Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats.

Mathilde Jeanbille,Jérôme Gury,Jean-Christophe Auguet,Jacek Tronczynski,Jean-François Ghiglione,Robert Duran,Hélène Agogué,Olfa Ben Saïd

doi:10.3389/fmicb.2016.01637

Abstract

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Highlights

Marine sediments cover more than two-thirds of the Earth’s surface
Particle size distribution, %total organic carbon (TOC), salinity, and temperature averages of the water column were significantly greater in the Mediterranean sites than in the Atlantic sites (Supplementary Figure S2)
polyaromatic hydrocarbons (PAHs) concentrations were strongly correlated to each other

Summary

INTRODUCTION

Marine sediments cover more than two-thirds of the Earth’s surface. Microorganisms play a central role in global biogeochemical cycling within these habitats (Nealson, 1997; Reed and Martiny, 2013), and in the biodegradation of undesirable compounds (Wiatrowski and Barkay, 2005; Fernández-Luqueño et al, 2010). The immense complexity of microbial communities have prevented the precise description of the species involved in these processes and how microbial communities respond to common contaminants such as polyaromatic hydrocarbons (PAHs; Nogales et al, 2011). These questions are relevant in the coastal ecosystems, which support numerous human activities exerting considerable anthropogenic pressures. We used 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from coastal sediment microbial communities sampled in chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea and the French Atlantic Ocean

MATERIALS AND METHODS

Molecular Methods and Sequence Processing

RESULTS AND DISCUSSION