Marine Biology

, Volume 146, Issue 1, pp 133–142 | Cite as

Phylogenetic diversity of Archaea in prawn farm sediment

  • Peng Shao
  • Yueqin Chen
  • Hui Zhou
  • Lianghu Qu
  • Ying Ma
  • Heyang Li
  • Nianzhi Jiao
Research Article


The structure and diversity of the Archaea collected from prawn farm sediment were investigated for the first time. A partial 16S ribosomal DNA library was constructed with Archaea-specific primers. Subsequently, 80 randomly selected archaeal clones from the library were analyzed by restriction fragment length polymorphism (RFLP), and resulted in 50 different RFLP patterns. Sequence analysis of representatives from each unique RFLP type revealed high diversity in the archaeal populations, and the majority of archaeal clones were either members of novel lineages or most closely related to uncultured clones. In the phylogenetic analysis, the archaeal clones could be grouped into discrete phylogenetic lineages within the two kingdoms Crenarchaeota and Euryarchaeota. Euryarchaeota dominated in our archaeal library, with up to 72.2% of the total clones, and Crenarchaeota represented 27.8%. Of all the Euryarchaeota clones, three clones (5.6%) were affiliated with Methanosarcinales, four clones (7.4%) were related to Methanomicrobiales, three clones (5.6%) were related to Halobacterium (with 93% similarity), and the remaining clones (81.5%) were related to those uncultured Euryarchaeota in the aquatic sediment ecosystem. None of the crenarchaeal clones were associated with any known cultured lineages. The selective dispersal of the archaeal population indicates that their ecological niches are associated with environmental characteristics. Novel phylotypes of Archaea would expand our understanding of the genetic diversity of Archaea in aquatic sediment systems and would be significant in the phylogenetic study of Archaea.


Archaea Archaeal Community Restriction Fragment Length Polymorphism Pattern Pond Sediment Sediment Environment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was supported by NSFC projects (no. 40176037, 40232021) and the Red Tide Key Project of the National Natural Science Foundation of Guangdong province, China (no. 011208). The experiments comply with current laws of the country in which the experiments were performed.


  1. Amann RI, Krumholz L, Stahl DA (1990) Flurorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762–770PubMedGoogle Scholar
  2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedGoogle Scholar
  3. Arahal DA, Dewhirst FE, Paster B, Volcani BE, Ventosa A (1996) Phylogenetic analyses of some extremely halophilic Archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences. Appl Environ Microbiol 62:3779–3786PubMedGoogle Scholar
  4. Barns SM, Fundyga RE, Jeffries MW, Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609–1613PubMedGoogle Scholar
  5. Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophily from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188–9193CrossRefPubMedGoogle Scholar
  6. Benson DA, Boguski MS, Lipman DJ, Lipman DJ, Ostell J, Ouellette BFF (1998) GenBank. Nucleic Acids Res 26:1–7CrossRefPubMedGoogle Scholar
  7. Bowman JP, Rea SM, McCammon SA, McMeekin TA (2000) Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, eastern Antarctica. Environ Microbiol 2:227–237CrossRefPubMedGoogle Scholar
  8. Boyd CE (1990) Water quality in ponds for aquaculture. Alabama Agricultural Experimental Station, Aubum University, Ala., USAGoogle Scholar
  9. Boyd CE (1992) Shrimp pond bottom soil and sediment management. In: Wyban J (ed) Proceedings special session on shrimp farming. World Aquaculture Society, Baton Rouge, L.A., USA, pp 166–181Google Scholar
  10. Boyd CE, Massaut L (1999) Risks associated with the use of chemicals in pond aquaculture. Aquacult Eng 20:113–132CrossRefGoogle Scholar
  11. Chou CL, Haya K, Paon LA (2002) Aquaculture-related trace metals in sediments and lobsters and relevance to environmental monitoring program ratings for near-field effects. Mar Pollut Bull 44:1259–1268CrossRefPubMedGoogle Scholar
  12. Cifuentes A, Anton J, Benlloch S, Donnelly A, Herbert RA, Rodriguez-Valera F (2000) Prokaryotic diversity in Zostera noltii—colonized marine sediments. Appl Environ Microbiol 66:1715–1719CrossRefPubMedGoogle Scholar
  13. Cytryn E, Dror M, Oremland RS, Cohen Y (2000) Distribution and diversity of Archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai, Egypt). Appl Environ Microbiol 66:3269–3276CrossRefPubMedGoogle Scholar
  14. Delong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689Google Scholar
  15. Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877PubMedGoogle Scholar
  16. Fuhrman JA, Davis AA (1997) Widespread Archaea and novel Bacteria from the deep-sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser 150:275–285Google Scholar
  17. Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R (1997) Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63:2802–2813PubMedGoogle Scholar
  18. Grant S, Grant WD, Jones BE, Kato C, Li L (1999) Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 3:139–145CrossRefPubMedGoogle Scholar
  19. Gräslund S, Bengtsson BE (2001) Chemicals and biological products used in south-east Asian shrimp farming, and their potential impact on the environment—a review. Sci Total Environ 280:93–131CrossRefPubMedGoogle Scholar
  20. Han JB, Mu YL, Wang LM (1999) Advances in research of marine aquaculture and coastal water pollution. Fish Sci (Tokyo) 18:40–43Google Scholar
  21. Hershberger KL, Barns SM, Reysenbach AL, Downson SC, Pace NR (1996) Wide diversity of Crenarchaeota. Nature 345:60–63Google Scholar
  22. Hinrichs KU, Hayes JM, Sylva SP, Brewer PG, DeLong EF (1999) Methane-consuming Archaebacteria in marine sediments. Nature 398:802–805CrossRefPubMedGoogle Scholar
  23. Hopkins JS, Sandifer PA, Browdy CL (1994) Sludge management in intensive pond culture of shrimp: effects of management regime on water quality, sludge characteristics, nitrogen extinction, and shrimp production. Aquacult Eng 13:11–30CrossRefGoogle Scholar
  24. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67CrossRefPubMedGoogle Scholar
  25. Hugenholtz P, Goebel BM, Pace NR (1998a) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774PubMedGoogle Scholar
  26. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998a) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376PubMedGoogle Scholar
  27. Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54:305–315PubMedGoogle Scholar
  28. Lyimo TJ, Pol A, Op den Camp HJM, Harhangi HR, Vogels GD (2000) Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int J Syst Evol Microbiol 50:171–178PubMedGoogle Scholar
  29. Macgregor BJ, Moser DP, Alm EW, Nealson KH, Stahl DA (1997) Crenarchaeota in Lake Michigan sediment. Appl Environ Microbiol 63:1178–1181PubMedGoogle Scholar
  30. Maguire GB, Allen G (1986) Pilot scale studies into New South Wales prawn farming. Aust Fish 45:26–32Google Scholar
  31. Massana R, Murray AE, Preston CM (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol 63:50–56PubMedGoogle Scholar
  32. Mau B, Newton M (1997) Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J Comput Graph Stat 6:122–131Google Scholar
  33. Mau B, Newton M, Larget B (1999) Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1–12CrossRefPubMedGoogle Scholar
  34. McCaig AE, Glover A, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730PubMedGoogle Scholar
  35. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ (1995) Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 40:148–158Google Scholar
  36. Munson MA, Nedwell DB, Embley TM (1997) Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63:4729–4733PubMedGoogle Scholar
  37. Nedwell DB (1984) The input and mineralization of organic carbon in anaerobic aquatic sediments. Adv Microb Ecol 7:93–130Google Scholar
  38. Ni S, Boone DR (1991) Isolation and characterization of a dimethyl sulfide-degrading methanogen, Methanolobus siciliae HI350, from an oil well, characterization of M. siciliae T4/MT, and emendation of M. siciliae. Int J Syst Bacteriol 41:410–416PubMedGoogle Scholar
  39. Ni S, Woese CR, Aldrich HC, Boone DR (1994) Transfer of Methanolobus siciliae to the genus Methanosarcina, naming it Methanosarcina siciliae, and emendation of the genus Methanosarcina. Int J Syst Bacteriol 44:357–359Google Scholar
  40. Oremland RS, Marsh LM, Polcin S (1982) Methane production and simultaneous sulfate reduction in anoxic, salt marsh sediments. Nature 296:143–145Google Scholar
  41. Paez-Osuna F (2001) The environmental impact of shrimp aquaculture: a global perspective. Environ Pollut 112:229–231CrossRefPubMedGoogle Scholar
  42. Pillay TVR (1992) Aquaculture and the environment. Wiley, New YorkGoogle Scholar
  43. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818CrossRefPubMedGoogle Scholar
  44. Rannala B, Yang ZH (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311PubMedGoogle Scholar
  45. Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68:3759–3770CrossRefPubMedGoogle Scholar
  46. Rodríguez F, Oliver JF, Marín A, Medina JR (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142:485–501PubMedGoogle Scholar
  47. Sako Y, Nomura N, Uchida A, Ishida Y, Morii H, Koga Y, Hoaki T, Maruyama T (1996) Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100°C. Int J Syst Bacteriol 46:1070–1077PubMedGoogle Scholar
  48. Schleper C, Holben W, Klenk HS (1997) Recovery of crenarchaeal ribosomal DNA sequences from freshwater lake sediments. Appl Environ Microbiol 63:321–323PubMedGoogle Scholar
  49. Smith PT (1993) Prawn farming in Australia—sediment is a major issue. Aust Fish 52:29–32Google Scholar
  50. Swofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer, Sunderland, Mass., USAGoogle Scholar
  51. Takai K, Horikoshi K (1999) Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–1297PubMedGoogle Scholar
  52. Thompson JD, Gibson TJ, Plewniak F (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedGoogle Scholar
  53. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal rRNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12:219–287Google Scholar
  54. Vetriani C, Reysenbach AL, Doré J (1998) Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol Lett 161:83–88CrossRefPubMedGoogle Scholar
  55. Vetriani C, Jannasch HW, Macgregor BJ, Stahl DA, Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 65:4375–4384PubMedGoogle Scholar
  56. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Peng Shao
    • 1
  • Yueqin Chen
    • 1
  • Hui Zhou
    • 1
  • Lianghu Qu
    • 1
  • Ying Ma
    • 2
  • Heyang Li
    • 2
  • Nianzhi Jiao
    • 2
  1. 1.Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research CenterZhongshan UniversityGuangzhouP.R. China
  2. 2.Key Laboratory for Marine Environmental Science of the Ministry Education, Environmental Science Research CenterXiamen UniversityXiamenP.R. China

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