Protocols for Mudflat and Algal Mat In Situ Analysis

Abstract

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.