Protocols for Mudflat and Algal Mat In Situ Analysis

  • Robert DuranEmail author
  • Cristiana Cravo-Laureau
Part of the Springer Protocols Handbooks book series (SPH)


Coastlines are subjected to a variety of pollution injuries from both sides, from the sea, predominantly by crude oil from shipping and offshore mining, and from the land, principally through agricultural practices, urban wastewaters and industrial activities. Hydrocarbon compounds and crude oil-derived products are the most abundant contaminants. The damaging effects of such contaminants to the environment and human health coupled with new societal pressures make the restoration of hydrocarbon-contaminated areas an urgent priority. Although they are frequently found at unacceptably high concentrations, hydrocarbons are ubiquitous compounds, and the collective catabolic diversity of microorganisms means that most of them can be biodegraded resulting generally in harmless products, thus making bioremediation an attractive option. However, our understanding of the particular microbes involved, their genetic and enzymatic capacities, their interactions as well as their functioning in the changing redox conditions is still limited.

It is thus pivotal to explore the hydrocarbon degradation capacities of microbial communities inhabiting coastal sediments developing and applying a suite of integrated cross-disciplinary approaches in order to understand the ecology of sediment ecosystems, particularly to know how the microbial communities degrade and/or detoxify hydrocarbons and how they are affected by the redox oscillations and alternating oxygen supply. Mudflats and algal mats are characterised by high spatial and temporal heterogeneity that should be taken into consideration when studying the microbial communities inhabiting such ecosystems. We present here sampling protocols to collect and preserve properly sediments for conducting a set of analyses including chemistry, microscopy and molecular diversity in order to characterise microbial communities inhabiting mudflats and algal mats.


Coastal sediments Hydrocarbon degradation Intertidal areas Microbial diversity Molecular ecology Sampling protocols Spatial–temporal heterogeneity 



We acknowledge the support of the French programme ANR DECAPAGE (project ANR-CESA-2011-006 01). We would like to thank all partners of the DECAPAGE project and MELODY group for their useful discussions. We acknowledge the Regional Platform for Environmental Microbiology PREMICE supported by the Aquitaine Regional Government Council (France) and the urban community of Pau-Pyrénées (France).


  1. 1.
    Duran R, Goñi-Urriza MS (2010) Impact of pollution on microbial mats. In: Timmis KN, McGenity TJ, van der Meer JR, de Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2339–2348CrossRefGoogle Scholar
  2. 2.
    Venosa AD, Campo P, Suidan MT (2010) Biodegradability of lingering crude oil 19 years after the Exxon Valdez oil spill. Environ Sci Technol 44:7613–7621CrossRefPubMedGoogle Scholar
  3. 3.
    Underwood GJC, Paterson DM (2003) The importance of extracellular carbohydrate production by marine epipelic diatoms. Adv Bot Res 40:183–240CrossRefGoogle Scholar
  4. 4.
    Underwood GJC, Kromkamp J (1999) Primary production by phytoplankton and microphytobenthos in estuaries. Adv Ecol Res 29:93–153CrossRefGoogle Scholar
  5. 5.
    Abed RMM, Safi NMD, Koster J et al (2002) Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl Environ Microbiol 68:1674–1683CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Coulon F, McKew BA, Osborn AM et al (2007) Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters. Environ Microbiol 9:177–186CrossRefPubMedGoogle Scholar
  7. 7.
    McKew BA, Coulon F, Osborn AM et al (2007) Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Environ Microbiol 9:165–176CrossRefPubMedGoogle Scholar
  8. 8.
    Prince RC (2010) Bioremediation of marine oil spills. In: Timmis KN, McGenity TJ, van der Meer JR, de Lorenzo V (eds) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2617–2630Google Scholar
  9. 9.
    Païssé S, Coulon F, Goñi-Urriza M et al (2008) Structure of bacterial communities along a hydrocarbon contamination gradient in coastal sediment. FEMS Microbiol Ecol 66:295–305CrossRefPubMedGoogle Scholar
  10. 10.
    Stauffert M, Cravo-Laureau C, Jézéquel R et al (2013) Impact of oil on bacterial community structure in bioturbated sediments. PLoS One 8:e65347. doi: 10.1371/journal.pone.0065347 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Timmis KN et al (2010) Handbook of hydrocarbon and lipid microbiology. Springer-Verlag, Heidelberg. doi:10.1007/978-3-540-77587-4
  12. 12.
    McGenity TJ, Folwell BD, Mckew B et al (2012) Marine crude-oil biodegradation: a central role for interspecies interactions. Aquat Biosyst 8:10. doi: 10.1186/2046-9063-8-10 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    McGenity TJ (2014) Hydrocarbon biodegradation in intertidal wetland sediments. Curr Opin Biotechnol 27:46–54CrossRefPubMedGoogle Scholar
  14. 14.
    Cravo-Laureau C, Duran R (2014) Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era. Front Microbiol 5:39CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Fourçans A, García de Oteyza T, Wieland A et al (2004) Characterization of functional bacterial groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France). FEMS Microbiol Ecol 51:55–70CrossRefPubMedGoogle Scholar
  16. 16.
    Fourçans A, Solé A, Diestra E et al (2006) Vertical migration of phototrophic SRB Spatio-temporal Distribution in Camargue Microbial Mat bacterial populations in a hypersaline microbial mat from Salins-de-Giraud (Camargue, France). FEMS Microbiol Ecol 57:367–377CrossRefPubMedGoogle Scholar
  17. 17.
    Wieland A, Kuhl M, McGowan L et al (2003) Microbial mats on the Orkney islands revisited: microenvironment and microbial community composition. Microb Ecol 46:371–390CrossRefPubMedGoogle Scholar
  18. 18.
    Prosser JI (2010) Replicate or lie. Environ Microbiol 12:1806–1810CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Equipe Environnement et Microbiologie, MELODY GroupUniversité de Pau et des Pays de l’Adour, IPREM UMR CNRS 5254Pau CedexFrance

Personalised recommendations