Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

Abstract

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

“…Proteobacteria, a phylum highly dependent on the abundance of primary producers such as algae in cold seawater [25] and sea ice [25,48,49] was dominant in all three metagenomes. In Ofotfjorden seawater, Alphaproteobacteria was the most dominant Proteobacterial class, in contrast with reports on Canadian Arctic seawater [25] and Svalbard seawater [36] where Gammaproteobacteria dominated in the prokaryotic community. This difference might be caused by the seasonal dynamics of seawater microbial communities [20], as the Ofotfjorden samples were collected in autumn (October-November), as opposed to spring (April-May) in the referred studies.…”

“…The most abundant gene in all metagenomes was the alkane degradation-related rubredoxin NAD + reductase encoding rubB, which was also found from all good-quality MAGs; however, its abundance was considerably higher (7-10%) in SIO compared to the SW metagenome and, in particular, the SI metagenome, coinciding with previous findings by Ribicic et al, 2018 [20]. Similar to this study, all these abundant genes were also detected from all MAGs recovered from the metagenomes of seawater close to Svalbard [36]. Moreover, the analyzed genes encoding electron transport subunits and ferredoxin reductases yielded substantially higher counts than the genes encoding structural subunits of enzymes.…”

“…The composition and structure of the bacterial and archaeal community were classified down to the species level with Kaiju [35] (v. 1.7.3; database: NCBI-nr-30.01.2020). To evaluate the proportion of oil hydrocarbon-degrading organisms (HDO) among prokaryotic genera in the studied metagenomes, the list of genera containing HDOs previously shown to be involved in oil hydrocarbon degradation [36] was updated (Table S2; n = 369) and used as a reference. MEGAHIT [37] (v. 1.2.9) was used to assemble quality-controlled reads into contigs (minimum length of 1000 bp).…”

“…In oil-contaminated sea ice, crude oil might provide the microorganisms that are able to use its components as an additional energy and carbon source with a competitive advantage over the other members of the community [64,65]. Moreover, some genera, such as Paraglaciecola and Shewanella, with known versatile potential for oil hydrocarbon degradation [36,66], emerged among the dominant HDO-containing genera only in the SIO metagenome. All three MAGs derived from the SIO metagenome were affiliated with taxa containing HDOs (Bermanella, Glaciecola, and Rhodobacteraceae) [67,68].…”

“…It has also been shown that interactions between the oil and the sea ice alters the oil's physical and thermodynamic properties and the availability of different oil compounds in the brine [73]. The abundance of the microbial community under nutrient-deficient conditions and the low availability of oil hydrocarbons, accompanied by possible hyperoxia conditions, may remain too low for notable oil biodegradation in sea ice [36,69]. However, oil-degrading bacteria from ice may contribute to the microbial community of seawater and to oil biodegradation once the ice melts [28].…”