Degradation of chlorinated biphenyl, dibenzofuran, and dibenzo-p-dioxin by marine bacteria that degrade biphenyl, carbazole, or dibenzofuran

Environmental contamination by heterocyclic Polynuclear aromatic hydrocarbons and their microbial degradation

Heterocyclic polynuclear aromatic hydrocarbons (PAHs) have been detected in all environmental matrices at few ppb to several ppm concentrations and they are characterized by high polarity. Some heterocyclic PAHs are mutagenic and carcinogenic to humans and various organisms. Despite being potent environmental pollutants, these compounds have received less attention. This paper focuses on the sources and occurrence of these compounds and their microbial degradation using diverse species of bacteria, fungi, and algae. Complete removal of 1.8 to 2614 mg/L of nitrogen heterocyclic PAH (PANH), 0.27 to 184 mg/L of sulfur heterocyclic PAH (PASH), and 0.6 to 120 mg/L of oxygen heterocyclic PAH (PAOH) compounds by various microbial species was observed between 3 h and 18 days, 8 h to 6 days, and 4 h to 250 h, respectively under aerobic condition. Strategies for enhancing the removal of heterocyclic PAHs from aquatic systems are also discussed along with the challenges.

Aerobic bacterial transformation and biodegradation of dioxins: a review

Waste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.

Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials

Biodiversity has been explored in the search for novel enzymes, including forests, savannas, tundras, deserts, and finally the sea. Marine microorganisms and their enzymes are capable of being active in high-salt concentration, large range of temperature, and high incidence of light and pressure, constituting an important source of unique biocatalysts. This review presents studies employing whole-cell processes of marine bacteria and fungi, aiming for new catalysts for different reactions in organic synthesis, such as reduction, oxidation, hydroxylation, hydrolysis, elimination, and conjugation. Genomics and protein engineering studies were also approached, and reactions employing isolated enzymes from different classes (oxidoreductases, hydrolases, lyases, and ligases) were described and summarized. Future biotechnological studies and process development should focus on molecular biology for the obtention of enzymes with interesting, fascinating and enhanced properties, starting from the exploration of microorganisms from the marine environment. This review approaches the literature about the use of marine-derived bacteria, fungi, and their enzymes for biocatalytic reactions of organic compounds, promoting a discussion about the possibilities of these microorganisms in the synthesis of different substances.

Aerobic cometabolism of tetrabromobisphenol A by marine bacterial consortia

The coastal environments worldwide are subjected to increasing TBBPA contamination, but current knowledge on aerobic biodegradability of this compound by marine microbes is lacking. The aerobic removal of TBBPA using marine consortia under eight different cometabolic conditions was investigated here. Results showed that the composition and diversity of the TBBPA-degrading consortia had diverged after 120-day incubation. Pseudoalteromonas, Alteromonas, Glaciecola, Thalassomonas, and Limnobacter were the dominant genera in enrichment cultures. Furthermore, a combination of beef extract- and peptone-enriched marine consortia exhibited higher TBBPA removal efficiency (approximately 60%) than the other substrate amendments. Additionally, Alteromonas macleodii strain GCW was isolated from a culture of TBBPA-degrading consortium. This strain exhibited about 90% of degradation efficiency toward TBBPA (10 mg L^-1) after 10 days of incubation under aerobic cometabolic conditions. The intermediates in the degradation of TBBPA by A. macleodii strain GCW were analyzed and the degradation pathways were proposed, involving β-scission, debromination, and nitration routes.

Properties, environmental fate and biodegradation of carbazole

The last two decades had witnessed extensive investigation on bacterial degradation of carbazole, an N-heterocyclic aromatic hydrocarbon. Specifically, previous studies have reported the primary importance of angular dioxygenation, a novel type of oxygenation reaction, which facilitates mineralization of carbazole to intermediates of the TCA cycle. Proteobacteria and Actinobacteria are the predominant bacterial phyla implicated in this novel mode of dioxygenation, while anthranilic acid and catechol are the signature metabolites. Several studies have elucidated the degradative genes involved, the diversity of the car gene clusters and the unique organization of the car gene clusters in marine carbazole degraders. However, there is paucity of information regarding the environmental fate as well as industrial and medical importance of carbazole and its derivatives. In this review, attempt is made to harness this information to present a comprehensive outlook that not only focuses on carbazole biodegradation pathways, but also on its environmental fate as well as medical and industrial importance of carbazole and its derivatives.

Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11

Metabolic pathway of biphenyl assimilation and the catabolic gene expression in a marine bacterium Pseudomonas aeruginosa JP-11, isolated from the coastal sediments of Odisha, India have been studied. This strain utilized 98.86% ± 2.29% of biphenyl within 72 h when supplied as the sole source of carbon, however, preferential utilization of glucose was observed over catechol and biphenyl when grown in a complex medium. Combination of chromatographic and spectrophotometric techniques confirmed the catechol pathway and identified 2-Hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate as the intermediate metabolic product. Assimilation of biphenyl was initiated by its dioxygenation, forming cis-2, 3-dihydro-2, 3-dihydroxybiphenyl subsequently transformed to 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate. In the lower pathway, cis-1, 6-dihydroxy-2, 4-cyclohexadiene-1-carboxylic acid was detected which formed catechol before entering into the Krebs cycle. Detection of key enzyme catechol-1, 2-dioxygenase in the cell-free extract of P. aeruginosa JP-11 supported the proposed degradation pathway. The primary enzyme for biphenyl assimilation, biphenyl dioxygenase encoded by bphA gene was found in the genome of the isolate. On increasing biphenyl stress (50, 100, 150 and 200 mg L(-1)), bphA gene showed a significant (P < 0.01) up-regulation upto 43.5 folds. Production of biosurfactant was confirmed and the rhamnolipid synthesizing gene rhlAB was amplified. This gene also showed a significant (P < 0.01) up-regulation upto 258 folds on increasing biphenyl stress.

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised) method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature's related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification.

Short-term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution

The changes caused by diesel oil pollution in the metabolically active bacterioplankton from an oligotrophic coastal location were analysed in laboratory microcosms (44 l) using 16S ribosomal RNA (16S rRNA) as molecular marker. The aim was to simulate typical hydrocarbon pollution events in a coastal area exploited for seasonal touristic activities. The experiment consisted in addition of low amounts of diesel oil without nutrients to seawater collected at different times (winter and summer). Bacterial diversity was analysed by terminal‐restriction fragment length polymorphism (T‐RFLP) profiling of 16S rRNAs after reverse transcription polymerase chain reaction (RT‐PCR), and by generation of 16S rRNA clone libraries in control and diesel‐polluted microcosms. Diesel addition caused a twofold increase in prokaryotic numbers in comparison with controls at the end of the experiment, both in winter and summer microcosms. Bacterioplankton composition, determined by 16S rRNA T‐RFLP data, changed rapidly (within 17 h) in response to treatment. The resulting communities were different in microcosms with water collected in summer and winter. A reduction in diversity (Shannon index, calculated on the basis of T‐RFLP data) was observed only in summer microcosms. This was due to the rapid increase of phylotypes affiliated to the Oceanospirillaceae, not observed in winter microcosms. After diesel treatment there was a reduction in the number of phylotypes related to SAR11, SAR86 and picocyanobacteria, while phylotypes of the Roseobacter clade, and the OMG group seemed to be favoured. Our results show that diesel pollution alone caused profound effects on the bacterioplankton of oligotrophic seawater, and explained many of the differences in diversity reported previously in pristine and polluted sites in this coastal area.

Cloning and nucleotide sequences of carbazole degradation genes from marine bacterium Neptuniibacter sp. strain CAR-SF

The marine bacterium Neptuniibacter sp. strain CAR-SF utilizes carbazole as its sole carbon and nitrogen sources. Two sets of clustered genes related to carbazole degradation, the upper and lower pathways, were obtained. The marine bacterium genes responsible for the upper carbazole degradation pathway, carAa, carBa, carBb, and carC, encode the terminal oxygenase component of carbazole 1,9a-dioxygenase, the small and large subunits of the meta-cleavage enzyme, and the meta-cleavage compound hydrolase, respectively. The genes involved in the lower degradation pathway encode the anthranilate dioxygenase large and small subunit AntA and AntB, anthranilate dioxygenase reductase AntC, 4-oxalocrotonate tautomerase, and catechol 2,3-dioxygenase. Reverse transcription-polymerase chain reaction confirmed the involvement of the isolated genes in carbazole degradation. Escherichia coli cells transformed with the CarAa of strain CAR-SF required ferredoxin and ferredoxin reductase for biotransformation of carbazole. Although carAc, which encodes the ferredoxin component of carbazole 1,9a-dioxygenase, was not found immediately downstream of carAaBaBbC, the carAc-like gene may be located elsewhere based on Southern hybridization. This is the first report of genes involved in carbazole degradation isolated from a marine bacterium.

Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations

The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity.

Novel marine carbazole-degrading bacteria

Eleven carbazole (CAR)-degrading bacterial strains were isolated from seawater collected off the coast of Japan using two different media. Seven isolates were shown to be most closely related to the genera Erythrobacter, Hyphomonas, Sphingosinicella, Caulobacter, and Lysobacter. Meanwhile, strains OC3, OC6S, OC9, and OC11S showed low similarity to known bacteria, the closest relative being Kordiimonas gwangyangensis GW14-5 (90% similarity). Southern hybridization analysis revealed that only five isolates carried car genes similar to those reported in Pseudomonas resinovorans CA10 (car(CA10)) or Sphingomonas sp. strain KA1 (car(KA1)). The isolates were subjected to GC-MS and the results indicated that these strains degrade CAR to anthranilic acid.

Obligate oil-degrading marine bacteria

Over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (OHCB) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)--which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temperature, salinity, redox and other prevailing physical-chemical factors. These blooms result in the rapid degradation of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic analysis of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecological success. These and other studies have revealed the potential of OHCB for multiple biotechnological applications that include not only oil pollution mitigation, but also biopolymer production and biocatalysis.

Microbial degradation of sulfur, nitrogen and oxygen heterocycles

Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.

Biodegradation of Dibenzofuran by Janibacter terrae Strain XJ-1

The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L(-1) DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.

Diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel gram-positive carbazole-degrading bacterium

Twenty-seven carbazole-utilizing bacterial strains were isolated from environmental samples, and were classified into 14 groups by amplified ribosomal DNA restriction analysis. Southern hybridization analyses showed that 3 and 17 isolates possessed the car gene homologs of Pseudomonas resinovorans CA10 and Sphingomonas sp. strain KA1, respectively. Of the 17 isolates, 2 isolates also have the homolog of the carAa gene of Sphingomonas sp. strain CB3. While the genome of one isolate, a Gram-positive Nocardioides sp. strain IC177, showed no hybridization to any car gene probes, PCR and sequence analyses indicated that strain IC177 had tandemly linked carAa and carC gene homologs whose deduced amino acid sequences showed 51% and 36% identities with those of strain KA1.

Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying thedbfA1A2gene homologues isolated from activated sludge

Thirteen dibenzofuran (DF)-utilizing bacteria carrying the DF terminal dioxygenase genes homologous to those of Terrabacter sp. strain DBF63 (dbfA1A2) were newly isolated from activated sludge samples. The amplified ribosomal DNA restriction analysis and the hybridization analyses showed that these strains were grouped into five genetically different types of bacteria. The sequence analyses of the 16S rRNA genes and the dbfA1A2 homologues from these five selected isolates revealed that the isolates belonged to the genus Rhodococcus, Terrabacter or Janibacter and that they shared 99-100% conserved dbfA1A2 homologues. We investigated the genetic organizations flanking the dbfA1A2 homologues and showed that the minimal conserved DNA region present in all five selected isolates consisted of an approximately 9.0-kb region and that their outer regions became abruptly non-homologous. Among them, Rhodococcus sp. strain DFA3 possessed not only the 9.0-kb region but also the 6.2-kb region containing dbfA1A2 homologues. Sequencing of their border regions suggested that some genetic rearrangement might have occurred with insertion sequence-like elements. Also, within their conserved regions, some insertions or deletions were observed.