An integrated metagenomic and metabolite profiling study of hydrocarbon biodegradation and corrosion in navy ships

Naval vessels regularly mix fuel and seawater as ballast, a practice that might exacerbate fuel biodegradation and metal biocorrosion. To investigate, a metagenomic characterization and metabolite profiling of ballast from U.S. Navy vessels with residence times of 1-, ~20-, and 31 weeks was conducted and compared with the seawater used to fill the tanks. Aerobic Gammaproteobacteria differentially proliferated in the youngest ballast tank and aerobic-specific hydrocarbon degradation genes were quantitatively more important compared to seawater or the other ballast tanks. In contrast, the anaerobic Deltaproteobacteria dominated in the eldest ballast fluid with anaerobic-specific hydrocarbon activation genes being far more prominent. Gene activity was corroborated by detection of diagnostic metabolites and corrosion was evident by elevated levels of Fe, Mn, Ni and Cu in all ballast samples relative to seawater. The findings argue that marine microbial communities rapidly shift from aerobic to anaerobic hydrocarbonoclastic-dominated assemblages that accelerate fuel and infrastructure deterioration.

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

SYNERGISM BETWEEN RHIZOSPHERE BACTERIA ISOLATES FROM Scleria sp., Clidemia sp., AND Panicum sp. TO INCREASE THE EFFECTIVENESS OF MIXED CULTURES IN HYDROCARBON BIODEGRADATION

The purpose of this research is to obtain hydrocarbon degrading bacteria that work synergistically in a consortium. Consortium microorganisms is mixture of microbial populations in the form of communities that have mutualistic relationships and doesn’t inhibition the growth of other microbes. In this study, isolates were obtained from the rhizosphere of soil contaminated with petroleum. The isolates obtained were tested for synergism to determine the relationship between bacterial isolates. Synergism testing was carried out using the spread plate method on agar media. The results of this study showed that isolate number one showed antagonistic properties to other bacterial isolates by forming a clear zone around the disc paper. A total of eight bacterial isolates showed the greatest percentage of synergism, namely ≥ 80% so that the eight rhizosphere bacterial isolates could be used as materials for mixed culture.

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L−1 and a phosphate content of 0.02mg.L−1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria (“Candidatus Acetothermia”) with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.

Effect of Aerating Duration on Hydrocarbon Biodegradation in a Simulated Crude-Oil Polluted Aquatic Environment Undergoing Bioremediation

The aim of this research work was to determine the aerating duration that would be effective in enhancing hydrocarbon biodegradation rate during bioremediation of crude-oil polluted river. Sediment and river-water were placed in four glass troughs labeled CT (control), A, B, and C. The setups were polluted with crude-oil, and allowed undisturbed for 2 weeks. Subsequently, accessible crude-oil on the surface was removed; bacteria and nutrients were then added. Air was bubbled for 3 hours into setups A, B, and C, at daily, 3 days, and 7 days interval respectively. Aeration was not applied to setup CT. On day 1, 7, 14, and 21, hydrocarbon concentration was determined; populations of total heterotrophic bacteria (THB) and hydrocarbon-utilizing bacteria (HUB) were also determined. The time it will take for hydrocarbons in the setups to biodegraded “completely” was calculated using first-order reaction equation. The results obtained showed that 71.43, 86.39, 83.17, and 15.42 % hydrocarbon degradation were obtained in setup A, B, C, and CT respectively. The time it will take for hydrocarbons in the setups to biodegrade “completely” were 129, 89, 101, and 1079 days for A, B, C, and CT respectively. There was slight reduction in population of HUB in setup CT, fairly stable population in setup A, and increase in population of HUB in setups B and C. It is concluded that aerating crude-oil polluted aquatic environment for 3 hours at 3 days interval will be more effective in enhancing hydrocarbon biodegradation rate during bioremediation.

Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from −20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.

Biodegradation of diesel and crude oil by Labrador Sea cold adapted microbial communities

Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed by petroleum product. Metagenomic sequencing revealed Paraperlucidibaca and Cycloclasticus harbour previously unrecognized capabilities for alkane biodegradation. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter , Pseudomonas _ D and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH 4 Cl; 1.47 mM KH 2 PO 4 ) was effective at enhancing n -alkane and PAH degradation following low concentration (0.1% v/v) diesel and crude oil amendments, while at higher concentrations (1% v/v) only n -alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid turnover in the microbial community in response to petroleum amendments, more than doubling the rates of CO 2 increase during the first few weeks of incubation. Importance Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.