The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats

https://doi.org/10.1016/j.marpolbul.2016.07.023Get rights and content

Highlights

  • Low seasonal variation was observed for chronically hydrocarbon-contaminated mats.

  • Hydrocarbon contents explained the differences in the microbial community structure.

  • Hydrocarbonoclastic bacteria are rare or transient in chronically polluted systems.

  • Obligate hydrocarbonoclastic bacteria should not be good indicators of chronic pollution.

Abstract

Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2 years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination.

Introduction

Microbial mats dominated by Cyanobacteria are considered to be the oldest structured ecosystem on Earth (Margulis et al., 1980). They are nearly auto-sufficient systems in terms of nutrient cycling, containing high taxonomic and metabolic diversity within few-millimeter scales (Bolhuis and Stal, 2011). Microbial populations within a mat are stratified by steep light, oxygen, sulfide, and pH gradients; in turn, their metabolisms participate in maintaining these gradients. Cyanobacteria play key roles within a photosynthetic mat. They are precursors of microbial mats, since they fix dinitrogen and carbon dioxide, supporting the community growth (Severin and Stal, 2010). Other functional groups in photosynthetic microbial mats are aerobic/anaerobic heterotrophs, fermenters, sulfide oxidizers, and methanogens (van Gemerden, 1993). The structure of the mats changes depending on season, as purple sulfur bacteria increase at the end of winter and spring and cyanobacteria at the end of summer and fall (Pinckney et al., 1996). Microbial mats can be found in a diverse range of environments around the world, including but not limited to hot springs (Coman et al., 2013, Roeselers et al., 2007), polar ponds (Vincent and Whitton, 2002), and hypersaline waters (Allen et al., 2009, Dillon et al., 2009, Schneider et al., 2013). They also have been observed in petroleum-contaminated areas (Barth, 2003, Paissé et al., 2008).

Previous studies on hydrocarbon-contaminated microbial mats showed a reduction of microbial diversity in the short term associated with the disappearance of certain groups of microorganisms and a strong selection for specialist hydrocarbon-degrading marine bacteria (i.e., Alcanivorax and Marinobacter) (Abed et al., 2007, Bordenave et al., 2007). Alcanivorax belong to the obligate hydrocarbonoclastic bacteria, which are known to feed exclusively on hydrocarbons (Yakimov et al., 2007). Other obligate hydrocarbonoclastic bacteria are Cycloclasticus spp., Oleiphilus spp., Oleispira spp., Thalassolituus spp., and some members of the genus Planomicrobium. Alcanivorax and related alkane degraders have been detected rapidly after an oil input (Head et al., 2006). Cycloclasticus spp., an aromatic hydrocarbon degrader, was shown to appear at later stages, when the alkanes have been degraded (Head et al., 2006). Microbial diversity in chronically or long-term hydrocarbon-polluted microbial mats is less documented. High diversity has been observed in chronically hydrocarbon-polluted microbial mats even though 16S rRNA gene sequences related to well-known hydrocarbon degraders (i.e., Alcanivorax and Cycloclasticus) were not (or rarely) detected (Paissé et al., 2008). Finally, microbial mats show a high resilience capacity after petroleum contamination (Bordenave et al., 2007), suggesting that the petroleum impact is only transient and that the mat structure and functioning are robust enough to recover.

The archaeal community has been tackled rarely in hydrocarbon-polluted environments. In oiled sediments, the Euryarchaeota dominated, with particular contributions of Methanococcoides, Methanosarcina, and Methanolobus sequences (Miralles et al., 2010). The Euryarchaeota have been also found to be dominant in an uncontaminated microbial mat developing on the Dutch barrier island Schiermonnikoog, mainly by the Methanobacteria and the Methanomicrobia (Bolhuis and Stal, 2011). As far as we know, the archaeal community never has been investigated in hydrocarbon-polluted microbial mats.

The goal of this study was to determine the impact of chronic hydrocarbon contamination on the biogeochemical functioning, structure, and activity of the prokaryotic community in natural microbial mats. In order to determine to which extent hydrocarbon contamination is able to drive the structure and activity of microbial mats, we compared a highly hydrocarbon-contaminated mat, whose in vitro hydrocarbon degradation capacity has been proven (Paissé et al., 2010), with a reference mat. The second mat is located in close proximity to the same lagoon and shows similar physical and chemical parameters but without a hydrocarbon contamination history. We performed an extensive biogeochemical characterization of both mats and deep phylogenetic and transcriptomic analyses using high-throughput sequencing of the bacterial and archaeal community 16S rRNA genes and transcripts. Hydrocarbonoclastic bacteria were specifically targeted, since previously they were poorly observed in the contaminated mat (Paissé et al., 2008). Because microbial mat functioning is influenced by seasonal variation, the analyses were performed in spring and autumn during 2 consecutive years in order to assess the seasonal variation of mat structure and activity and to determine the impact of hydrocarbon contamination.

Section snippets

Sampling sites and procedure

The Berre lagoon is located on the French coast of the Mediterranean Sea near Marseille. Microbial mat samples were collected from two sites within the lagoon at a distance of 4.9 km: a contaminated site located in a retention basin receiving hydrocarbon wastewaters from a petrochemical industry (EDB1) and a non-hydrocarbon-contaminated site located within the “Les salins du Lion” bird reserve (SL) considered as a reference. The EDB1 retention basin had been collecting hydrocarbon-charged waters

Biogeochemical description of the mats

Hydrocarbon contents at EDB1 were 4–7-fold higher for alkanes and 28–330-fold higher for PAHs than those at SL (Table S1). As such, Cr and Cu contents were also higher at EDB1, with concentrations above the low effect range (ERL) and above the medium effect range (ERM) for Pb, Zn, and Ni (USA Environmental Protection Agency guidelines defined by Long et al. (1995)). The Hg was very abundant at both sites, with concentrations over the ERM; SL showed Cd, Zn, and Ni concentrations above the ERL

Discussion

Most of the studies related to polluted environments mainly have focused on the capacity of biodegradation of contaminated sediments through the isolation of hydrocarbonoclastic bacteria or the detection of hydrocarbonoclastic bacteria or genes involved in biodegradation (Bordenave et al., 2008, Paissé et al., 2012, Todorova et al., 2014). Microcosm studies have demonstrated that hydrocarbon contamination induces an increase of hydrocarbonoclastic bacterial community abundance (Coulon et al.,

Conclusion

This comparative in situ study showed that chronic hydrocarbon contamination in natural conditions induces only minor perturbations in the biogeochemical functioning and the bacterial composition of microbial mats. Although the classical seasonal variation was observed in the reference mat (phototrophic community dominant in autumn and sulfur cycle-related bacteria and methanogens dominant in spring), the contaminated site showed a progressive increase of the cyanobacterial component and no

Author contributions

MG, RG and OP conceived the study, JA, OP, PB and MG collected samples, JA, OP, BD, OB and PB conducted lab work, JA, NB, EB, PS and CK analyzed data, and JA wrote the manuscript with contributions from MG, RG, OP, PB, CK and PS. All authors read and approved the final manuscript.

Acknowledgments

This work was supported by the French National Research Agency (ANR FUNHYMAT ANR11 BSV7 014 01). The authors received support with linguistic proofreading from a professional proofreading service.

References (73)

  • L. Pastor et al.

    Influence of the organic matter composition on benthic oxygen demand in the Rhône River prodelta (NW Mediterranean Sea)

    Cont. Shelf Res.

    (2011)
  • O. Pringault et al.

    Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat

    Chemosphere

    (2015)
  • N.H. Todorova et al.

    Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments

    Mar. Pollut. Bull.

    (2014)
  • H. van Gemerden

    Microbial mats: a joint venture

    Mar. Geol.

    (1993)
  • M.M. Yakimov et al.

    Obligate oil-degrading marine bacteria

    Current Opinion in Biotechnology, Energy Biotechnology/Environmental Biotechnology

    (2007)
  • R.M.M. Abed et al.

    Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds

    Appl. Environ. Microbiol.

    (2002)
  • R.M.M. Abed et al.

    Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland

    PLoS ONE

    (2014)
  • A. Acosta-González et al.

    Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after the prestige oil spill

    Environ. Microbiol.

    (2013)
  • M. Alexander

    Aging, bioavailability, and overestimation of risk from environmental pollutants

    Environ. Sci. Technol.

    (2000)
  • M.A. Allen et al.

    Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay

    Geobiology

    (2009)
  • P. Ardilly

    Les techniques de sondage

    (2006)
  • R.M. Atlas

    Microbial degradation of petroleum hydrocarbons: an environmental perspective

    Microbiol. Rev.

    (1981)
  • C. Barranguet et al.

    Factors controlling primary production and photosynthetic characteristics of intertidal microphytobenthos

    Mar. Ecol. Prog. Ser.

    (1998)
  • N. Beau-Monvoisin

    Déversement accidentel d'hydrocarbures, sur l'étang de Berre suite à un débordement des bassins d'orage de la Compagnie Pétrochimique de Berre (CPB). Brest : Cedre (Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux)

    (2009)
  • M. Benthien et al.

    Oil-contamination effects on a hypersaline microbial mat community (Camargue, France) as studied with microsensors and geochemical analysis

    Ophelia

    (2004)
  • G.F. Blanchard et al.

    Quantifying the short-term temperature effect on light-saturated photosynthesis of intertidal microphytobenthos

    Mar. Ecol. Prog. Ser.

    (1996)
  • H. Bolhuis et al.

    Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

    ISME J.

    (2011)
  • P.C. Bonin et al.

    Nitrogen budget in a microbial mat in the Camargue (southern France)

    Mar. Ecol. Prog. Ser.

    (2006)
  • S. Bordenave et al.

    Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat

    Appl. Environ. Microbiol.

    (2007)
  • S. Bordenave et al.

    Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels

    Environ. Microbiol.

    (2008)
  • J.D. Cline

    Spectrophotometric determination of hydrogen sulfide in natural waters

    Limnol. Oceanogr.

    (1969)
  • C. Coman et al.

    Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania

    Extremophiles

    (2013)
  • R. Core Team

    R: A Language and Environment for Statistical Computing

    (2015)
  • F. Coulon et al.

    Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters

    Environ. Microbiol.

    (2007)
  • J.G. Dillon et al.

    Spatial and temporal variability in a stratified hypersaline microbial mat community

    FEMS Microbiol. Ecol.

    (2009)
  • R.C. Edgar

    UPARSE: highly accurate OTU sequences from microbial amplicon reads

    Nat. Methods

    (2013)
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