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).
Similar content being viewed by others
References
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
Thamdrup B, Hansen JW, Jørgensen B B. Temperature dependence of aerobic respiration in a coastal sediment. FEMS Microbiol Ecol, 1998, 25: 189–200
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
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
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
Glud R N, Middelboe M. Virus and bacteria dynamics of coastal sediment: Implication for benthic carbon cycling. Limnol Oceanogr, 2004, 49: 2073–2081
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
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 Volcano Mar Geol, 2007, 243(1–4): 1–17
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
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
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
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
Marsh T L. Terminal restriction fragment length polymorphism (TRFLP): An emerging method for characterizing diversity among homologous populations of implication products. Curr Opin Microbiol, 1999, 2(3): 323–327
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
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
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
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
Bray J R, Curtis J T. An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr, 1957, 27(2): 325–349
Schiffman S S, Reynolds M L. Introduction to multidimensional scaling. Theory, Methods and Applications. London: Academic Press, 1981
Hope A C A. A simplified Monte Carlo significance test procedure. J Roy Stat Soc B, 1968, 30(3): 580–598
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
Clarke K R, Warwick R M. Change in marine communities: An approach to statistical analysis and interpretation. Plymouth: Primer-E, 2001
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
Edlund A, Soule T, Sjoling S, Jansson, J K. Microbial community structure in polluted Baltic Sea sediments. Environ Microbiol, 2006, 8(2): 223–232
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 analysis. Appl Environ Microbiol., 2000, 66(7): 2943–2950
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
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wang, H., Jiang, X., He, Y. et al. Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis. Front. Environ. Sci. Eng. China 3, 194–199 (2009). https://doi.org/10.1007/s11783-009-0018-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11783-009-0018-3