuary, south India. J Earth Syst Sci 115:451-460 (Pubitemid 44269879)
44. Sorensen KB, Teske A (2006) Stratified communities of active archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596-4603 (Pubitemid 44078783)
45. Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67:5750-5760 (Pubitemid 33641014)
46. Teske A, Sorensen K (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2:3-18
47. Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882 (Pubitemid 28022245)
48. Tian XP (1994) The distribution characteristics of temperature in the Lingdingyang, estuary of Zhujiang. Trop Oceanol 13:76-80 (in Chinese)
49. Treude T, Kruger M, Boetius A, Jørgensen BB (2005) Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic). Limnol Oceanogr 50:1771-1786 (Pubitemid 41692185)
50. Upstill-Goddard RC, Barnes J, Frost T, Punshon S, Owens NJP (2000) Methane in the southern North Sea: low-salinity inputs, estuarine removal, and atmospheric flux. Global Biogeochem Cycles 14:1205-1217 (Pubitemid 32281834)
51. Walsh DA, Papke RT, Doolittle WF (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environ Microbiol 7:1655-1666 (Pubitemid 41345907)
52. Wang P, Xiao X, Wang FP (2005) Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool. Extremophiles 9:209-217 (Pubitemid 40938363)
53. Yan B, Hong K, Yu ZN (2006) Archaeal communities in mangrove soil characterized by 16S rRNA gene clones. J Microbiol 44:566-571 (Pubitemid 46409817)
54. Ye GB, Wang SF, Jiang LJ, Xiao X, Wang FP, Noakes J, Zhang CL (2009) Distribution and diversity of bacteria and archaea in marine sediments affected by gas hydrates at Mississippi Canyon in the Gulf of Mexico. Geomicrobiol J 26:370-381
55. Zhang J, Yu ZG, Wang JT, Ren JL, Chen HT, Xiong H, Dong LX, Xu WY (1999) The subtropical Zhujiang (Pearl River) estuary: nutrient, trace species and their relationship to photosynthesis. Estuar Coast Shelf Sci 49:385-400 (Pubitemid 29475339)
56. Zhao H (1990) Evolution of the Pearl River Estuary. Ocean Press, Beijing, p 357 (in Chinese)