18S rDNA Sequences from Microeukaryotes Reveal Oil Indicators in Mangrove Sediment

Abstract

BackgroundMicroeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group.Methodology/Principal FindingsWe evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment.Conclusions/SignificanceWe believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies.

Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex

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Genetic diversity patterns of microbial communities in a subtropical riverine ecosystem (Jiulong River, southeast China)

“…Recently, this method has become routinely used to study microbial ecology and diversity in a number of different aquatic ecosystems (Diez et al, 2001;Sakami, 2008;Wu et al, 2009). However, previous studies of microbial communities have largely focused on the analysis of prokaryotic 16S rRNA genes; in comparison studies using eukaryotic 18S rRNA genes are strikingly scarce (Santos et al, 2010). Further, DGGE has rarely been applied in lotic (running water) systems, and we have limited knowledge about the spatial patterns of microbial communities and the factors that influence them in lotic systems (Cody et al, 2000;Leff, 2002;Passy, 2007).…”

Cyanobacterial and microeukaryotic profiles of healthy, diseased, and dead Millepora alcicornis from the South Atlantic

“…To analyze the microeukaryotic community, the specific amplification of the gene encoding the 18S ribosome subunit in eukaryotes was performed using the primers Ek7F-GC and EK516R (Díez et al 2001, Moon-van der Staay et al 2001, Santos et al 2010. The amplification was performed in a solution contain ing 1× PCR buffer, 0.4 mM dNTPs, 2.5 mM MgCl 2 , 2.75 U recombinant Taq DNA polymerase (Fermentas), 400 µmol of each primer, 2 to 4 ng total DNA and sterile Milli-Q water to a final volume of 50 µl.…”