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

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.

Optimality of extracellular enzyme production and activity in dynamic flux balance modeling

In microbial communities, many vital metabolic functions, including the degradation of cellulose, proteins and other complex macromolecules, are carried out by costly, extracellularly secreted enzymes. While significant effort has been dedicated to analyzing genome-scale metabolic networks for individual microbes and communities, little is known about the interplay between global allocation of metabolic resources in the cell and extracellular enzyme secretion and activity. Here we introduce a method for modeling the secretion and catalytic functions of extracellular enzymes using dynamic flux balance analysis. This new addition, implemented within COMETS (Computation Of Microbial Ecosystems in Time and Space), simulates the costly production and secretion of enzymes and their diffusion and activity throughout the environment, independent of the producing organism. After tuning our model based on data for a Saccharomyces cerevisiae strain engineered to produce exogenous cellulases, we explored the dynamics of the system at different cellulose concentrations and enzyme production rates. We found that there are distinct rates of constitutive enzyme secretion which maximize either growth rate or biomass yield. These optimal rates are strongly dependent on enzyme kinetic properties and environmental conditions, including the amount of cellulose substrate available. Our framework will facilitate the development of more realistic simulations of microbial community dynamics within environments rich in complex macromolecules, with applications in the study of soil and plant-associated ecosystems, and other natural and engineered microbiomes.

Structure-Based Long-Term Biodegradation of the Azo Dye: Insights from the Bacterial Community Succession and Efficiency Comparison

In this study, microbial community dynamics were explored during biological degradation of azo dyes with different chemical structures. The effect of the different molecular structures of the azo dyes was also assessed against the simultaneous removal of color and the bacterial community. Winogradsky columns were inoculated with dewatered sludge and separately fed with six different azo dyes to conduct the sludge acclimatization process, and nine bacterial decolorizing strains were isolated and identified. The decolorization and biodegradation performances of the acclimated system and isolated strains were also determined. Results showed that the bacterial isolates involved in decolorization and the degradation of the azo dyes were mainly associated with the azo dye structure. After 24 h acclimatization at room temperature without specific illumination, immediate decolorization of methyl red (89%) and methyl orange (78%) was observed, due to their simple structure compared to tartrazine (73%). However, after 8 days of acclimatization, methyl red was easily decolorized up to 99%, and about 87% decolorization was observed for orange G (87%), due to its complex chemical structure. Higher degrees of degradation and decolorization were achieved with Pseudomonas geniculate strain Ka38 (Proteobacteria), Bacillus cereus strain 1FFF (Firmicutes) and Klebsiella variicola strain RVEV3 (Proteobacteria) with continuous shaking at 30 °C. The azo dyes with benzene rings were found to be easier to decolorize and degrade with similar microbial communities. Moreover, it seems that the chemical structures of the azo dyes, in a sense, drove the divergent succession of the bacterial community while reducing the diversity. This study gives a deep insight into the feasible structure-based artificial manipulation of bacterial communities and offers theoretical guidance for decolorizing azo dyes with mixed bacteria cultures.