Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea

Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx104 g-1 after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.

Bioaugmentation failed to enhance oil bioremediation in three soil samples from three different continents

Soil samples from Kuwait, Lebanon, Egypt and Germany were polluted with 3% crude oil. Series of samples were left unbioaugmented, others were bioaugmented with Kuwaiti desert soil with a long history of oil pollution and still others with Kuwaiti marine biofouling material. In the samples from Kuwait, Egypt, and Germany, bioaugmentation did not enhance oil removal, whereas it did in the sample from Lebanon. Taxa from the desert-soil bioaugmented batches, but none of those from the biofouling-material bioaugmented ones, succeeded in colonizing the four studied soils. The dynamics of the hydrocarbonoclastic communities during bioremediation were monitored. Those communities differed in composition, not only according to the type of soil, but also for the same soil; at various phases of bioremediation. Although each soil seemed to have its characteristic microflora, they all were similar in harboring lower and higher actinomycetes and pseudomonads in addition to many other taxa. None of the taxa prevailed through all phases of bioremediation. The most powerful isolate in oil-removal; was Rhodococcus erythropolis (Germany), and the weakest was Arthrobacter phenanthrenivorans (Lebanon). The pure hydrocarbonoclastic isolates tolerated unusually high oil concentrations, up to 30%.

Cross-Bioaugmentation Among Four Remote Soil Samples Contaminated With Oil Exerted Just Inconsistent Effects on Oil-Bioremediation

Soil samples were collected from Kuwait, Lebanon, Egypt, and Germany, and artificially polluted with 3% (w/w) crude oil. Cross-bioaugmentation was done among them, and the oil-consumption and the constituent communities of hydrocarbonoclastic bacteria were monitored periodically through 6 months. The results showed that cross-bioaugmentation did not bring about reproducible effects on oil-removal in the four soils. After 6 months, oil-removal values reached between 82 and 95% in most of the samples including the unbioaugmented controls. The numbers of hydrocarbonoclastic bacteria showed significant increases followed by significant decreases during the course of bioremediation also in the unbioaugmented controls. In most cases, the inoculated bacterial taxa failed to colonize the soils, and oil-removal was achieved mainly by the native (autochthonous) soil bacterial communities. those belonged to the genera Mycolicibacterium, Mycobacterium, Xanthobacter, Pseudoxanthomonas, Pseudomonas, Zavarzinia, and others. The microbial communities in the four soils also comprised nitrogen fixing bacteria belonging to the genera Gordonia, Rhizobium, Kocuria, and Azospirillum. Such diazotrophs are known to enrich the soils with fixed nitrogen and thus, contribute to enhancing the microbiological hydrocarbon-consumption. It was concluded that cross-bioaugmentation leads to unpredictable and inconsistent effects on oil removal. Therefore, it could not beregarded as the technology of choice for oil-bioremediation.

Ferric Sulfate and Proline Enhance Heavy-Metal Tolerance of Halophilic/Halotolerant Soil Microorganisms and Their Bioremediation Potential for Spilled-Oil Under Multiple Stresses

The aim of this study was to explore the heavy-metal resistance and hydrocarbonoclastic potential of microorganisms in a hypersaline soil. For this, hydrocarbonoclastic microorganisms were counted on a mineral medium with oil vapor as a sole carbon source in the presence of increasing concentrations of ZnSO₄, HgCl₂, CdSO₄, PbNO₃, CuSO₄, and Na₂HAsO_4. The colony-forming units counted decreased in number from about 150 g^-1 on the heavy-metal-free medium to zero units on media with 40-100 mg l^-1 of HgCl₂, CdSO₄, PbNO₃, or Na₂HAsO₄. On media with CuSO₄ or ZnSO₄ on the other hand, numbers increased first reaching maxima on media with 50 mg l^-1 CuSO₄ and 90 mg l^-1 ZnSO₄. Higher concentrations reduced the numbers, which however, still remained considerable. Pure microbial isolates in cultures tolerated 200-1600 mg l^-1 of HgCl₂, CdSO₄, PbNO₃, CuSO₄, and Na₂HAsO₄ in the absence of crude oil. In the presence of oil vapor, the isolates tolerated much lower concentrations of the heavy metals, only 10-80 mg l^-1. The addition of 10 Fe₂(SO₄)₃ and 200 mg l^-1 proline (by up to two- to threefold) enhanced the tolerance of several isolates to heavy metals, and consequently their potential for oil biodegradation in their presence. The results are useful in designing bioremediation technologies for oil spilled in hypersaline areas.

Gelatinizing oil in water and its removal via bacteria inhabiting the gels

When crude oil samples were shaken (200 rpm) in seawater samples from the Arabian Gulf at 30 °C, usually oil-gels were produced spontaneously leaving the water quite clear. The gelators could probably be based on cholesteryl derivatives. Microscopic examination of the established gels revealed nanofibrellar structures similar to those described by earlier workers for artificially synthesized gelators. Communities of bacteria including prosthetic and stalked members as well as oil-degrading bacteria were recorded in such gels. Chemical analysis revealed that 88.5% of the oil entrapped by gelation was biodegraded after 40 days at 30 °C. Individual bacterial species isolated from the oil-gels biodegraded in batch cultures between 17.8 and 33.3% of the oil added at time zero in 12 days at 30 °C. Gelation is a promising approach, not only for clean, physical removal of oil spilled in aquatic habitats, as so far suggested, but also in its effective microbiological biodegradation, as the current study revealed.

Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples

Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank. The plating method offered the advantages of capturing the targeted hydrocarbonoclastic microorganisms, counting them and providing cultures for further study. However, this technique could not capture more than a total of 15 different prokaryotic taxa. Those taxa belonged predominantly to the genera Alcanivorax, Pseudoxanthomonas, Bosea, Halomonas, and Marinobacter. The individual isolates in culture consumed between 19 and 50% of the available crude oil in 10 days. Although the culture-independent approach revealed much more microbial diversity, it was not problem-free. The subdivision primers exhibited satisfactory specificity, but they failed to capture all the available taxa. The universal bacterial primer pair ignored Actinobacteria altogether, although the primer pair specific for Actinobacteria captured many of them, for example, the genera Geodermatophilus, Streptomyces, Mycobacterium, Pontimonas, Rhodococcus, Blastococcus, Kocuria, and many others. Because most researchers worldwide use universal primers for PCR, this finding should be considered critically to avoid misleading interpretations.

Biostimulation of indigenous microorganisms for bioremediation of oily hypersaline microcosms from the Arabian Gulf Kuwaiti coasts

Hypersaline soil and water samples were collected in summer and winter from the "sabkha" area at the Kuwaiti shore of the Arabian Gulf. Physicochemical parameters were analyzed, and found suitable for microbial oil-removal. Summer- and winter-microcosms were treated with individual cation (K⁺, Ca²⁺, Mg²⁺, Fe³⁺) salts, and with animal blood and commercial yeast, as cost-effective vitamin sources. Those microcosms were exposed to the open environment for six winter and six summer months, and analyzed for their hydrocarbonoclastic microorganisms at time zero and in two month intervals. The hydrocarbonoclastic microbial communities in the microcosms consisted of halophilic bacteria and haloarchaea. The constituent bacterial species varied according to the season. Three species, Dietzia kunjamensis, Marinobacter lacisalsi and Halomonas oxialensis consistently occurred both in summer- and winter-samples, but the remaining species were different. On the other hand, the haloarchaeal communities in summer and winter were quite similar, and consisted mainly of Haloferax spp and Halobacterium spp. Treating the microcosms with cations and with vitamin-containing natural products enhanced microbial numbers and oil-removal. The effectiveness of the cations in oil-removal was in the order; Fe³⁺ (94%) > Ca²⁺ (89%) > Mg²⁺ (85%) > K⁺ (82%). Thus, oily microcosms amended with trivalent and divalent cations lost most of the oil, and those amended with commercial yeast and with animal blood, as vitamin sources, lost 78% and 72% oil, respectively.

Biofilms constructed for the removal of hydrocarbon pollutants from hypersaline liquids

Hydrocarbonoclastic biofilms were established on sterile glass plates vertically submerged for 1 month in a hypersaline soil/water suspension containing 0.3% crude oil. The culture-dependent analysis of the microbial community in those biofilms revealed hydrocarbonoclastic species in the magnitude of 10(3) cells cm(-2). Those species belonged to the halophilic bacterial genera Marinobacter, Halomonas, Dietzia, Bacillus, Arhodomonas, Aeromonas and Kocuria as well as to the haloarchaeal genera Haloferax and Halobacterium. Those organisms were not evenly distributed over the biofilm surface area. The culture-independent analysis revealed a different community composition, which was based on four uncultured and four cultured taxa. Depending on the culture conditions and the sort of chemical amendments, the biofilms succeeded in removing in 2 weeks up to about 60-70% of crude oil, pure n-hexadecane and pure phenanthrene in hypersaline pond water samples. The amendment with KCl, MgSO4 and a vitamin mixture composed of thiamin, pyridoxine, vitamin B12, biotin, riboflavin and folic acid was most effective.

Enhanced bioremediation of oil-polluted, hypersaline, coastal areas in Kuwait via vitamin-fertilization

There is no research published sofar on managements that could bioremediate hypersaline soils and water polluted with hydrocarbons. The objective of this study was to assess the effect of vitamin amendment on hydrocarbon removal by microorganisms indigenous to such hypersaline environments. We used in this study ten hydrocarbonoclastic bacterial species and five archaeal species that had been isolated by the conventional plating method on media containing oil as a sole carbon source, from a hypersaline (3-4 M NaCl) coastal area in Kuwait, and characterized by sequencing of their 16S rRNA coding genes. The oil and pure hydrocarbon consumption was measured by gas-liquid chromatography. The oil and pure hydrocarbon consumption potential of all microorganisms in media with hypersalinity was enhanced by vitamin fertilization. This was true for individual microorganisms in pure cultures as well as for microbial consortia in hypersaline soil and water samples used as inocula. Most effective vitamins were thiamin, pyridoxine and vitamin B12. Vitamin fertilization using vitamin rich wastes or byproducts could be an effective practice for enhancing bioremediation of oil contaminated hypersaline environments.

Oil-bioremediation potential of two hydrocarbonoclastic, diazotrophic Marinobacter strains from hypersaline areas along the Arabian Gulf coasts

Two halophilic, hydrocarbonoclastics bacteria, Marinobacter sedimentarum and M. flavimaris, with diazotrophic potential occured in hypersaline waters and soils in southern and northern coasts of Kuwait. Their numbers were in the magnitude of 10(3) colony forming units g(-1). The ambient salinity in the hypersaline environments was between 3.2 and 3.5 M NaCl. The partial 16S rRNA gene sequences of the two strains showed, respectively, 99 and 100% similarities to the sequences in the GenBank. The two strains failed to grow in the absence of NaCl, exhibited best growth and hydrocarbon biodegradation in the presence of 1 to 1.5 M NaCl, and still grew and maintained their hydrocarbonoclastic activity at salinities up to 5 M NaCl. Both species utilized Tween 80, a wide range of individual aliphatic hydrocarbons (C9-C40) and the aromatics benzene, biphenyl, phenanthrene, anthracene and naphthalene as sole sources of carbon and energy. Experimental evidence was provided for their nitrogen-fixation potential. The two halophilic Marinobacter strains successfully mineralized crude oil in nutrient media as well as in hypersaline soil and water microcosms without the use of any nitrogen fertilizers.

Phytoremediation of mercury in pristine and crude oil contaminated soils: Contributions of rhizobacteria and their host plants to mercury removal

The rhizospheric soils of three tested legume crops: broad beans (Vicia faba), beans (Phaseolus vulgaris) and pea (Pisum sativum), and two nonlegume crops: cucumber (Cucumis sativus) and tomato, (Lycopersicon esculentum) contained considerable numbers (the magnitude of 10(5)g(-1) soil) of bacteria with the combined potential for hydrocarbon-utilization and mercury-resistance. Sequencing of the 16S rRNA coding genes of rhizobacteria associated with broad beans revealed that they were affiliated to Citrobacter freundii, Enterobacter aerogenes, Exiquobacterium aurantiacum, Pseudomonas veronii, Micrococcus luteus, Brevibacillus brevis, Arthrobacter sp. and Flavobacterium psychrophilum. These rhizobacteria were also diazotrophic, i.e. capable of N(2) fixation, which makes them self-sufficient regarding their nitrogen nutrition and thus suitable remediation agents in nitrogen-poor soils, such as the oily desert soil. The crude oil attenuation potential of the individual rhizobacteria was inhibited by HgCl(2), but about 50% or more of this potential was still maintained in the presence of up to 40 mgl(-1) HgCl(2). Rhizobacteria-free plants removed amounts of mercury from the surrounding media almost equivalent to those removed by the rhizospheric bacterial consortia in the absence of the plants. It was concluded that both the collector plants and their rhizospheric bacterial consortia contributed equivalently to mercury removal from soil.

Oil phytoremediation potential of hypersaline coasts of the Arabian Gulf using rhizosphere technology

The rhizosphere and phyllosphere of the halophyte Halonemum strobilaceum naturally inhabiting hypersaline coastal areas of the Arabian Gulf harbor up to 8.1 x 10(4)g(-1) and 3 x 10(2)g(-1), respectively, of extremely halophilic oil-utilizing microorganisms. Such organisms were 14- to 38-fold more frequent in the rhizosphere than in the plant-free soil. Frequent genera in the rhizosphere were affiliated to the archaea Halobacterium sp. and Halococcus sp., the firmicute Brevibacillus borstenlensis, and the proteobacteria Pseudoalteromonas ruthenica and Halomonas sinaensis. The phyllospheric microflora consisted of the dimorphic yeast Candida utilis and the two proteobacteria Ochrobactrum sp. and Desulfovibrio sp. Individual strains grew on a range of pure aliphatic and aromatic hydrocarbons, as sole sources of carbon and energy. All the strains, except C. utilis which could not tolerate salinities >2M NaCl, grew also in media with salinities ranging between 1 and 4M NaCl, with optimum growth between 1 and 2M NaCl. With the exception of the two archaeal genera, all isolates could grow in a nitrogen-free medium. The total rhizospheric and phyllospheric microbial consortia could attenuate crude oil in complete (nitrogen-containing) medium, but also equally well in a nitrogen-free medium. It was concluded that H. strobilaceum could be a valuable halophyte for phytoremediation of oil-polluted hypersaline environments via rhizosphere technology.

The 2-oxoacid dehydrogenase multienzyme complex of Haloferax volcanii

Those aerobic archaea whose genomes have been sequenced possess four adjacent genes that, by sequence comparisons with bacteria and eukarya, appear to encode the component enzymes of a 2-oxoacid dehydrogenase multienzyme complex. However, no catalytic activity of any such complex has ever been detected in the archaea. In Thermoplasma acidophilum, evidence has been presented that the heterologously expressed recombinant enzyme possesses activity with the branched chain 2-oxoacids and, to a lesser extent, with pyruvate. In the current paper, we demonstrate that in Haloferax volcanii the four genes are transcribed as an operon in vivo. However, no functional complex or individual enzyme, except for the dihydrolipoamide dehydrogenase component, could be detected in this halophile grown on a variety of carbon sources. Dihydrolipoamide dehydrogenase is present at low catalytic activities, the level of which is increased three to fourfold when Haloferax volcanii is grown on the branched-chain amino acids valine, leucine and isoleucine.