Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

Abstract

Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, HhaI and MspI, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from HhaI and MspI both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With HhaI as the sample, the pair wise T-tests also revealed that variations were minor between each pair of marine environments, with R ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites (R ranging from 0.282 to 0.349).

Keywords

terminal restriction fragment length polymorphism (T-RFLP) / bacterial community structure / marine microbial diversity / HhaI / MspI

References

[1] Pringault O, Duran R, Jacquet S, Torréton J P. Temporal variations of microbial activity and diversity in marine tropical sediments (New Caledonia Lagoon). Microbiol Ecol, 2008, 55: 247-258

[2] Thamdrup B, Hansen J W, Jørgensen B B. Temperature dependence of aerobic respiration in a coastal sediment. FEMS Microbiol Ecol, 1998, 25: 189-200

[3] Fischer H, Wanner S C, Pusch M. Bacterial abundance and production in river sediments as related to the biochemical composition of particulate organic matter (POM). Biogeochemistry, 2002, 61: 37-55

[4] Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M, Jacobs E, Roske I. Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol Ecol, 2003, 46: 331-347

[5] Hondeveld B J M, Bak R P M, van Raaphorst W, Van Duyl F C. Impact of grazing by benthic eukaryotic organisms on the nitrogen sediment—water exchange in the North Sea. J Sea Res, 1999, 41: 255-268

[6] Glud R N, Middelboe M. Virus and bacteria dynamics of coastal sediment: Implication for benthic carbon cycling. LimnolOceanogr, 2004, 49: 2073-2081

[7] Tanaka T, Zohary T, Krom M D, Law CS, Pitta P, Psarra S, Rassoulzadegan F, Thingstad F, Tselepides A, Woodward E M S, Flaten G A F, Skjoldal E F, Zodiatis G. Microbial community structure and function in the Levantine Basin of the eastern Mediterranean. Deep-Sea Res. I, 2007, 54(10): 1721-1743

[8] Jerosch K, Schlüter M, Foucher J P, Allais A G, Klages M, Edy C. Spatial distribution of mud flows, chemoautotrophic communities, and biogeochemical habitats at Håkon Mosby Mud VolcanoMar Geol, 2007, 243(1-4): 1-17

[9] Fogel G B, Collins C R, Li J, Brunk, C F. Prokaryotic genome size and SSU rDNA copy number: Estimation of microbial relative abundance from a mixed population. Microbiol Ecol, 1999, 38(1): 93-113

[10] Dunbar J, White S, Forney L J. Genetic diversity through the looking glass: Effect of enrichment bias. Appl Environ Microbiol, 1997, 63(4): 1326-1331

[11] Muyzer G, de Waal E C, Unitterlinden A G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl Environ Microbiol, 1993, 59(3): 695-700

[12] Wintzingerode F V, Göbel U B, Satackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev, 1997, 21(2): 213-229

[13] Marsh T L. Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of implication products. Curr Opin. Microbiol, 1999, 2(3): 323-327

[14] Kitts C L. Terminal restriction fragment patterns: A tool for comparing microbial communities and assessing community dynamics. Curr Iss Intest Microbiol, 2001, 2(1): 17-25

[15] Wilson B, Danilowicz B S, Meijer W G. The diversity of bacterial communities associated with atlantic cod Gadus morhua. Microbiol Ecol, 2008, 55: 425-434

[16] Massana R, Murray A E, Preston C M, de Long E F. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol, 1997, 63(1): 50-56

[17] Blackwood C B, Marsh T, Kim S H, Paul E A. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of Microbial communities. Appl Environ Microbiol., 2003, 69(2): 926-932

[18] Bray J R, Curtis J T. An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr, 1957, 27(2): 325-349

[19] Schiffman S S, Reynolds M L. Introduction to multidimensional scaling. Theory, Methods and Applications. London: Academic Press, 1981

[20] Hope A C A. A simplified Monte Carlo significance test procedure. J Roy Stat Soc B, 1968, 30(3): 580-598

[21] Wolsing M, Priemé A. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiol Ecol, 2004, 48(2): 261-271

[22] Clarke K R, Warwick R M. Change in marine communities: An approach to statistical analysis and interpretation. Plymouth: Primer-E, 2001

[23] Osborne C A, Rees G N, Bernstein Y, Janssen. P H. New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol, 2006, 72(2): 1270-1278

[24] Edlund A, Soule T, Sjoling S, Jansson. J K. Microbial community structure in polluted Baltic Sea sediments. Environ Microbiol, 2006, 8(2): 223-232

[25] Dunbar J, Ticknor L O, Kuske C R. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysisAppl Environ. Microbiol, 2000, 66(7): 2943-2950

[26] Urakawa H, Yoshida T, Nishimura M, Ohwada K. Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinine profiling.Environ Microbiol, 2000, 2(5): 542-554

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