Isolation and description of a stable carbazole-degrading microbial consortium consisting of Chryseobacterium sp. NCY and Achromobacter sp. NCW

Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges

The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.

Phenanthrene Degradation by Photosynthetic Bacterial Consortium Dominated by Fischerella sp

Microbial degradation of aromatic hydrocarbons is an emerging technology, and it is well recognized for its economic methods, efficiency, and safety; however, its exploration is still scarce and greater emphasis on cyanobacteria-bacterial mutualistic interactions is needed. We evaluated and characterized the phenanthrene biodegradation capacity of consortium dominated by Fischerella sp. under holoxenic conditions with aerobic heterotrophic bacteria and their molecular identification through 16S rRNA Illumina sequencing. Results indicated that our microbial consortium can degrade up to 92% of phenanthrene in five days. Bioinformatic analyses revealed that consortium was dominated by Fischerella sp., however different members of Nostocaceae and Weeksellaceae, as well as several other bacteria, such as Chryseobacterium, and Porphyrobacter, were found to be putatively involved in the biological degradation of phenanthrene. This work contributes to a better understanding of biodegradation of phenanthrene by cyanobacteria and identify the microbial diversity related.

Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

Salicylate or Phthalate: The Main Intermediates in the Bacterial Degradation of Naphthalene

Polycyclic aromatic hydrocarbons (PAHs) are widely presented in the environment and pose a serious environmental threat due to their toxicity. Among PAHs, naphthalene is the simplest compound. Nevertheless, due to its high toxicity and presence in the waste of chemical and oil processing industries, naphthalene is one of the most critical pollutants. Similar to other PAHs, naphthalene is released into the environment via the incomplete combustion of organic compounds, pyrolysis, oil spills, oil processing, household waste disposal, and use of fumigants and deodorants. One of the main ways to detoxify such compounds in the natural environment is through their microbial degradation. For the first time, the pathway of naphthalene degradation was investigated in pseudomonades. The salicylate was found to be a key intermediate. For some time, this pathway was considered the main, if not the only one, in the bacterial destruction of naphthalene. However, later, data emerged which indicated that gram-positive bacteria in the overwhelming majority of cases are not capable of the formation/destruction of salicylate. The obtained data made it possible to reveal that protocatechoate, phthalate, and cinnamic acids are predominant intermediates in the destruction of naphthalene by rhodococci. Pathways of naphthalene degradation, the key enzymes, and genetic regulation are the main subjects of the present review, representing an attempt to summarize the current knowledge about the mechanism of the microbial degradation of PAHs. Modern molecular methods are also discussed in the context of the development of “omics” approaches, namely genomic, metabolomic, and proteomic, used as tools for studying the mechanisms of microbial biodegradation. Lastly, a comprehensive understanding of the mechanisms of the formation of specific ecosystems is also provided.

Elucidation of substrate interaction effects in multicomponent systems containing 3-ring homocyclic and heterocyclic polynuclear aromatic hydrocarbons

Bacterial growth and degradation experiments were conducted on carbazole (CBZ), fluorene (FLU) and dibenzothiophene (DBT) individually and in various mixture combinations using an efficient polynuclear aromatic hydrocarbon (PAH) degrading bacterial strain, Pseudomonas aeruginosa RS1. In single component systems, bacterial growth on CBZ (specific growth rate, μ = 0.99 day^-1) was much higher compared to that on FLU (μ = 0.38 day^-1) and DBT (μ = 0.33 day^-1) and bacterial growth was inhibited in the presence of FLU and DBT in binary (μ = 0.64 day^-1) and ternary (μ = 0.75 day^-1) mixtures. Multisubstrate additive modelling indicated growth inhibition in all the systems. The degradation of the compounds was significantly inhibited in binary mixtures. While the degradation of the compounds in binary mixtures varied from 35 ± 4% to 73 ± 3%, their degradation varied from 61 ± 5% to 91 ± 4%, when applied as sole substrates and from 77 ± 3% to 96 ± 3%, when applied in a ternary mixture. Degradation experiments were also conducted in ternary mixtures using a 2³ full factorial design and the results were examined using analysis of variance (ANOVA) and Tukey's honest significant difference (HSD) tests. At a low concentration of the heterocyclics, CBZ and DBT (5 mg L^-1 each), the degradation of the PAH, FLU, was significantly enhanced (from 81 ± 1% to 93 ± 0.3%) when its concentration was increased from 5 to 30 mg L^-1. The full factorial design can provide valuable insights into substrate interaction effects in mixtures.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.

Facilitated bio-mineralization of N,N-dimethylformamide in anoxic denitrification system: Long-term performance and biological mechanism

Due to highly recalcitrant and toxicological nature of N,N-dimethylformamide (DMF), efficient removal of DMF is challenging for biological wastewater treatment. In this study, an anoxic denitrification system was developed and continuously operated for 220 days in order to verify the enhanced DMF biodegradation mechanism. As high as 41.05 mM DMF could be thoroughly removed in the anoxic denitrification reactor at hydraulic residence time (HRT) of 24 h, while the total organic carbon (TOC) and nitrate removal efficiencies were as high as 95.7 ± 2.5% and 98.4 ± 1.1%, respectively. Microbial community analyses indicated that the species related to DMF hydrolysis (Paracoccus, Brevundimonas and Chryseobacterium) and denitrification (Paracoccus, Arenimonas, Hyphomicrobium, Aquamicrobium and Bosea) were effectively enriched in the anoxic denitrification system. Transcriptional analysis coupled with enzymatic activity assay indicated that both hydrolysis and mineralization of DMF were largely enhanced in the anoxic denitrification system. Moreover, the occurrence of microbial denitrification distinctly facilitated carbon source utilization to produce electron and energy, which was rather beneficial for better reactor performance. This study demonstrated that the anoxic denitrification system would be a potential alternative for efficient treatment of wastewater polluted by recalcitrant pollutants such as DMF.

Impact of necrophytoremediation on petroleum hydrocarbon degradation, ecotoxicity and soil bacterial community composition in diesel-contaminated soil

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degradation, toxicity and the associated bacterial community structure and composition in diesel-contaminated soil. A significant reduction in total petroleum hydrocarbon (TPH) concentration was detected in both treatments; however, PS-treated soil showed more rapid degradation (87%) after 5 months together with a significant reduction in soil toxicity (EC50 = 91 mg diesel/kg). Quantitative PCR analysis revealed an increase in the number of 16S rRNA and alkB genes in the PS-amended soil. Substantial shifts in soil bacterial community were observed during the bioremediation, including an increased abundance of numerous hydrocarbon-degrading bacteria. The bacterial community shifted from dominance by Alphaproteobacteria and Gammaproteobacteria in the original soil to Actinobacteria during bioremediation. The dominance of two genera of bacteria, Sphingobacteria and Betaproteobacteria, in both NA- and PS-treated soil demonstrated changes occurring within the soil bacterial community through the incubation period. Additionally, pea straw itself was found to harbour a diverse hydrocarbonoclastic community including Luteimonas, Achromobacter, Sphingomonas, Rhodococcus and Microbacterium. At the end of the experiment, PS-amended soil exhibited reduced ecotoxicity and increased bacterial diversity as compared with the NA-treated soil. These findings suggest the rapid growth of species stimulated by the bioremediation treatment and strong selection for bacteria capable of degrading petroleum hydrocarbons during necrophytoremediation. Graphical abstract.

Efficient elimination of sulfadiazine in an anaerobic denitrifying circumstance: Biodegradation characteristics, biotoxicity removal and microbial community analysis

Sulfadiazine (SDZ) is widely used in clinical treatment, livestock husbandry and aquaculture as an antibacterial agent, resulting in environmental risks. In this work, batch experiments were conducted to investigate the characteristics of SDZ biodegradation and reaction mechanisms in a nitrate anaerobic denitrifying system for the first time. The results showed that 98.52% of the SDZ, which had an initial concentration of 50 mg L^-1, was degraded after 70 h, indicating that the removal efficiency of SDZ in anaerobic denitrifying system was 55.27% higher than that in anaerobic system. Furthermore, LC-MS-MS analysis confirmed that SDZ could be degraded into 16 byproducts via 3 main degradation pathways that contained 6 different reactions. After analyzing the microbial communities of the reactor, the denitrifying bacteria and desulfurizing bacteria Desulforhabdus, Ignavibacterium, SBR1031_norank, Nocardioides, etc. were highly associated with the removal of SDZ in the system. The biological toxicity test of the effluent indicated that the remaining organic matter and inorganic matter of the effluent could provide nutrients for E. coli and promote its growth. In other words, anaerobic denitrifying systems are highly efficient, simple and environmentally friendly, and have an impressive prospect in the biodegradation of sulfonamide antibiotics.

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.

Isolation of aluminum-tolerant bacteria capable of nitrogen removal in activated sludge

Four strains of bacteria capable of withstanding 20mM concentration of aluminum were isolated from activated sludge in a bioreactor. 16S rRNA identification and morphological characteristics indicated that these strains were Chryseobacterium sp. B1, Brevundimonas diminuta B3, Hydrogenophaga sp. B4, and Bacillus cereus B5. Phylogenetic analysis revealed the position and interrelationships of these bacteria. B. diminuta B3 and Hydrogenophaga sp. B4 could achieve nitrate nitrogen removal of 94.0% and 76.8% within 36h of its initial concentration of 148.8 and 151.7mg/L, respectively. Meanwhile, B3 and B4 could degrade ammonia with little nitrite accumulation. Results of this study provide more information about aluminum-resistant bacteria and laid the foundation for aluminum salt when it is simultaneously used for chemical precipitation.

Biotic inactivation of the Pseudomonas aeruginosa quinolone signal molecule

In Pseudomonas aeruginosa, quorum sensing (QS) regulates the production of secondary metabolites, many of which are antimicrobials that impact on polymicrobial community composition. Consequently, quenching QS modulates the environmental impact of P. aeruginosa. To identify bacteria capable of inactivating the QS signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), a minimal medium containing PQS as the sole carbon source was used to enrich a Malaysian rainforest soil sample. This yielded an Achromobacter xylosoxidans strain (Q19) that inactivated PQS, yielding a new fluorescent compound (I-PQS) confirmed as PQS-derived using deuterated PQS. The I-PQS structure was elucidated using mass spectrometry and nuclear magnetic resonance spectroscopy as 2-heptyl-2-hydroxy-1,2-dihydroquinoline-3,4-dione (HHQD). Achromobacter xylosoxidans Q19 oxidized PQS congeners with alkyl chains ranging from C1 to C5 and also N-methyl PQS, yielding the corresponding 2-hydroxy-1,2-dihydroquinoline-3,4-diones, but was unable to inactivate the PQS precursor HHQ. This indicates that the hydroxyl group at position 3 in PQS is essential and that A. xylosoxidans inactivates PQS via a pathway involving the incorporation of oxygen at C2 of the heterocyclic ring. The conversion of PQS to HHQD also occurred on incubation with 12/17 A. xylosoxidans strains recovered from cystic fibrosis patients, with P. aeruginosa and with Arthrobacter, suggesting that formation of hydroxylated PQS may be a common mechanism of inactivation.

Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya Bay, southern China

Microorganisms play an important role in the biodegradation of petroleum contaminants, which have attracted great concern due to their persistent toxicity and difficult biodegradation. In this paper, a novel hydrocarbon-degrading bacterium HZ01 was isolated from the crude oil-contaminated seawater at the Daya Bay, South China Sea, and identified as Achromobacter sp. Under the conditions of pH 7.0, NaCl 3% (w/v), temperature 28 °C and rotary speed 150 rpm, its degradability of the total n-alkanes reached up to 96.6% after 10 days of incubation for the evaporated diesel oil. Furthermore, Achromobacter sp. HZ01 could effectively utilize polycyclic aromatic hydrocarbons (PAHs) as its sole carbon source, and could remove anthracene, phenanthrene and pyrence about 29.8%, 50.6% and 38.4% respectively after 30 days of incubation. Therefore, Achromobacter sp. HZ01 may employed as an excellent degrader to develop one cost-effective and eco-friendly method for the bioremediation of marine environments polluted by crude oil.

Technoeconomic assessment of phenanthrene degradation by Pseudomonas stutzeri CECT 930 in a batch bioreactor

Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent pollutants that accumulate in natural environment mainly as a result of anthropogenic activities. Therefore, the improvement of the available bank of microbial resources and information is crucial to the proper management of PAHs-polluted sites and effluents. In this work, Pseudomonas stutzeri CECT 930 was selected for aerobically degrading an aqueous effluent containing phenanthrene (PHE). Maximum PHE degradation of 90% was obtained both at flask and stirred tank bioreactor scale. All the experimental data were fitted to logistic and Luedeking and Piret models, and licensed to quantitatively ascertain a stronger dependence on the biomass of the metabolites triggering the bioremediation process. In addition, PHE degradation via protocatechuate pathway was elucidated through GC-MS data. Finally, based on the promising results of biodegradation, a preliminary economic evaluation of this process at industrial scale was approached by means of simulation data obtained with SuperPro Designer.

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

Toxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0-500 mg kg(-1)) followed by dose-response and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC(50) values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC(50) concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.

Bacterial degradation of aromatic compounds

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.