Effect of petrochemical sludge concentrations on microbial communities during soil bioremediation

Effects of organic matter addition on chronically hydrocarbon-contaminated soil

Soil is the recipient of organic pollutants as a consequence of anthropogenic activities. Hydrocarbons are contaminants that pose a risk to human and environmental health. Bioremediation of aging contaminated soils is a challenge due to the low biodegradability of contaminants as a result of their interaction with the soil matrix. The aim of this work was to evaluate the effect of both composting and the addition of mature compost on a soil chronically contaminated with hydrocarbons, focusing mainly on the recovery of soil functions and transformations of the soil matrix as well as microbial community shifts. The initial pollution level was 214 ppm of polycyclic aromatic hydrocarbons (PAHs) and 2500 ppm of aliphatic hydrocarbons (AHs). Composting and compost addition produced changes on soil matrix that promoted the release of PAHs (5.7 and 15 % respectively) but not the net PAH elimination. Interestingly, composting stimulated AHs elimination (about 24 %). The lack of PAHs elimination could be attributed to the insufficient PAHs content to stimulate the microbial degrading capacity, and the preferential consumption of easily absorbed C sources by the bacterial community. Despite the low PAH catabolic potential of the aging soil, metabolic shift was driven by the addition of organic matter, which could be monitored by the ratio of Proteobacteria to Actinobacteria combined with E₄/E₆ ratio. Regarding the quality of the soil, the nutrients provided by the exogenous organic matter contributed to the recovery of the global functions and species diversity of the soil along with the reduction of phytotoxicity.

Study of microbial diversity in plant-microbe interaction system with oil sludge contamination

A 90 days greenhouse experiment was conducted for evaluation of soil microbial diversity in different treatments of rhizospheric and nonrhizospheric oil sludge contaminated soil. Various pot treatments (T1-T5) were as follows: 2% oil sludge contaminated soil was considered as control (T1); augmentation of control with preadapted microbial consortium was T2; addition of Vetiver zizanioide to control was T3; bioaugmentation of control along with V. zizanioide was T4; and bioaugmentation with V. zizanioide and bulking agent was T5. During the study, different microbial populations were determined in all treatments. Additionally, soil microbial diversity using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA was carried out. At the end of experimental period, significant increase in microbial number in bioaugmented rhizospheric treatments (T4 and T5) was observed as compared to non-rhizospheric and non-bioaugmented treatments (T2 and T3). The community and sequencing results revealed that combined treatment of plant and microbes resulted in improved microbial species and number. The dominant phyla belonged to γ proteobacteria, β proteobacteria, Chloroflexi, firmicutes, and uncultured bacteria. It is concluded that plant-microbe-soil system supports immense oil degrading microbial diversity and can be used as an effective indicator tool for remediation of oil sludge contaminated sites.

Remediation of a soil chronically contaminated with hydrocarbons through persulfate oxidation and bioremediation

The impact of remediation combining chemical oxidation followed by biological treatment on soil matrix and microbial community was studied, of a chronically hydrocarbon contaminated soil sourced from a landfarming treatment. Oxidation by ammonium persulfate produced a significant elimination of polycyclic aromatic hydrocarbons (PAHs) and an increase in PAH bioavailability. Organic-matter oxidation mobilized nutrients from the soil matrix. The bacterial populations were affected negatively, with a marked diminution in the diversity indices. In this combined treatment with oxidation and bioremediation working in tandem, the aliphatic-hydrocarbon fractions were largely eliminated along with additional PAHs. The chemical and spectroscopic analyses indicated a change in soil nutrients. In spite of the high residual-sulfate concentration, a rapid recovery of the cultivable bacterial population and the establishment of a diverse and equitable microbial community were obtained. Pyrosequencing analysis demonstrated a marked succession throughout this twofold intervention in accordance with the chemical and biologic shifts observed. These remediation steps produced different effects on the soil physiology. Spectroscopic analysis became a useful tool for following and comparing those treatments, which involved acute changes in a matrix of such chronically hydrocarbon-contaminated soil. The combined treatment increased the elimination efficiency of both the aliphatic hydrocarbons and the PAHs at the expense of the mobilized organic matter, thus sustaining the recovery of the resilient populations throughout the treatment. The high-throughput-DNA-sequencing techniques enabled the identification of the predominant populations that were associated with the changes observed during the treatments.

Assessment of hydrocarbon degradation potentials in a plant-microbe interaction system with oil sludge contamination: A sustainable solution

A pot culture experiment was conducted for 90 days for the evaluation of oil and total petroleum hydrocarbon (TPH) degradation in vegetated and non-vegetated treatments of real-field oil-sludge-contaminated soil. Five different treatments include (T1) control, 2% oil-sludge-contaminated soil; (T2), augmentation of microbial consortium; (T3), Vertiveria zizanioides; (T4), bio-augmentation along with V. zizanioides; and (T5), bio-augmentation with V. zizanioides and bulking agent. During the study, oil reduction, TPH, and degradation of its fractions were determined. Physico-chemical and microbiological parameters of soil were also monitored simultaneously. At the end of the experimental period, oil content (85%) was reduced maximally in bio-augmented rhizospheric treatments (T4 and T5) as compared to control (27%). TPH reduction was observed to be 88 and 89% in bio-augmented rhizospheric soil (T4 and T5 treatments), whereas in non-rhizospheric and control (T2 and T1), TPH reduction was 78 and 37%, respectively. Degradation of aromatic fraction after 90 days in bio-augmented rhizosphere of treatments T4 and T5 was found to 91 and 92%, respectively. In microbial (T2) and Vertiveria treatments (T3), degradation of aromatic fraction was 83 and 68%, respectively. A threefold increase in soil dehydrogenase activity and noticeable changes in organic carbon content and water-holding capacity were also observed which indicated maximum degradation of oil and its fractions in combined treatment of plants and microbes. It is concluded that the plant-microbe soil system helps to restore soil quality and can be used as an effective tool for the remediation of oil-sludge-contaminated sites.

Synergistic influence of Vetiveria zizanioides and selected rhizospheric microbial strains on remediation of endosulfan contaminated soil

Application of endosulfan tolerant rhizospheric bacterial strain isolated from pesticide contaminated area, Ghaziabad in combination with V. zizanioides for the remediation of endosulfan is described herein. The dissipation of endosulfan from soil was considerably enhanced in the presence of bacterial strain and Vetiveria zizanioides together when compared to the dissipation in presence of either of them alone. Four strains- EAG-EC-12 (M1), EAG-EC-13(M2), EAG-EC-14(M3) and EAG-EC-15(M4) are used for this purpose. V. zizanioides was grown in garden soil spiked with 1500 µg g(-1) of endosulfan and inoculated with 100 ml of microbial culture of above motioned strains. Effect of microbial inoculation on plant growth, endosulfan uptake and endosulfan removal efficiency were analyzed. The microbial inoculation significantly enhances the growth of test plant and endosulfan dissipation from soil (p < 0.05). The addition of bacterial strain M1, M2, M3 and M4 in treated pots showed enhanced root length by 13, 33 35, 20.2 and 4.3 %, above ground plant length by 16.38, 35.56, 24.92 and 9.8 % and biomass by 33.69, 49.63, 39.24 and 17.09 % respectively when compared with endosulfan treated plants. After 135 days of exposure, a decline in endosulfan concentration by 59.12, 64.56, 62.69 and 56.39 % was obtained in the spiked soil inoculated with bacterial strains M1, M2, M3 and M4 respectively whereas, decrease in endosulfan concentration by 72.78, 85.25, 76.91 and 65.44 % in the vegetative spiked soil inoculated with same strains was observed during same exposure period. After 135 days of growth period, enhanced removal of endosulfan from experimental soil by 13.66, 20.69, 14.22 and 9.05 % was found in vegetative experiment inoculated with same strains when compared with non vegetative experiment. Result of the study showed that use of toletant plant and tolerant bacterial strains could be the better strategy for the remediation of endosulfan contaminated soil.

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing

The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.

Different substrates and starter inocula govern microbial community structures in biogas reactors

The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes

To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with (13)C-labeled Spirulina biomass (130 mg per 21 g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output reached its maximum (55 μW), while primary fermentation products were formed (in μmol) as follows: acetate 440, ethanol 195, butyrate 128, propionate 112, H(2) 127 and smaller amounts of valerate, propanol and butanol. Sulfate was depleted within 7 days. Thereafter, methanogenesis was observed and secondary fermentation proceeded. H(2) and alcohols disappeared completely, whereas fatty acids decreased in concentration. Three main degraders were identified by RNA-based SIP and denaturant gradient gel electrophoresis. After 12 h, two phylotypes clearly enriched in (13)C: (i) Psychrilyobacter atlanticus, a fermenter known to produce hydrogen and acetate and (ii) bacteria distantly related to Propionigenium. A Cytophaga-related bacterium was highly abundant after day 3. Sulfate reduction appeared to be performed by incompletely oxidizing species, as only sulfate-reducing bacteria related to Desulfovibrio were labeled as long as sulfate was available.

Bioprospection and selection of bacteria isolated from environments contaminated with petrochemical residues for application in bioremediation

The use of microorganisms with hydrocarbon degrading capability and biosurfactant producers have emerged as an alternative for sustainable treatment of environmental passives. In this study 45 bacteria were isolated from samples contaminated with petrochemical residues, from which 21 were obtained from Landfarming soil contaminated with oily sludge, 11 were obtained from petrochemical industry effluents and 13 were originated directly from oily sludge. The metabolization capability of different carbon sources, growth capacity and tolerance, biosurfactant production and enzymes detection were determined. A preliminary selection carried out through the analysis of capability for degrading hydrocarbons showed that 22% of the isolates were able to degrade all carbon sources employed. On the other hand, in 36% of the isolates, the degradation of the oily sludge started within 18-48 h. Those isolates were considered as the most efficient ones. Twenty isolates, identified based on partial sequencing of the 16S rRNA gene, were pre-selected. These isolates showed ability for growing in a medium containing 1% of oily sludge as the sole carbon source, tolerance in a medium containing up to 30% of oily sludge, ability for biosurfactant production, and expression of enzymes involved in degradation of aliphatic and aromatic compounds. Five bacteria, identified as Stenotrophomonas acidaminiphila BB5, Bacillus megaterium BB6, Bacillus cibi, Pseudomonas aeruginosa, and Bacillus cereus BS20 were shown to be promising for use as inoculum in bioremediation processes (bioaugmentation) of areas contaminated with petrochemical residues since they can use oily sludge as the sole carbon source and produce biosurfactants.

Acetogens and acetoclastic methanosarcinales govern methane formation in abandoned coal mines

In abandoned coal mines, methanogenic archaea are responsible for the production of substantial amounts of methane. The present study aimed to directly unravel the active methanogens mediating methane release as well as active bacteria potentially involved in the trophic network. Therefore, the stable-isotope-labeled precursors of methane, [(13)C]acetate and H(2)-(13)CO(2), were fed to liquid cultures from hard coal and mine timber from a coal mine in Germany. Guided by methane production rates, samples for DNA stable-isotope probing (SIP) with subsequent quantitative PCR and denaturing gradient gel electrophoretic (DGGE) analyses were taken over 6 months. Surprisingly, the formation of [(13)C]methane was linked to acetoclastic methanogenesis in both the [(13)C]acetate- and the H(2)-(13)CO(2)-amended cultures of coal and timber. H(2)-(13)CO(2) was used mainly by acetogens related to Pelobacter acetylenicus and Clostridium species. Active methanogens, closely affiliated with Methanosarcina barkeri, utilized the readily available acetate rather than the thermodynamically more favorable hydrogen. Thus, the methanogenic microbial community appears to be highly adapted to the low-H(2) conditions found in coal mines.

Temporal changes in Sphingomonas and Mycobacterium populations in mangrove sediments contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs)

The change in community diversity and structure of the indigenous, dominant, polycyclic aromatic hydrocarbon (PAH)-degrading bacterial genera, Sphingomonas and Mycobacterium, due to contamination in the environment is not very well known. A combination of PCR-DGGE with specific primers and a cultivation-dependent microbiological method was used to detect different populations of Sphingomonas and Mycobacterium in mangrove sediments. The structure of the entire bacterial community (including Sphingomonas) did not show a shift due to environmental contamination, whereas the diversity of Mycobacterium populations in mangrove sediments with higher PAH contamination increased from exposure between Day 0 and Day 30. The isolated Mycobacterium strains migrated to the same position as the major bands of the bacterial communities in Mycobacterium-specific DGGE. A dioxygenase gene system, nidA, which is commonly found in PAH-degrading Mycobacterium strains, was also detected in the more highly contaminated sediment slurries. The present study revealed that Mycobacterium species were the dominant PAH-degraders and played an important role in degrading PAHs in contaminated mangrove sediments.

Effects of nonionic surfactant addition on populations of polycyclic aromatic hydrocarbon-degrading bacteria in a bioreactor treating contaminated soil

We studied the effects of two polyethoxylated nonionic surfactants, Brij 30 and C(12)E(8), on populations of polycyclic aromatic hydrocarbon- (PAH-) degrading bacteria from a bioreactor treating PAH-contaminated soil. Each surfactant was evaluated at doses that corresponded to aqueous-phase concentrations both above and below the critical micelle concentration (CMC) after mixing with reactor slurry. Real-time quantitative PCR was used to quantify 16S rRNA (rRNA) gene sequences representing degraders of salicylate, naphthalene, phenanthrene, or pyrene previously identified in the bioreactor community by stable-isotope probing. Sequences representing two groups of organisms associated with degradation of naphthalene and/or salicylate in the bioreactor increased in abundance by more than an order of magnitude after incubation with either surfactant at each dose tested. In contrast, the abundance of a group of uncultivated pyrene-degrading bacteria, whose relative abundance in the soil without surfactant addition was up to 9% of the total 16S rRNA genes, decreased by an order of magnitude or more in the presence of each surfactant at each dose. These results indicate that surfactant addition can have substantial, differential effects on populations of organisms responsible for contaminant degradation within a microbial community.

Leachability of arsenic and heavy metals from mine tailings of abandoned metal mines

Mine tailings from an abandoned metal mine in Korea contained high concentrations of arsenic (As) and heavy metals [e.g., As: 67,336, Fe: 137,180, Cu: 764, Pb: 3,572, and Zn: 12,420 (mg/kg)]. US EPA method 6010 was an effective method for analyzing total arsenic and heavy metals concentrations. Arsenic in the mine tailings showed a high residual fraction of 89% by a sequential extraction. In Toxicity Characteristic Leaching Procedure (TCLP) and Korean Standard Leaching Test (KSLT), leaching concentrations of arsenic and heavy metals were very low [e.g., As (mg/L): 0.4 for TCLP and 0.2 for KSLT; cf. As criteria (mg/L): 5.0 for TCLP and 1.5 for KSLT].

Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.

Effect of sludges on bacteria in agricultural soil. Analysis at laboratory and outdoor lysimeter scale

The effect of composted (CS), digested (DS) and liquid raw (LRS) sludges unspiked or spiked with benzo[a]pyrene(BaPYR), dibuthyl phthalate (DBP) or nonyl phenol (NP) on the structure of the bacterial communities of an agricultural soil was estimated by using thermal temporal gel electrophoresis (TTGE). At the laboratory scale, DS and especially LRS modified the composition of the bacterial communities (irrespective of the addition of BaPYR, DBP or NP or not). Sludges, especially LRS, very probably acted both as a bacterial inoculum and a nutrient source. The combined effect was transient in the laboratory conditions probably due to the favorable conditions of mineralization. The results observed with soil amended with the same sludges and cultivated or not with carrots in outdoor lysimeters were similar to those observed in the laboratory experiments. Thus, this bioassay allowed predicting the potential effect of various sludges on the structure of the bacterial communities within a few days.

Photodegradation of soil organic matter and its effect on gram-negative bacterial growth

To learn more about the role of the reactive oxygen species (ROS) in the production of bioavailable products of the dissolved organic matter, we investigate here the effect of the photolysis (lambda(exc) > 320 nm) of a soil extract (SE) on the growth of bacteria isolated from the same soil as used for obtaining the extract. Comparative experiments with Aldrich humic acid (AHA) as substrate were performed. The photodegradation of the SE was evaluated with different techniques-UV-visible absorption spectroscopy, fluorescence excitation emission matrices (EEM) and Fourier transform infrared spectroscopy (FTIR). Known ROS scavengers were employed to study the effect of photochemically produced ROS on the photodegradation of the substrates. To evaluate the effect of irradiation on the bioavailability of the SE and AHA, photolyzed and nonphotolyzed substrates were added to different culture media and the growth of Pseudomonas sp. isolated from the soil and a strain of Escherichia coli were studied. The different results obtained were assigned to the dissimilar metabolisms of both bacteria.

Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea

The anoxic layers of marine sediments are dominated by sulfate reduction and methanogenesis as the main terminal oxidation processes. The aim of this study was to analyze the vertical succession of microbial populations involved in these processes along the first 4.5 m of a tidal-flat sediment. Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA). The sampling site was characterized by an unusual sulfate peak at 250 cm depth resulting in separate sulfate-methane transition zones. Methane and sulfate profiles were diametrically opposed, with a methane maximum in the sulfate-depleted zone showing high numbers of archaea and methanogens. The methane-sulfate interfaces harbored elevated numbers of sulfate reducers, and revealed a slight increase in mcrA and archaeal 16S rRNA genes, suggesting sulfate-dependent anaerobic oxidation of methane. A diversity analysis of both functional genes by PCR-denaturing gradient gel electrophoresis revealed a vertical succession of subpopulations that were governed by geochemical and sedimentologic conditions. Along the upper 200 cm, sulfate-reducing populations appeared quite uniform and were dominated by the Deltaproteobacteria. In the layers beneath, an apparent increase in diversity and a shift to the Firmicutes as the predominant group was observed.

Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

Effects of naphthalene on microbial community composition in the Delaware estuary

The effects of naphthalene on microbial communities in the bottom boundary layer of the Delaware Bay estuary were investigated in microcosms using denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) with oligonucleotide probes. Three days after the addition of naphthalene, rates of bacterial production and naphthalene mineralization were higher than in no-addition controls and than in cases where glucose was added. Analyses using both DGGE and FISH indicated that the bacterial community changed in response to the addition of naphthalene. FISH data indicated that a few major phylogenetic groups increased in response to the glucose addition and especially to the naphthalene addition. DGGE also demonstrated differences in community composition among treatments, with four phylotypes being unique to naphthalene-amended treatments and three of these having 16S rRNA genes similar to known hydrocarbon degraders. The bacterial community in the naphthalene-amended treatment was distinct from the communities in the glucose-amended treatment and in the no-addition control. These data suggest that polycyclic aromatic hydrocarbons may have large effects on microbial community structure in estuaries and probably on microbially mediated biogeochemical processes.