Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study

Abstract

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon‐degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil‐degrading consortia, we have established a series of identical oil‐degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil‐degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A. borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil‐degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations.

Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads

“…Most obvious is the separation of the early sampling points (days 0-10) in the upper right section of Fig. 2 from the bulk of the late sampling points (days [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28]. This trend coincides with the peaks of both emulsification (days 10-12 in both treatments) and protein production (days [12][13][14][15][16][17][18][19][20], which is strongly supported by the ANOSIM results presented in Supplementary Table 1c.…”

“…Sequencing was performed at Macrogen (Amsterdam, Netherlands) with primers F530 and R1492. The processing and assembly of DNA sequences as well as testing for chimeric sequences was conducted using BioEdit as described before [2,16]. Sequence alignment was performed against a database of validly published reference DNA sequences of typed strains using ClustalW [30].…”

“…Sequence alignment was performed against a database of validly published reference DNA sequences of typed strains using ClustalW [30]. The sequences were clustered by maximum parsimony according to the recommendation of the MODELTEST software [45] and phylogenetic tree was constructed using MEGA 4.0 as previously described [16]. DNA sequences of Halomonas isolates were submitted to the European Nucleotide Archive (ENA) under the accession numbers HG803097 to HG803140.…”

“…To generate high DNA yields required for sequencing analysis, a series of up-scaled microcosms was set up (microcosms [13][14][15][16][17][18][19][20]. One-litre Erlenmeyer flasks were filled with 150 g of sand (Sigma-Aldrich, St. Louis, USA), sterilized and spiked with 10 mL of sterile filtered Arabian light crude oil.…”

Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

“…Studies performed after the marine BP Deepwater Horizon oil spill in 2010 in the Gulf of Mexico in the United States showed that the oil leak resulted in the enrichment of bacteria belonging to the Oceanospirillales order and Colwellia and Cycloclasticus genera (5)(6)(7). In addition, members of the Oceanospirillales were detected as the major constituents of the bacterial community in different studies on oil-polluted marine ecosystems (8,9). However, microbial succession in petroleum-contaminated environments depends on the hydrocarbon fractions available to the microbial community, as suggested previously by McKew et al (10).…”