In Situ Aerobic Bioremediation of Sediments Polluted with Petroleum Hydrocarbons: A Critical Review

Oil pollution has been a worldwide concern especially in environments where treatment is quite difficult to apply. Marine polluted sediments, in particular, constitute one of the most recalcitrant environments for bioremediation and are often the final repository of petroleum contaminants, as a result of runoff and deposition. Aerobic hydrocarbon degraders present in the sediments are tackling the pollution under oxygen-limited or oxygen-depleted conditions. Research has focused on new ways to enhance bioremediation under anoxic conditions, however aerobic bioremediation is faster, and hence more effort should be made to sustain oxygen concentration levels. In this review, the different bioremediation techniques used for the decontamination of marine sediments are briefly discussed, and focus is primarily given to the different oxygenation methods used for enhancing aerobic bioremediation and the aeration methods that are suitable for in situ application, as well as state of the art technologies that make in situ aeration an appealing approach. Based on the technologies analyzed, suggestions are made for sediment bioremediation techniques in different marine environments.

Biodegradation of Escravos light crude oil by three indigenous bacteria, isolated from mechanic workshop in Lagos State Nigeria

Introduction: Petroleum hydrocarbons can be degraded by microorganisms such as bacteria, fungi, yeast and microalgae. However, bacteria play an imperative role in hydrocarbon degradation. Microorganisms are endowed with metabolism machinery to use petroleum products as a carbon and energy source Aims: The aim of the study is to isolate hydrocarbon degrading bacteria from hydrocarbon polluted site (mechanic workshops) in Lagos state. Materials and Methods: The physical, chemical and microbiological properties of the three soil sample were analyzed using standard procedure. Hydrocarbon degraders were isolated on 1% crude oil mineral salt medium via enrichment technique. The best hydrocarbon degrader were identified on the basis of their colonial morphology, biochemical characteristics and complemented with analytical profile index (API) kit. Hydrocarbon degradation were monitored using total viable count and residual oil was determined by Gas Chromatography equipped with Flame Ionized detector (GC-FID). Results: Alkaline pH were observed for all three soil samples, the total nitrogen detected were 0.07, 0.04 and 0.1. The total heterotrophic bacteria (THB) estimated were 3 x 1010, 6.5 x 109 and 1.7 x 1010 cfu/ml while the total hydrocarbon utilizing bacteria estimated via vapour phase were 1.89 x 106 , 4x104 and 9.62 x 107 cfu/ml for Ikeja, Iyana-Iba and Mushin sample. The organisms had a generation time of 5.56, 9.09 and 10.9 (d), the degradation half-life were 3.85, 6.3 and 7.5 (d) respectively. Over 60% hydrocarbon degradation were determined within 10 days for all three isolates. The Gc-fid prints shows reduction in peak area of various hydrocarbon fractions with a decrease in pH of the medium. Conclusion: The study showed that hydrocarbon degraders are ubiquitously distributed in the hydrocarbon polluted soil sample. Their degradation potential can be optimized so as curtail the adverse effect of petroleum in the environment

Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition

Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.

Effect of polymer type on the colonization of plastic pellets by marine bacteria

Plastic is omnipresent in the oceans and serves as a surface for biofilm-forming microorganisms. Plastic debris comprises different polymers, which may influence microbial colonization; here, we evaluated whether polymer type affects bacterial biofilm formation. Quantifying the biofilm on polyethylene (PE), polypropylene (PP) or polystyrene (PS) pellets by six marine bacterial strains (Vibrio,Pseudoalteromonas,Phaeobacter) demonstrated that each strain had a unique colonization behavior with either a preference for PS or PP over the other polymer types or no preference for a specific plastic type. PE, PP and PS pellets were exposed to natural seawater microbiota using free-living or total communities as inoculum. Microbial assembly as determined by 16S rRNA (V4) amplicon sequencing was affected by the composition of the initial inoculum and also by the plastic type. Known polymer and hydrocarbon degraders such as Paraglaciecola, Oleibacter and Hydrogenophaga were found in the plastic biofilms. Thus, on a community level, bacterial colonization on plastic is influenced by the microorganisms as well as the polymer type, and also individual strains can demonstrate polymer-specific colonization.

Revealing of Non-Cultivable Bacteria Associated with the Mycelium of Fungi in the Kerosene-Degrading Community Isolated from the Contaminated Jet Fuel

Fuel (especially kerosene) biodamage is a challenge for global industry. In aviation, where kerosene is a widely used type of fuel, its biodeterioration leads to significant damage. Six isolates of micromycetes from the TS-1 aviation kerosene samples were obtained. Their ability to grow on the fuel was studied, and the difference between biodegradation ability was shown. Micromycetes belonged to the Talaromyces, Penicillium, and Aspergillus genera. It was impossible to obtain bacterial isolates associated with their mycelium. However, 16S rRNA metabarcoding and microscopic observations revealed the presence of bacteria in the micromycete isolates. It seems to be that kerosene-degrading fungi were associated with uncultured bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were abundant in the fungal cultures isolated from the TS-1 jet fuel samples. Most genera among these phyla are known as hydrocarbon degraders. Only bacteria-containing micromycete isolates were able to grow on the kerosene. Most likely, kerosene degradation mechanisms are based on synergism of bacteria and fungi.

Marine Sediments Harbor Diverse Archaea and Bacteria With Potentials for Anaerobic Hydrocarbon Degradation via Fumarate Addition

Background: Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. Previous gene- and genome-based surveys have detected ubiquitous and novel fumarate-adding enzymes (FAE), but these were neither confirmed as occurring within full degradation pathways nor affiliated with known organisms. The identity and ecological roles of a significant fraction of anaerobic hydrocarbon degraders in marine sediments therefore remains unknown.Results: By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available and newly sequenced metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Deltaproteobacteria that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. The biogeography survey reveals these bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems.Conclusions: Our results expand the knowledge of novel microbial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons, and shed new light on the importance of marine sedimentary archaea in hydrocarbon degradation.

Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes

The invasion of aquifer microbial communities by aboveground microorganisms, a phenomenon known as community coalescence, is likely to be exacerbated in groundwaters fed by stormwater infiltration systems (SISs). Here, the incidence of this increased connectivity with upslope soils and impermeabilized surfaces was assessed through a meta-analysis of 16S rRNA gene libraries. Specifically, DNA sequences encoding 16S rRNA V5-V6 regions from free-living and attached aquifer bacteria (i.e., water and biofilm samples) were analysed upstream and downstream of a SIS and compared with those from bacterial communities from watershed runoffs and surface sediments from the SIS detention and infiltration basins. Significant bacterial transfers were inferred by the SourceTracker Bayesian approach, with 23 % to 57 % of the aquifer bacterial biofilms being composed of taxa from aboveground sediments and urban runoffs. Sediments from the detention basin were found more significant contributors of taxa involved in the buildup of these biofilms than soils from the infiltration basin. Inferred taxa among the coalesced biofilm community were predicted to be high in hydrocarbon degraders such as Sphingobium and Nocardia. The 16S rRNA-based bacterial community structure of the downstream-SIS aquifer waters showed lower coalescence with aboveground taxa (8 % to 38 %) than those of biofilms and higher numbers of taxa predicted to be involved in the N and S cycles. A DNA marker named tpm enabled the tracking of bacterial species from 24 genera including Pseudomonas, Aeromonas and Xanthomonas, among these communities. Several tpm sequence types were found to be shared between the aboveground and aquifer samples. Reads related to Pseudomonas were allocated to 50 species, of which 16 were found in the aquifer samples. Several of these aquifer species were found to be involved in denitrification but also hydrocarbon degradation (P. aeruginosa, P. putida and P. fluorescens). Some tpm sequence types allocated to P. umsongensis and P. chengduensis were found to be enriched among the tpm-harbouring bacteria, respectively, of the aquifer biofilms and waters. Reads related to Aeromonas were allocated to 11 species, but only those from A. caviae were recovered aboveground and in the aquifer samples. Some tpm sequence types of the X. axonopodis phytopathogen were recorded in higher proportions among the tpm-harbouring bacteria of the aquifer waters than in the aboveground samples. A significant coalescence of microbial communities from an urban watershed with those of an aquifer was thus observed, and recent aquifer biofilms were found to be significantly colonized by runoff-opportunistic taxa able to use urban C sources from aboveground compartments.

Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders

ABSTRACT Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.