Biodegradation of Dibenzofuran by Janibacter terrae Strain XJ-1

Environmental persistence assessment of heterocyclic polyaromatic hydrocarbons - Ultimate and primary biodegradability using adapted and non-adapted microbial communities

Heterocyclic polyaromatic hydrocarbons (heterocyclic PAHs) are of increasing concern and their environmental and human health impacts should be assessed due to their widespread presence and potential persistence in the environment. This study investigated the ultimate and primary biodegradability of ten heterocyclic PAHs, nine of which were found to be non-readily biodegradable. To generate a microbial community capable of degrading such compounds, a bacterial inoculum isolated from the effluent of a wastewater treatment plant (WWTP) was adapted to a mixture of heterocyclic PAHs for one year. Throughout the adaptation process, bacterial samples were collected at different stages to conduct primary biodegradation, ultimate biodegradation, and inoculum toxicity tests. Interestingly, after one year of adaptation, the community developed the ability to mineralize carbazole, but in the same time showed an increasing sensitivity to the toxic effects of benzo[c]carbazole. In two consecutive primary biodegradation experiments, degradation of four heterocycles was observed, while no biodegradation was detected for five compounds in any of the tests. Furthermore, the findings of this work were compared with predictions from in silico models regarding biodegradation timeframe and sorption, and it was found that the models were partially successful in describing these processes. The results of study provide valuable insights into the persistence of a representative group of heterocyclic PAHs in aquatic environments, which contributes to the hazard assessment of this particular class of substances.

Investigation on Metabolites in Structure and Biosynthesis from the Deep-Sea Sediment-Derived Actinomycete Janibacter sp. SCSIO 52865

For exploring structurally diverse metabolites and uniquely metabolic mechanisms, we systematically investigated the chemical constituents and putative biosynthesis of Janibacter sp. SCSIO 52865 derived from the deep-sea sediment based on the OSMAC strategy, molecular networking tool, in combination with bioinformatic analysis. As a result, one new diketopiperazine (1), along with seven known cyclodipeptides (2-8), trans-cinnamic acid (9), N-phenethylacetamide (10) and five fatty acids (11-15), was isolated from the ethyl acetate extract of SCSIO 52865. Their structures were elucidated by a combination of comprehensive spectroscopic analyses, Marfey's method and GC-MS analysis. Furthermore, the analysis of molecular networking revealed the presence of cyclodipeptides, and compound 1 was produced only under mBHI fermentation condition. Moreover, bioinformatic analysis suggested that compound 1 was closely related to four genes, namely jatA-D, encoding core non-ribosomal peptide synthetase and acetyltransferase.

Short-Term Biodegradation of Crude Petroleum Oil in Water by Photostimulated Janibacter terrae Strain S1N1

Biodegradation is a sustainable green strategy that gives the opportunity for remediation of water contaminated with petroleum products. In this study, 12 bacterial isolates were recovered from River Nile, Egypt and screened for their potential to degrade a mixture of paraffinic petroleum crude oil. The most promising isolate was identified according to 16S rRNA sequencing as Janibacter terrae strain S1N1 (GenBank accession No. KX570955.1). In order to boost the biodegradation efficiency, the bacterial suspension was photostimulated by exposure to different irradiation doses using a low-power helium-neon (He-Ne) laser (λ = 632.8 nm). Maximum biodegradation was achieved after 4 min of exposure (134.07 J cm^-2) at optimized pH value (6) and temperature (35 °C). The gas chromatography-mass spectrometry (GC-MS) analysis revealed the biodegradation of 96.5% of the substrate after only 48 h of incubation. The n-C₁₇/Pr and n-C₁₈/Ph ratios indicated a preferential biodegradation of iso-paraffines over normal ones. Meanwhile, pristane/phytane (Pr/Ph) ratios were indicative of selective biodegradation for pristane. The carbon preference index (CPI) was nearly around unity indicating the ability of Janibacter terrae to attack the odd and even n-alkanes simultaneously. These results support the superiority of irradiated bacteria in optimizing the biodegradation efficiency and shortening the time of treatment, thus proposing an eco-friendly technique in water bioremediation programs.

Janibacter endophyticus sp. nov., an Endophytic Actinobacterium Isolated from the Root of Paris polyphylla Smith var. Yunnanensis

A novel endophytic actinobacterium, designated as strain YIM B02568^T, was isolated from the root of Paris polyphylla Smith var. Yunnanensis obtained from Yunnan Province, southwest China. Strain YIM B02568^T was characterized using a polyphasic approach. Phylogenetic analysis indicated that this isolate belonged to the genus Janibacter. The 16S rRNA gene sequence similarity values of strain YIM B02568^T to the type strains of members of this genus ranged from 95.8 to 98.6%. However, overall genome relatedness indices were significantly lower than the widely accepted species-defined threshold. The cell wall of strain YIM B02568^T contained meso-diaminopimelic acid. The major menaquinone was MK-8(H₄). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The major cellular fatty acids were comprised of iso-C_16:0 and C_18:1 ω9c. The DNA G + C content was 71.6 mol%. Based on the data from the polyphasic studies, we propose that strain YIM B02568^T represents a novel species within the genus Janibacter, Janibacter endophyticus sp. nov. The type strain is YIM B02568^T (= JCM 34639^T = CGMCC 1.18658^T).

Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment

Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.

Cloning, expression and characterization of catechol 1,2-dioxygenase from Burkholderia cepacia

The present study reports on the cloning, expression and characterization of catechol 1,2-dioxygenase (CAT) of bacterial strains isolated from dioxin-contaminated soils in Vietnam. Two isolated bacterial strains DF2 and DF4 were identified as Burkholderia cepacia based on their 16S rRNA sequences. Their genes coding CAT was amplified with a specific pair of primers. Recombinant CAT (rCAT) was expressed in E. coli M15 cells and its activity was confirmed by the detection of cis,cis-muconic acid, a product from catechol, by high-performance liquid chromatography (HPLC) analysis. The rCAT of DF4 had an optimal pH and temperature of 7 and 30°C, respectively. Metal ions, such as Zn²⁺ and Mn²⁺, and surfactants, such as SDS, Tween 20 and Triton X100, strongly inhibited enzyme activity, while K⁺ slightly increased the activity.

Complete Genome Sequence of Janibacter melonis M714, a Janus-Faced Bacterium with Both Human Health Impact and Industrial Applications

Janibacter, a member of the Intrasporangiaceae family of Actinobacteria, is a Janus-faced bacterium that has both antibiotic resistance/pathogenicity and the ability to degrade pollutants, with significant research value. Here, we isolated the novel strain Janibacter melonis M714 from an irradiated area in Xinjiang Uygur Autonomous Region, China. J. melonis M714 contains one circular chromosome of 3,426,637 bp with a GC content of 72.98% and one plasmid of 54,436 bp with a GC content of 67.80%. The genome of J. melonis M714 contains 2,859 CDSs, 47 tRNA genes, and 6 rRNA genes. Genome assembly and annotation indicated that strain M714 has a high GC content and contains multiple notable functional genes, including a beta-lactam resistance gene and dioxygenase gene, which may be the key determinants of the strain's antibiotic resistance and xenobiotic degradation ability, respectively. The whole genome sequences of J. melonis M714 provide information that is useful for its potential applications in the degradation of pollutants and environmental remediation.

Aerobic degradation of dichlorinated dibenzo-p-dioxin and dichlorinated dibenzofuran by bacteria strains obtained from tropical contaminated soil

Bacterial diversity and aerobic catabolic competence of dioxin-degrading bacterial strains isolated from a polluted soil in the tropics were explored. Isolation of bacteria occurred after 12 months of consecutive enrichment, with dioxin congeners serving as the only sources of carbon and energy. Seventeen strains that were isolated were subsequently screened for dioxin metabolic competence. Among these isolates, five had unique amplified ribosomal DNA restriction analysis (ARDRA) patterns out of which two exhibiting good metabolic competence were selected for further investigation. The two strains were identified as Bacillus sp. SS2 and Serratia sp. SSA1, based on their 16S rRNA gene sequences. Bacterial growth co-occurred with dioxin disappearance and near stoichiometric release of chloride for one ring of the chlorinated congeners. The overall percentage removal of dibenzofuran (DF) by strain SS2 was 93.87%; while corresponding values for 2,8-dichlorodibenzofuran (2,8-diCDF) and 2,7-dichlorodibenzo-p-dioxin (2,7-diCDD) were 86.22% and 82.30% respectively. In the case of strain SSA1, percentage removal for DF, 2,8-diCDF and 2,7-diCDD were respectively 98.9%, 80.97% and 70.80%. The presence of two dioxin dioxygenase catabolic genes (dxnA1 and dbfA1) was investigated. Only the dbfA1 gene could be amplified in SS2 strain. Results further revealed that strain SS2 presented higher expression levels for the alpha-subunit of DF dioxygenase (dbfA1) gene during growth with dioxins. The expression level for dbfA1 gene was higher when growing on DF than on the other chlorinated analogs. This study gives an insight into dioxin degradation, with the catabolic potential of strains SS2 and SSA1 (an enteric bacterium) within the sub-Sahara Africa. It further shows that dioxin catabolic potential might be more prevalent in different groups of microorganisms than previously believed. Few reports have demonstrated the degradation of chlorinated congeners of dioxins, particularly from sub-Saharan African contaminated systems.

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.

Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process

Pentachlorophenol (PCP) is a toxic and persistent wood and cellulose preservative extensively used in the past decades. The production process of PCP generates polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) as micropollutants. PCDD/Fs are also known to be very persistent and dangerous for human health and ecosystem functioning. Several physico-chemical and biological technologies have been used to remove PCP and PCDD/Fs from the environment. Bacterial degradation appears to be a cost-effective way of removing these contaminants from soil while causing little impact on the environment. Several bacteria that cometabolize or use these pollutants as their sole source of carbon have been isolated and characterized. This review summarizes current knowledge on the metabolic pathways of bacterial degradation of PCP and PCDD/Fs. PCP can be successfully degraded aerobically or anaerobically by bacteria. Highly chlorinated PCDD/Fs are more likely to be reductively dechlorinated, while less chlorinated PCDD/Fs are more prone to aerobic degradation. The biochemical and genetic basis of these pollutants’ degradation is also described. There are several documented studies of effective applications of bioremediation techniques for the removal of PCP and PCDD/Fs from soil and sediments. These findings suggest that biodegradation can occur and be applied to treat these contaminants.

Pentachlorophenol degradation by Janibacter sp., a new actinobacterium isolated from saline sediment of arid land

Many pentachlorophenol- (PCP-) contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, and high salt concentrations. PCP-degrading microorganisms, adapted to grow and prosper in these environments, play an important role in the biological treatment of polluted extreme habitats. A PCP-degrading bacterium was isolated and characterized from arid and saline soil in southern Tunisia and was enriched in mineral salts medium supplemented with PCP as source of carbon and energy. Based on 16S rRNA coding gene sequence analysis, the strain FAS23 was identified as Janibacter sp. As revealed by high performance liquid chromatography (HPLC) analysis, FAS23 strain was found to be efficient for PCP removal in the presence of 1% of glucose. The conditions of growth and PCP removal by FAS23 strain were found to be optimal in neutral pH and at a temperature of 30 °C. Moreover, this strain was found to be halotolerant at a range of 1-10% of NaCl and able to degrade PCP at a concentration up to 300 mg/L, while the addition of nonionic surfactant (Tween 80) enhanced the PCP removal capacity.

Isolation and characterization of a newly isolated polycyclic aromatic hydrocarbons-degrading Janibacter anophelis strain JY11

The PAHs-degradation bacterium strain JY11 was newly isolated from the polluted soil in Jinan Oil Refinery Factory, Shandong Province of China. The isolate was identified as Janibacter anophelis with respect to its 16S rDNA sequence, DNA-DNA relatedness and fatty acid profiles, as well as various physiological characteristics. The strain was Gram-positive, non-motile, non-spore-forming, short rods in young culture, 0.8-1.0 microm in diameter and 1.3-1.6 microm long, and coccoid cells in the stationary phase of growth that are 1.0-1.2 microm in diameter and 1.3-1.5 microm long, occurred in pairs and sometimes in chains or in group, aerobic, oxidase-week positive, catalase-positive. J. anophelis strain JY11 can utilize naphthalene, phenanthrene, anthracene, pyrene, xylene, methanol, ethanol and salicylic acid as sole carbon source. The strain could remove 98.5% of phenanthrene, 82.1% of anthracene, and 97.7% of pyrene with an initial concentration of 500 ppm in five days without adding co-metabolism substrates and surfactants.

Crystal structure and mutagenic analysis of GDOsp, a gentisate 1,2-dioxygenase from Silicibacter pomeroyi

Dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. Here we report the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) at a 2.8 A resolution. The enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. However, each subunit of GDOsp unusually contained two ferrous centers that were located in its two homologous cupin domains, respectively. Further mutagenic analysis indicated that the enzyme activity of GDOsp depends on the microenvironment in both metal-binding sites. Moreover, homologous structural comparison and functional study on GDOsp variants unveiled a group of functionally essential residues and suggested that the active site of the enzyme is located in the amino-terminal domain, but could be influenced by changes in the carboxyl domain. Therefore, GDOsp may provide a working model for studying long-distance communication within a protein (or its complex).

Characterization of diverse Acinetobacter isolates for utilization of multiple aromatic compounds

This study demonstrates the multiple catabolic capacities of lab isolates belonging to the genus Acinetobacter. Thirty-one Acinetobacter strains were screened initially for their capacity to utilize ten substrates that includes monocyclic, heterocyclic and polycyclic aromatic compounds. These bacteria were isolated from activated biomass of different effluent treatment plants (ETPs) treating wastewater generated at different industries and selected based on partial sequence data of the 16S rRNA gene. Of these 31 isolates, preliminary plate assay results showed eleven isolates that could utilize multiple substrates. Analytical studies demonstrated multiple degradation of hydrocarbons dibenzothiophene, fluorene, dibenzofuran, benzyl sulfide, and sodium benzoate by two isolates, HPC311 and HPC159.

Two angular dioxygenases contribute to the metabolic versatility of dibenzofuran-degrading Rhodococcus sp. strain HA01

Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% +/- 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.

Isolation and characterization of dibenzofuran-degrading Serratia marcescens from alkalophilic bacterial consortium of the chemostat

Alkalophilic bacterial consortium developed by continuous enrichment in the chemostat in presence of 4-chlorosalicylic acid as sole source of carbon and energy contained six bacterial strains, Micrococcus luteus (csa101), Deinococcus radiothilus (csa102), csa103 (Burkholderia gladioli), Alloiococcus otilis (csa104), Micrococcus diversus (csa105), Micrococcus luteus (csa106), identified by the Biolog test method. The strains were tested for utilization of organic compounds in which one of the strains (csa101) had higher potency to utilize dibenzofuran (DF) as sole carbon and energy source identified as Serratia marcescens on the basis of 16S rDNA. The degradation of DF by bacterial strain proceeded through an oxidative route as indicated by 2,2'3-trihydroxybiphenyl, 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid, salicylic acid, and catechol, which was identified by gas chromatography-mass spectrometry.