Biodegradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments

Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil

Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.

Petroleum-contaminated soil: environmental occurrence and remediation strategies

Soil is an environmental matrix that carries life for all living things. With the rise of human activities and the acceleration of population, the soil has been exposed in part to pollution by the discharge of various xenobiotics and persistent pollutants into it. The disposal of toxic substances such as polycyclic aromatic hydrocarbons (PAHs) alters soil properties, affects microbial biodiversity, and damages objects. Considering the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and clean-up of PAH-polluted sites represents an important technological and environmental challenge for sustainable growth and development. Though several treatment methods to remediate PAH-polluted soils exist, interesting bacteria, fungi, and their enzymes receive considerable attention. The aim of the present review is to discuss PAHs' impact on soil properties. Also, this review illustrates physicochemical and biological remediation strategies for treating PAH-contaminated soil. The degradation pathways and contributing factors of microbial PAH-degradation are elucidated. This review also assesses the use of conventional microbial remediation compared to the application of genetically engineered microorganisms (GEM) that can provide a cost-effective and eco-friendly PAH-bioremediation strategy.

Identifying bioaugmentation candidates for bioremediation of polycyclic aromatic hydrocarbons in contaminated estuarine sediment of the Elizabeth River, VA, USA

Estuarine sediments near former creosoting facilities along the Elizabeth River (Virginia, USA) are contaminated by polycyclic aromatic hydrocarbons (PAHs). In this study, we interrogated the bacterial community of the Elizabeth River with both culture-based and culture-independent methods to identify potential candidates for bioremediation of these contaminants. DNA-based stable isotope probing (SIP) experiments with phenanthrene and fluoranthene using sediment from the former Republic Creosoting site identified relevant PAH-degrading bacteria within the Azoarcus, Hydrogenophaga, and Croceicoccus genera. Targeted cultivation of PAH-degrading bacteria from the same site recovered 6 PAH-degrading strains, including one strain highly similar to Hydrogenophaga sequences detected in SIP experiments. Other isolates were most similar to organisms within the Novosphingobium, Sphingobium, Stenotrophomonas, and Alcaligenes genera. Lastly, we performed 16S rRNA gene amplicon microbiome analyses of sediment samples from four sites, including Republic Creosoting, with varying concentrations of PAHs. Analysis of these data showed a striking divergence of the microbial community at the highly contaminated Republic Creosoting site from less contaminated sites with the enrichment of several bacterial clades including those affiliated with the Pseudomonas genus. Sequences within the microbiome libraries similar to SIP-derived sequences were generally found at high relative abundance, while the Croceicoccus sequence was present at low to moderate relative abundance. These results suggest that Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation, while Croceicoccus spp. might be good targets for bioaugmentation in these sediments. Furthermore, this study demonstrates the value of culture-based and culture-independent methods in identifying promising bacterial candidates for use in a precision bioremediation scheme. KEY POINTS: • This study highlights the importance of using multiple strategies to identify promising bacterial candidates for use in a precision bioremediation scheme. • We used both selective cultivation techniques and DNA-based stable isotope probing to identify bacterial degraders of prominent PAHs at a historically contaminated site in the Elizabeth River, VA, USA. • Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation in Elizabeth River sediments, while Croceicoccus spp. might be good targets for bioaugmentation.

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.

Optimization of Crude Oil Biodegradation by Brevibacterium sp. Isolated from the Native Sponges of the Persian Gulf

Background:

The native sponges of Persian Gulf are unique species facing difficult climate conditions and environmental contamination. It is necessary to investigate these native sponges because global warming most probably destroyed many of these creatures. Therefore, the study of the microorganisms associated with sponges will introduce new bacterial strains with various industrial and environmental applications and, in this way, a part of the Persian Gulf biodiversity will be preserved for posterity.

Objective:

The aim of this study was the isolation and molecular identification of bacteria associated with the ability of biodegrading crude oil from the native sponges of the Persian Gulf. Also, optimization of crude oil biodegradation was done for one of the most efficient bacterial strains.

Materials and Methods:

Isolated species were compared in terms of E24 index and growth rate in a culture medium containing at least 2% of oil as the sole carbon source. Molecular identification was done for five bacterial strains. Using the Taguchi experimental design, the effects of 4 factors, namely, carbon source auxiliary, organic and inorganic nitrogen sources, salinity and pH, were evaluated at 3 levels. GC-Mass analysis was performed on the remaining oil in the culture medium.

Results:

In the initial screening of two native species of sponges, 22 bacterial strains were isolated which were capable of decomposing oil. Five bacterial strains showed the best results and were recorded in NCBI with access numbers KY283126, KY283128, KY285290, KY285289, and KY285288. Brevibacterium sp. (KY283128) showed the highest level of oil degradation (about 97%) and growth rate. The results showed that the optimal oil degradation occurs in the absence of carbon source auxiliary, at 0.5% of salinity, with NH₄Cl as the nitrogen source and at a pH of 6.5.

Conclusions:

This bacterial strain can be used for biodegradation in oil-contaminated areas and oil refineries. By isolating the oil degrading gene in this bacterial strain and cloning it in other bacterial strains, the efficiency of eliminating oil contamination can be increased.

Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.

Multilevel changes in bacterial properties on long-term exposure to hydrocarbons and impact of these cells on fresh-water communities

To handle the impact of habitat transformations, the microbial cells developed mechanisms aimed at adjustment of their biological processes in response to signals indicating environmental changes. One of the first changes in their properties is observed on their surface, which has direct contact with the dynamically varying surroundings. In this study, we present results of changes in the cell surface properties which may have a decisive impact on the xenobiotics' bioavailability and microbial cell survival. These changes influence their ability to remove xenobiotics by accelerating and empowering this process. Moreover, the application of microorganisms exposed for long-term to hydrocarbons in bioremediation processes might have positive impact on biodegradation of the latter in the natural environment as well as natural microbial community diversity. This study demonstrates a variety of microbial cell mechanisms of adaptation to long-term exposure to hydrocarbons and their potential as the bioremediation tools.

The influence of heavy metals on the bioremediation of polycyclic aromatic hydrocarbons in aquatic system by a bacterial-fungal consortium

Co-contamination of polycyclic aromatic hydrocarbons (PAHs) with heavy metals (HMs) in aquatic environments is a global threat; however, little is understood about PAH biodegradation in these sites. In this study, PAHs' biodegradation in the presence of HMs in water by a metal-tolerant consortium composed of Bacillus subtilis and fungus Acremonium sp. was investigated. The consortium demonstrated higher tolerance to the tested HMs (Fe²⁺, Al³⁺, Ni²⁺, Cu²⁺, Mn²⁺ and Zn²⁺) than the individual consortium components, and the tolerance to individual metals decreased with increasing metal concentrations. In the absence of HMs in aquatic systems, the consortium efficiently degraded naphthalene, fluorine, phenanthrene, anthracene and fluoranthene individually (50 mmol/L) over 10 days. However, while Ni²⁺ supplementation (5 mmol/L) suppressed phenanthrene and anthracene removal (p ≤ 0.01), enhanced fluoranthene degradation relative to the control was observed. Cu²⁺, Zn²⁺, Fe²⁺ and Al³⁺ supplementation demonstrated significant inhibition against individual phenanthrene, anthracene and fluoranthene removal, and Cu²⁺ showed a more significant effect on the degradation of these PAH compounds compared to other metals. Conversely, Mn²⁺ significantly enhanced the removal of fluorene, phenanthrene and fluoranthene, but inhibited anthracene degradation. HM contamination in aquatic systems did not show any effect on naphthalene bioremediation, possible due to its rapid degradation over a short time. Thus, metals affect PAH aquatic biodegradation by consortia, depending on metal species and PAH compound, underlining the complex nature of co-contaminated systems containing HMs and PAHs. To our knowledge, this is the first study to examine the influence of HMs on PAHs' bioremediation by such PAH-degrading consortia in water.

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment

Coastal sediments contaminated by polycyclic aromatic hydrocarbons (PAHs) can be candidates for remediation via an approach like land farming. Land farming converts naturally anaerobic sediments to aerobic environments, and the response of microbial communities, in terms of community structure alterations and corresponding effects on biodegradative activities, is unknown. A key goal of this study was to determine if different sediments exhibited common patterns in microbial community responses that might serve as indicators of PAH biodegradation. Sediments from three stations in the Lagos Lagoon (Nigeria) were used in microcosms, which were spiked with a mixture of four PAH, then examined for PAH biodegradation and for shifts in microbial community structure by analysis of diversity in PAH degradation genes and Illumina sequencing of 16S rRNA genes. PAH biodegradation was similar in all sediments, yet each exhibited unique microbiological responses and there were no microbial indicators of PAH bioremediation common to all sediments.

Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis

This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg^-1 of each PAH), and acenaphthene (600 mg kg^-1). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.

Bioactivity of a Novel Glycolipid Produced by a Halophilic Buttiauxella sp. and Improving Submerged Fermentation Using a Response Surface Method

An antimicrobial glycolipid biosurfactant (GBS), extracted and identified from a marine bacterium, was studied to inhibit pathogenic microorganisms. Production of the GBS was optimized using a statistical method, a response surface method (RSM) with a central composite design (CCD) for obtaining maximum yields on a cost-effective substrate, molasses. The GBS-producing bacterium was identified as Buttiauxella Species in terms of biochemical and molecular characteristics. This compound showed a desirable antimicrobial activity against some pathogens such as E. coli, Bacillus subtilis, Bacillus cereus, Candida albicans, Aspergilus niger, Salmonella enterica. The rheological studies described the stability of the GBS at high values in a range of pH (7-8), temperature (20-60) and salinity (0%-3%). The statistical optimization of GBS fermentation was found to be pH 7, temperature 33 °C, Peptone 1%, NaCl 1% and molasses 1%. The potency of the GBS as an effective antimicrobial agent provides evidence for its use against food and human pathogens. Moreover, favorable production of the GBS in the presence of molasses as a cheap substrate and the feasibility of pilot scale fermentation using an RSM method could expand its uses in food, pharmaceutical products and oil industries.

Bioremediation of Crude Oil Using Bacterium from the Coastal Sediments of Kish Island, Iran

BACKGROUND

Much of the environment is affected by petroleum contamination. It imposes serious health problems for humans as well as serious environmental impact. Bioremediation is an important consideration for removing environmental pollutants because, compared with other technologies, it incurrs lower costs and is environmentally compatible.

METHODS

Crude oil degrading bacteria were isolated using serial dilutions of a bacterial consortium. The Taguchi experimental design L16 (4(5)) was used to optimize the biodegradation process of crude oil by the isolated strain. This investigation applied the parameters of temperature, salinity, pH, NH4Cl and FeSO4.7H2O. Modeling the kinetics of crude oil biodegradation included five batch cultivation experiments (2.5 ml/L to 40 ml/L) using crude oil as a single limiting substrate.

RESULTS

Halomonas sp. MS1 was identified using identification tests. Maximum biodegradation efficiency was predicted to occur at pH=9, temperature=30 °C, salinity=2%, NH4Cl concentration=0.4 g/L and FeSO4.7H2O=0.04 g/L. After optimization, biodagradation was significantly (P<0.05) higher (i.e. 90.65%) than it results under the original conditions. Furthermore, growth kinetics modelling of bacteria in various concentrations of crude oil showed a positive correlation between increased concentration, up to 10 ml/L and bacterial growth, but this was not evident at higher concentrations (20-40 mL/L).

CONCLUSION

Overall, bacteria in surface sediment samples from Kish Island have been determined as having good potential for application in oil biodegradation. Optimum amounts of the studied factors were determined successfully by applying the Taguchi experimental design and the models of Teissier and Haldane are suggested as kinetic models to describe the batch crude oil degradation behavior of MS1.