Marine bacteria and omic approaches: A novel and potential repository for bioremediation assessment

Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio-remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques used for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e. heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better used for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, using the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists and decision-makers to develop a holistic understanding regarding their utility in bioremediation assessment.     

近海柴油降解菌群的构建及其对柴油的降解特性

【目的】实施近海柴油污染的生物治理。【方法】以柴油为唯一碳源,从深圳港口海域富集筛选柴油降解菌;采用复配、正交试验等方式构建混合菌群;通过单因素试验研究环境因素对菌群降解柴油的影响;使用气相色谱-氢火焰检测器(GC-FID)分析降解前后柴油各组分的变化;通过生理生化试验和16S rRNA基因序列分析对菌株进行鉴定。【结果】获得了16株柴油降解菌,7 d内对柴油的降解率最高达40.8%;选择菌株C1-8、C2-10、C3-13构建了混合菌群CQ1,投加量分别为0.5%、2.0%和1.0%,CQ1对柴油去除率比单菌提高了10%以上;CQ1的最适环境条件为：温度30 °C、pH 7.6、摇床转速220 r/min、柴油浓度20 g/L,优化后9 d内对柴油去除率达60%以上;GC-FID结果显示,菌群CQ1可降解大部分C11?C27的正构烷烃,对C21?C27的烷烃降解可达100%。经鉴定,菌株C1-8、C2-10和C3-13分别为微杆菌(Microbacterium sp.)、剑菌(Ensifer sp.)和变异棒杆菌(Corynebacterium variabile)。【结论】CQ1在近海柴油污染的生物修复中具有良好的应用前景。     

X-ray structure and mechanism of ZgHAD,a l-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans

Haloacid dehalogenases are potentially involved in bioremediation of contaminated environments and few have been biochemically characterized from marine organisms. The l -2-haloacid dehalogenase (l -2-HAD) from the marine Bacteroidetes Zobellia galactanivorans Dsij^T (ZgHAD) has been shown to catalyze the dehalogenation of C2 and C3 short-chain l -2-haloalkanoic acids. To better understand its catalytic properties, its enzymatic stability, active site, and 3D structure were analyzed. ZgHAD demonstrates high stability to solvents and a conserved catalytic activity when heated up to 60°C, its melting temperature being at 65°C. The X-ray structure of the recombinant enzyme was solved by molecular replacement. The enzyme folds as a homodimer and its active site is very similar to DehRhb, the other known l -2-HAD from a marine Rhodobacteraceae. Marked differences are present in the putative substrate entrance sites of the two enzymes. The H179 amino acid potentially involved in the activation of a catalytic water molecule was confirmed as catalytic amino acid through the production of two inactive site-directed mutants. The crystal packing of 13 dimers in the asymmetric unit of an active-site mutant, ZgHAD-H179N, reveals domain movements of the monomeric subunits relative to each other. The involvement of a catalytic His/Glu dyad and substrate binding amino acids was further confirmed by computational docking. All together our results give new insights into the catalytic mechanism of the group of marine l -2-HAD.     

Marine bacteria: potential candidates for enhanced bioremediation

Bacteria are widespread in nature as they can adapt to any extreme environmental conditions and perform various physiological activities. Marine environments are one of the most adverse environments owing to their varying nature of temperature, pH, salinity, sea surface temperature, currents, precipitation regimes and wind patterns. Due to the constant variation of environmental conditions, the microorganisms present in that environment are more suitably adapted to the adverse conditions, hence, possessing complex characteristic features of adaptation. Therefore, the bacteria isolated from the marine environments are supposed to be better utilized in bioremediation of heavy metals, hydrocarbon and many other recalcitrant compounds and xenobiotics through biofilm formation and production of extracellular polymeric substances. Many marine bacteria have been reported to have bioremediation potential. The advantage of using marine bacteria for bioremediation in situ is the direct use of organisms in any adverse conditions without any genetic manipulation. This review emphasizes the utilization of marine bacteria in the field of bioremediation and understanding the mechanism behind acquiring the characteristic feature of adaptive responses.     

Bioremediation of a petroleum‐contaminated cryic soil: Effects of phosphorus,nitrogen, and temperature

Bioremediation has been shown to be an effective means of treating petroleum‐contaminated soils in cold areas, although the conditions required to maximize bioremediation in cold region (cryic) soils are not well documented. A laboratory study was conducted to investigate the effects of nitrogen and phosphorus levels and temperature on petroleum bioremediation. A cryic entisol contaminated with diesel fuel was treated with nitrogen (0, 400, 800, or 1200 mg/kg of soil) and phosphorus (0, 60, 120, or 180 mg/kg of soil) and incubated at two temperatures (10 and 20°C). At 10°C, bioremediation rates were not affected by fertility treatments. At 20°C, reaction rates were increased by the addition of P, but unaffected by N. Regardless of fertility regime, the rate of diesel loss was much greater in soil incubated at 20°C than in soil incubated at 10°C.     

Filtration and clearance rates of Anadara grandis juveniles (Pelecypoda, Arcidae) with different temperatures and suspended matter concentrations

The mangrove cockle Anadara grandis (Broderip and Sowerby, 1829) is a potential candidate for aquaculture and for bioremediation of aquaculture effluents in the tropical and subtropical coastal areas of the eastern Pacific Ocean. Laboratory-produced spat are available, but there is no information on their responses to the range of environmental conditions to which they might be subject during the growth cycle. The aim of this study was to evaluate the filtration and clearance rates ofA. grandis spat (shell length 9.50+/-0.37 mm) with a food concentration (7.5 mgxl(-1)) at four different temperatures (22, 25, 28 and 31 degrees C, with pH=7.5+/-0.2 and O2 concentration of 6.4+/-0.5 mgxl(-1); experiment one); and with a temperature (25 degrees C) and five concentrations of suspended matter (from 7.5 to 29 mgxl(-1) and pH and O2 values of 7.9+/-0.2 and 6.8+/-0.4 mgxl(-1); experiment two). Filtration and clearance rates were highest at 25 degrees C and significantly different (p<.05) from those obtained at 22, 28 and 31 degrees C; the clearance rates had the same tendency but the differences were not significant (p>.05). In the second experiment filtration increased according to the amount of food available, but there were no significant differences (p>.05) between 7.5 and 11 mgxl(-1) and from 22.4 to 29 mgxl(-1). The trend was similar for clearance, and in this case significant differences were found (p<.05) between 7.5, 22.4 and 29 mgxl(-1). Filtration at 31 degrees C was close to 80% at the optimum temperature of 25 degrees C, which indicates that A. grandis is a good candidate for tropical aquaculture. Clearance increased with high concentrations of suspended solids, but the production of biodeposits could be a source of environmental concern. Therefore, the possibility of using this species for bioremediation of aquaculture effluents should be studied with larger specimens and at higher seston concentrations.     

Phylogenetic diversity of bacterial communities associated with bioremediation of crude oil in microcosms

Bioremediation, mainly by indigenous bacteria, has been regarded as an effective way to clean up oil pollution after an oil spill. In order to obtain a systematic understanding of the succession of bacterial communities associated with oil bioremediation, sediments collected from the Penglai 19-3 oil platform were co-incubated with crude oil. Oil biodegradation was assessed on the basis of changes in oil composition monitored by GC–MS. Changes in the bacterial community structure were detected by two 16S rRNA gene based culture-independent methods, denaturing gradient gel electrophoresis (DGGE) and clone library. The results suggested that crude oil was rapidly degraded during the 30-day bioremediation period. Bacteria affiliated with the genus Pseudomonas dominated all three clone libraries. But dramatic changes were also detected in the process of biodegradation of crude oil. The “professional hydrocarbonocastic bacteria” (e.g., Alcanivorax) became abundant in the two samples during the bioremediation period. Meanwhile, δ-proteobacteria was only detected in the two samples. Information on the bacterial community revealed in this study will be useful in developing strategies for bioremediation of crude oil dispersed in the marine ecosystem.     

Characterization of antarctic hydrocarbon-degrading bacteria capable of producing bioemulsifiers.

During screening for biosurfactant-producing, n-alkane-degrading marine bacteria, two heterotrophic bacterial strains were isolated from enriched mixed cultures, obtained from Terra Nova Bay (Ross sea, Antarctica) by using aliphatic and artomatic hydrocarbons as the principal carbon source. These gram-positive, aerobic, cocci-shaped bacteria use a various number of organic compounds, including aliphatic hydrocarbons, volatile fatty acids, and biphenyl. During cultivation on n-alkanes as sole source of carbon and energy, all strains produced both an extracellular and cell-bound surface-active mixture of trehalose lipids which reduced the surface tension of water from 72 mN/m to 32mN/m. This class of glycolipids was found to be produced only by marine rhodococci. The 16S-rRNA gene sequence analysis showed that both strains are members of the G + C rich gram-positive group of the phylum Proteobacteria and was found to be almost identical to that of Rhodococcus fascians DSM 20669. The potential of these strains for in situ bioremediation of contaminated cold marine environment is discussed in the present study.     

Salmonella DNA persistence in natural seawaters using PCR analysis

The risks of false-positive responses were examined when using the polymerase chain reaction (PCR) method for the detection of Salmonella in the marine environment (water and shellfish). The degradation rates of DNA, both free and from dead Salmonella , were evaluated in natural seawaters maintained at 10° and 20°C, using PCR with Vir and invA primers. The DNA of dead Salmonella was detected up to 55 d in seawater collected in winter and stored at 10°C. But in summer, the persistence was shorter: 10 d or even 2 d for a smaller inoculum (3 × 10³ Salmonella ml⁻¹). The role of the planktonic organisms present in spring and summer was pinpointed. For free DNA, the persistence times were shorter: from 2 to 4 d at 20°C, and from 3 to 8 d at 10°C showing that the nuclease activity of marine organisms is higher at warm temperatures. These data led us to recommend careful interpretations of direct PCR results, especially during cold periods and for samples collected close to terrestrial discharges of high concentrations of live, dead or lysed Salmonella . PCR is a rapid, specific and sensitive method, but should be applied with care to marine samples, in order to avoid false-positive responses.     

Bioremediation of Cr(VI) from Chromium-Contaminated Wastewater by Free and Immobilized Cells of Cellulosimicrobium cellulans KUCr3

In this report, possible utilization of a chromium-reducing bacterial strain Cellulosimicrobium cellulans KUCr3 for effective bioremediation of hexavalent chromium (Cr(VI))-containing wastewater fed with tannery effluents has been discussed. Cr(VI) reduction and bioremediation were found to be related to the growth supportive conditions in wastewater, which is indicative of cell mass dependency for Cr(VI) reduction. Cr(VI) reduction was determined by measuring the residual Cr(VI) in the cell-free supernatant using colorimetric reagent S-diphenylcarbazide. Nutrient availability and initial cell density showed a positive relation with Cr(VI) reduction, but it was inhibited with increasing concentration of Cr(VI) under laboratory condition. The optimum temperature and pH for effective Cr(VI) reduction in wastewater were found to be 35°C and 7.5, respectively. The viable cells of KUCr3 were successfully entrapped in an agarose bead that was used in continuous column and batch culture for assaying Cr(VI) reduction. In packed bed column (continuous flow) experiment, approximately 25% Cr(VI) reduction occurred after 144 h. Cr(VI) was almost 75% and 52% reduced at concentrations of 0.5 mM and 2 mM Cr(VI), respectively, after 96 h in batch culture experiment in peptone-yeast extract-glucose medium, whereas it could decrease the Cr(VI) content up to 40% from the water containing tannery waste. This study suggests that KUCr3 could be used as a candidate for possible environmental clean up operation with respect to Cr(VI) bioremediation.     

Effects of hypoxia on alveolar fluid transport capacity in rat lungs.

There is little information regarding the effect of hypoxia on alveolar fluid clearance capacity. We measured alveolar fluid clearance, lung water volume, plasma catecholamine concentrations, and serum osmolality in rats exposed to 10% oxygen for up to 120 h and explored the mechanisms responsible for the increase in alveolar fluid clearance. The principal results were 1) alveolar fluid clearance did not change for 48 h and then increased between 72 and 120 h of exposure to hypoxia; 2) although nutritional impairment during hypoxia decreased basal alveolar fluid clearance, endogenous norepinephrine increased net alveolar fluid clearance; 3) the changes of lung water volume and serum osmolality were not associated with those of alveolar fluid clearance; 4) an administration of beta-adrenergic agonists further increased alveolar fluid clearance; and 5) alveolar fluid clearance returned to normal within 24 h of reoxygenation after hypoxia. In conclusion, alveolar epithelial fluid transport capacity increases in rats exposed to hypoxia. It is likely that a combination of endogenous norepinephrine and nutritional impairment regulates alveolar fluid clearance under hypoxic conditions.     

Mixotrophy in the newly described phototrophic dinoflagellate Woloszynskia cincta from western Korean waters: feeding mechanism, prey species and effect of prey concentration

Woloszynskia species are dinoflagellates in the order Suessiales inhabiting marine or freshwater environments; their ecophysiology has not been well investigated, in particular, their trophic modes have yet to be elucidated. Previous studies have reported that all Woloszynskia species are photosynthetic, although their mixotrophic abilities have not been explored. We isolated a dinoflagellate from coastal waters in western Korea and established clonal cultures of this dinoflagellate. On the basis of morphology and analyses of the small/large subunit rRNA gene (GenBank accession number=FR690459), we identified this dinoflagellate as Woloszynskia cincta. We further established that this dinoflagellate is a mixotrophic species. We found that W. cincta fed on algal prey using a peduncle. Among the diverse prey provided, W. cincta ingested those algal species that had equivalent spherical diameters (ESDs) ≤12.6 μm, exceptions being the diatom Skeletonema costatum and the dinoflagellate Prorocentrum minimum. However, W. cincta did not feed on larger algal species that had ESDs≥15 μm. The specific growth rates for W. cincta increased continuously with increasing mean prey concentration before saturating at a concentration of ca. 134 ng C/ml (1,340 cells/ml) when Heterosigma akashiwo was used as food. The maximum specific growth rate (i.e. mixotrophic growth) of W. cincta feeding on H. akashiwo was 0.499 d(-1) at 20 °C under illumination of 20 μE/m(2) /s on a 14:10 h light-dark cycle, whereas its growth rate (i.e. phototrophic growth) under the same light conditions without added prey was 0.040 d(-1). The maximum ingestion and clearance rates of W. cincta feeding on H. akashiwo were 0.49 ng C/grazer/d (4.9 cells/grazer/d) and 1.9 μl/grazer/h, respectively. The calculated grazing coefficients for W. cincta on co-occurring H. akashiwo were up to 1.1 d(-1). The results of the present study suggest that grazing by W. cincta can have a potentially considerable impact on prey algal populations.     

Inoculants and Biodegradation of Crude Oil Floating on Marsh Sediments

The efficacy of ten commercial bioremediation products in enhancing the biodegradation of crude oil was investigated in the laboratory at 10 or 30a°C for 90 d with and without supplemental nitrogen and phosphorus. Oil was added to a 1-cm layer of water covering sediments from a salt marsh. The products did not increase the numbers of hydrocarbon-degrading microorganisms in water and sediments but did increase heterotrophic populations at 21 d. Some bioremediation products more than doubled the quantity of hydrocarbons degraded in 45 d at 10°C. At 30°C, no product increased degradation compared to the fertilized control in which 70% of the added hydrocarbons were degraded. Two products increased the percentage of hydrocarbons degraded from 42% to approximately 65% in 45 d at 30°C when supplemental fertilizer was not provided. The hydrocarbon concentration was not significantly reduced between 45 and 90 d for most product treatments at either temperature. At 10°C, products seemed to have the greatest potential for enhancing oil bioremediation compared to the control.     

Evaluation of the Gastrointestinal Tract as Potential Route of Primary Polyomavirus Infection in Mice

Background

Detection of Polyomavirus (PyV) DNA in metropolitan rivers worldwide has led to the suggestion that primary viral infection can occur by the oral route. The aim of this study was to test this notion experimentally.

Methods

Mouse PyV (MPyV) was used to infect C57BL/6J mice by the nasal or intragastric route. Viral load kinetics was studied 3, 7, 10, 14, 21 and 28 days post-infection (dpi) using quantitative PCR.

Results

Following nasal infection, MPyV DNA was readily detected in many organs including lung, heart, aorta, colon, and stool with viral loads in the range of 10³–10⁶ copies/mg wet weight that peaked 7–10 dpi. Complete viral clearance occurred in the serum and kidney by 28 dpi, while clearance in other organs was partial with a 10–100 fold decrease in viral load. In contrast, following intragastric infection peak detection of PyV was delayed to 21 dpi, and viral loads were up to 3 logs lower. There was no detectable virus in the heart, colon, or stool.

Conclusions

The intragastric route of MPyV infection is successful, not as efficacious as the respiratory route, and associated with delayed viral dissemination as well as a lower peak MPyV load in individual organs.     

Improved production of the anticancer compound 1403C by glucose pulse feeding of marine Halorosellinia sp. (No. 1403) in submerged culture

Effects of different pulse fed-batch methods on production of the anti-cancer compound 1403C by marine mangrove endophytic fungus Halorosellinia sp. (No. 1403) in a 5-L bioreactor were investigated. Since high glucose concentrations improved mycelial growth but inhibited 1403C production, the cultures were pulse fed with glucose solutions to keep the residual glucose lower than 4 g/L but higher than 0.5 g/L during rapid growth phase (0-50 h). In this way, a maximum dry biomass, 1403C production and yield coefficient (Y1403C/X) of up to 4.5 g/L, 2.64 g/L and 0.59 g/g dry cell weight, respectively were achieved. These values are 22.7%, 98.0% and 61.4%, respectively higher than those obtained with batch cultures. This strategy is valuable for fermentation scale-up of Halorosellinia sp. (No. 1403) for 1403C production, and might also be applicable to other marine fungi cultures.     

Bioremediation Potential of Terrestrial Fuel Spills

A bioremediation treatment that consisted of liming, fertilization, and tilling was evaluated on the laboratory scale for its effectiveness in cleaning up a sand, a loam, and a clay loam contaminated at 50 to 135 mg g of soil⁻¹ by gasoline, jet fuel, heating oil, diesel oil, or bunker C. Experimental variables included incubation temperatures of 17, 27, and 37°C; no treatment; bioremediation treatment; and poisoned evaporation controls. Hydrocarbon residues were determined by quantitative gas chromatography or, in the case of bunker C, by residual weight determination. Four-point depletion curves were obtained for the described experimental variables. In all cases, the disappearance of hydrocarbons was maximal at 27°C and in response to bioremediation treatment. Poisoned evaporation controls underestimated the true biodegradation contribution, but nevertheless, they showed that biodegradation makes only a modest contribution to gasoline disappearance from soil. Bunker C was found to be structurally recalcitrant, with close to 80% persisting after 1 year of incubation. The three medium distillates, jet fuel, heating oil, and diesel oil, increased in persistence in the listed order but responded well to bioremediation treatment under all test conditions. With bioremediation treatment, it should be possible to reduce hydrocarbons to insignificant levels in contaminated soils within one growing season.     

Bioremediation of soil polluted with fuels by sequential multiple injection of native microorganisms: Field-scale processes in Poland

Research was conducted to estimate impact of the multiple bioaugmentation on the treatment of soil contaminated by fuels - diesel oil and aircraft fuel. The bacteria used to inoculate the remediation plots were isolated from the polluted soil and proliferated in field conditions. The amount of biomass applied to the polluted soil was set to ensure the total number of bacteria in soil 10⁷-10⁸ cfu/g d.w. The multiple inoculation of soil with indigenous bacteria active in diesel oil and engine oil (plot A) degradation increased bioremediation effectiveness by 50% in comparison to the non-inoculated control soil and by 30% in comparison to the soil that was inoculated only once. The multiple inoculation of soil with indigenous microorganisms was then applied in bioremediation of the soil polluted with double high concentration of diesel oil (soil B) and in bioremediation of the soil polluted with aircraft fuel (soil C). The process efficiency was 80% and 98% removal of TPH for soil B and C, respectively.     

Engineering Deinococcus geothermalis for bioremediation of high-temperature radioactive waste environments

Deinococcus geothermalis is an extremely radiation-resistant thermophilic bacterium closely related to the mesophile Deinococcus radiodurans, which is being engineered for in situ bioremediation of radioactive wastes. We report that D. geothermalis is transformable with plasmids designed for D. radiodurans and have generated a Hg(II)-resistant D. geothermalis strain capable of reducing Hg(II) at elevated temperatures and in the presence of 50 Gy/h. Additionally, D. geothermalis is capable of reducing Fe(III)-nitrilotriacetic acid, U(VI), and Cr(VI). These characteristics support the prospective development of this thermophilic radiophile for bioremediation of radioactive mixed waste environments with temperatures as high as 55 degrees C.     

Bioremediation of oil contaminated beach sediments using indigenous microorganisms in singapore

The potential of using indigenous microorganisms in beach sediments to degrade petroleum hydrocarbons emanating from marine oil spillages in the Straits of Singapore was investigated. A field trial was conducted using oil contaminated beach sediments from Pulau Semakau – a small island 15 km south of Singapore. The results clearly show that the addition of inorganic nutrients to beach sediments significantly enhanced the activity of indigenous microorganisms (measured using the dehydrogenase enzyme assay and viable cell count techniques), as well as the removal of total recoverable petroleum hydrocarbons (TRPH) over a 50-day study period (with up to 44% in the case of nutrient addition). The potential of exploiting in-situ bioremediation techniques for oil spill clean-up operations in tropical marine environments is discussed.     

Rhamnolipid biosurfactants: evolutionary implications,applications and future prospects from untapped marine resource

Rhamnolipid-biosurfactants are known to be produced by the genus Pseudomonas, however recent literature reported that rhamnolipids (RLs) are distributed among diverse microbial genera. To integrate the evolutionary implications of rhamnosyl transferase among various groups of microorganisms, a comprehensive comparative motif analysis was performed amongst bacterial producers. Findings on new RL-producing microorganism is helpful from a biotechnological perspective and to replace infective P. aeruginosa strains which ultimately ensure industrially safe production of RLs. Halotolerant biosurfactants are required for efficient bioremediation of marine oil spills. An insight on the exploitation of marine microbes as the potential source of RL biosurfactants is highlighted in the present review. An economic production process, solid-state fermentation using agro-industrial and industrial waste would increase the scope of biosurfactants commercialization. Potential and prospective applications of RL-biosurfactants including hydrocarbon bioremediation, heavy metal removal, antibiofilm activity/biofilm disruption and greener synthesis of nanoparticles are highlighted in this review.