Isolation and characteristics of a novel biphenyl-degrading bacterial strain, Dyella ginsengisoli LA-4

doi:10.1016/S1001-0742(08)62253-6

Journal of Environmental Sciences

Volume 21, Issue 2, 2009, Pages 211-217

https://doi.org/10.1016/S1001-0742(08)62253-6 Get rights and content

Abstract

A novel biphenyl-degrading bacterial strain LA-4 was isolated from activated sludge. It was identified as Dyella ginsengisoli according to phylogenetic similarity of 16S rRNA gene sequence. This isolate could utilize biphenyl as sole source of carbon and energy, which degraded over 95 mg/L biphenyl within 36 h. The major metabolites formed from biphenyl, such as 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and benzoic acid, were identified by LC-MS. The crude cell extract of strain LA-4 exhibited the activity of 2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD) and the kinetic parameters K_m was 26.48 μmol/L and V_max was 8.12 U/mg protein. A conserved region of the biphenyl dioxygenase gene bphA1 of strain LA-4 was amplified by PCR and confirmed by DNA sequencing.

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Biodegradation of expanded polystyrene and low-density polyethylene foams in larvae of Tenebrio molitor Linnaeus (Coleoptera: Tenebrionidae): Broad versus limited extent depolymerization and microbe-dependence versus independence
2021, Chemosphere
Citation Excerpt :
Dyella sp. increased in the larvae fed with PS (Fig. 5 B). Dyella ginsengisoli strain LA-4 was isolated from the activated sludge, which can utilize biphenyl as the sole source of carbon and energy, which degrades over 95 mg/L of biphenyl in 36 h (Li et al., 2009). Dyella sp. may involve in degradation of PS intermediates in T. molitor.
Yellow mealworms (Tenebrio molitor larvae) are capable of biodegrading polystyrene (PS) and low-density polyethylene (LDPE). This study tested biodegradation of one expanded PS (EPS) with a weight-average molecular weight (M_w) 256.4 kDa and two LDPE foams with respective M_w of 130.6 kDa (PE-1) and 288.7 kDa (PE-2) in T. monitor larvae obtained in Beijing, China. The larvae consumed EPS and both LDPEs over a 60 day. Fourier transform infrared spectroscopy and thermogravimetric analyses of frass confirmed the formation of new oxygen-containing functional groups, as well as a change in physical property and chemical modification, indicating that biodegradation of EPS and LDPE occurred. Gel permeation chromatography analysis confirmed broad depolymerization of EPS and PE-1 (i.e., a decrease in both M_w and a number-average molecular weight (M_n)) but revealed limited extent depolymerization of PE-2 (i.e., increase in M_n and decrease in M_w). For all materials, the size-average molecular weight (M_z) was decreased. Biodegradation and oxidation of EPS and LDPE were confirmed using FTIR and TGA analysis. Depression of gut microbes by the antibiotic gentamicin resulted in significant inhibition of EPS depolymerization but did not stop LDPE depolymerization, resulting in the increase in M_n and revealing that PS biodegradation was gut microbe-dependent but LDPE biodegradation was less dependent or independent of gut microbes. Gut microbial community analysis indicated that, as expected, under different dietary conditions, the intestinal flora significantly shifted to communities associated with biodegradation of EPS and LDPE. The results indicated the complexity and limitation of biodegradation of plastics in plastics-eating T. molitor larvae.
Fate of di (2‑ethylhexyl) phthalate in different soils and associated bacterial community changes
2018, Science of the Total Environment
Citation Excerpt :
In addition, the study of Iwata et al. (2016) recently reported that the MEHP hydrolase (EG-5 MehpH) isolated from Rhodococcus species showed similarity with C–C hydrolase from Ralstonia, suggesting potential degradation capacity towards MEHP by Ralstonia. Dyella and Lysobacter strains have also been reported to degrade various aromatic compounds (Li et al., 2009; Maeda et al., 2009) and thus might play a role in DEHP degradation. In the other acidic soil S2, the largest enrichment was observed for unclassified bacteria, followed by Bradyrhizobium, Sphingomonas, Nocardia and Azoarcus.
Di (2‑ethylhexyl) phthalate (DEHP) is a ubiquitous organic pollutant, which has caused considerable pollution in arable soils. In this study, the relationship between DEHP degradation potential and soil properties in 12 agricultural soils (S1-S12) was examined in a microcosm based experiment. Six of these soils were then selected to monitor patterns in bacterial community responses. It was found that DEHP degradation was positively correlated with bacterial counts in the original soils, suggesting a key role for bacteria in degradation. However, DEHP metabolism did not always lead to complete degradation. Its monoester metabolite, mono (2‑ethylhexyl) phthalate (MEHP), was present at appreciable levels in the two acidic soils (S1 and S2) during the incubation period of 35 days. Based on high-throughput sequencing data, we observed a greater impact of DEHP contamination on bacterial community structure in acidic soils than in the other soils. Nocardioides, Ramlibacter and unclassified Sphingomonadaceae were enriched in the two near-neutral soils where degradation was highest (S4 and S7), suggesting that these organisms might be efficient degraders. The relative abundance of Tumibacillus was greatly reduced in 50% of the six soils examined, demonstrating a high sensitivity to DEHP contamination. Furthermore, putative organic-matter decomposing bacteria (including Tumebacillus and other bacteria taxa such as members from Micromonosporaceae) were greatly reduced in the two acidic soils (S1 and S2), possibly due to the accumulation of MEHP. These results suggest a crucial role of soil acidity in determining the fate and impact of DEHP in soil ecosystems, which deserves further investigation. This work contributes to a better understanding of the environmental behavior of DEHP in soil and should facilitate the development of appropriate remediation technologies.
Phenol removal performance and microbial community shift during pH shock in a moving bed biofilm reactor (MBBR)
2018, Journal of Hazardous Materials
A moving bed biofilm reactor (MBBR) effectively removes pollutants and even runs under extreme conditions. However, the pH shock resistance of a biofilm in MBBRs has been rarely reported. In this study, simulated phenol wastewater with acidic shock (pH 7.5–3.0) was used. In the pH shock phase, the phenol and COD removal efficiencies initially decreased and gradually increased to more than 90%. Microscopic studies showed that the superficial biofilm was mainly composed of fungi (yeasts) in the acidic pH shock phase. The microbial community composition in the acidic pH shock phase was significantly different from those in other phases. Firmicutes and Ascomycota were the dominant bacterial and fungal phyla in this stage, respectively. 16S rRNA gene-based functional annotation indicated that functional profiles related to aromatic compound degradation existed in all of the stages. Therefore, MBBRs show potential for the treatment of phenolic wastewater exposed to pH shock.
Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil
2018, Chemosphere
Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%–95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation.
Gene manipulation and regulation of catabolic genes for biodegradation of biphenyl compounds
2018, New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Genes Biochemistry and Applications
Polychlorinated biphenyls (PCBs) are organic compounds that find a large number of applications at industrial level. Due to their low bioavailability and stability, they are persistent in the environment and also impose deleterious effects on animals and plants. Degradation of these compounds by microbes is a cost-effective strategy to remove these hazardous compounds from the environment and is also receiving greater attention. A number of microbes belonging to phylum Actinobacteria, Ascomycota, Bacteroidetes, Basidiomycota Firmicutes, and Proteobacteria of the genera Achromobacter, Arthrobacter, Aspergillus, Bacillus, Janibacter, Janthinobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Rhodococcus, Shigella, Sphingobium, Sphingomonas, Stenotrophomonas, Talaromyces, Trametes, and Williamsia have been reported to degrade PCBs. There are many reports on the study of the degradation pathways used by the microbes to degrade these compounds as well as the detailed enzymatic steps involved. Further, the catabolic genes (bph) responsible for the degradation in diverse microbes have been studied, which shows a greater diversity in the arrangement of these genes. Also, bph genes have been cloned from different bacterial strains. The study of biodegradation is a complex process and requires the combined study of microbial ecology, biochemistry, and genetic engineering with the aim that the efficient strains may be improved for enhanced degradation and to understand how microbes acquire novel degradation capabilities.
Isolation of bacterial strains able to degrade biphenyl, diphenyl ether and the heat transfer fluid used in thermo-solar plants
2017, New Biotechnology
Citation Excerpt :
These results demonstrate that the isolated bacterial strains are not only able to degrade HTF but also to tolerate extremely high concentrations of this technical mixture, being appropriate candidates to be used in possible bioremediation processes. It is worth noting that most BP- or DE-degrading bacteria usually grow with BP or DE concentrations less than 2000 ppm [6–8,10–12,16], whereas the Pseudomonas strains isolated in this work tolerated HTF concentrations 75-fold higher. For this reason, the possible utilisation of these native bacteria for bioremediation of soils contaminated with the organic technical mixture used in thermo-solar plants is proposed.
Thermo-solar plants use eutectic mixtures of diphenyl ether (DE) and biphenyl (BP) as heat transfer fluid (HTF). Potential losses of HTF may contaminate soils and bioremediation is an attractive tool for its treatment. DE- or BP-degrading bacteria are known, but up to now bacteria able to degrade HTF mixture have not been described. Here, five bacterial strains which are able to grow with HTF or its separate components DE and BP as sole carbon sources have been isolated, either from soils exposed to HTF or from rhizospheric soils of plants growing near a thermo-solar plant. The organisms were identified by 16S rRNA gene sequencing as Achromobacter piechaudii strain BioC1, Pseudomonas plecoglossicida strain 6.1, Pseudomonas aeruginosa strains HBD1 and HBD3, and Pseudomonas oleovorans strain HBD2. Activity of 2,3-dihydroxybiphenyl dioxygenase (BphC), a key enzyme of the biphenyl upper degradation pathway, was detected in all isolates. Pseudomonas strains almost completely degraded 2000 ppm HTF after 5-day culture, and even tolerated and grew in the presence of 150,000 ppm HTF, being suitable candidates for in situ soil bioremediation. Degradation of both components of HTF is of particular interest since in the DE-degrader Sphingomonas sp. SS3, growth on DE or benzoate was strongly inhibited by addition of BP.

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Journal of Environmental Sciences

Abstract

References (28)

Polychlorinated biphenyls and their biodegradation

Process Biochemistry

A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

Analytical Biochemistry

Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase

Journal of Biological Chemistry

Cloning and expression of the polychlorinated biphenyl-degradation gene cluster from Arthrobacter M5 and comparison to analogous genes from Gram-negative bacteria

Gene

Decolorization of bromoamine acid by a newly isolated strain of Sphingomonas xenophaga QYY and its resting cells

Biochemical Engineering Journal

Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases

Gene

A toxicological study of biphenyl, a citrus fungistat

Food Research

Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR

Applied and Environmental Microbiology

2-Hydroxy-6-oxo-phenylhexa-2,4-dienoate: the meta-cleavage product from 2,3-dihydroxybiphenyl by Pseudomonas putida

Biochemical Journal

Microbial degradation of aromatic hydrocarbons used as reactor coolants

Experientia

Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400

Journal of Bacteriology

Biphenyl dioxygenases: functional versatilities and directed evolution

Journal of Bacteriology

Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes

Journal of Bacteriology

Cited by (31)

Biodegradation of expanded polystyrene and low-density polyethylene foams in larvae of Tenebrio molitor Linnaeus (Coleoptera: Tenebrionidae): Broad versus limited extent depolymerization and microbe-dependence versus independence

Fate of di (2‑ethylhexyl) phthalate in different soils and associated bacterial community changes

Phenol removal performance and microbial community shift during pH shock in a moving bed biofilm reactor (MBBR)

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Gene manipulation and regulation of catabolic genes for biodegradation of biphenyl compounds

Isolation of bacterial strains able to degrade biphenyl, diphenyl ether and the heat transfer fluid used in thermo-solar plants