Isolation and characterization of a novel 2-sec-butylphenol-degrading bacterium Pseudomonas sp. strain MS-1

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides

Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.

A comprehensive study of conditions of the biodegradation of a plastic additive 2,6-di-tert-butylphenol and proteomic changes in the degraderPseudomonas aeruginosasan ai

ThePseudomonas aeruginosasan ai strain was investigated for its capability to degrade the 2,6-di-tert-butylphenol (2,6-DTBP) plastic additive, a hazardous and toxic substance for aquatic life.

Construction and analysis of an intergeneric fusion from Pigmentiphaga sp. strain AAP-1 and Pseudomonas sp. CTN-4 for degrading acetamiprid and chlorothalonil

Pseudomonas sp. CTN-4 degrades chlorothalonil (CTN) but not acetamiprid (AAP), and Pigmentiphaga sp. strain AAP-1 degrades AAP but not CTN. A functional strain, AC, was constructed through protoplast fusion of two parental strains (Pseudomonas sp. CTN-4 and Pigmentiphaga sp. strain AAP-1) in order to simultaneously improve the degradation efficiency of AAP and CTN. Fusant-AC with eight transfers on plates containing two antibiotics and CTN was obtained. For the purpose of identifying and confirming the genetic relationship between fusant-AC and its parents, randomly amplified polymorphic DNA (RAPD), scanning electron microscopy (SEM), and 16S ribosomal DNA (rDNA) analysis were performed. In toto, RAPD fingerprint analysis produced 194 clear bands with 9 primers, which not only had bands in common with strains CTN-4 and AAP-1, but also had its own novel fusant-specific bands. The genetic similarity indices between fusant-AC and parental strains CTN-4 and AAP-1 were 0.40 and 0.69, respectively. The result of SEM indicated that the cell morphology of fusant-AC differed from both its parents. The fusant strain AC possesses a strong capability for AAP and CTN degradation. At AAP concentration (50-300 mg L(-1)), the degradation was achieved within 5 h. At the initial dose of 50 and 100 mg L(-1) CTN, the percentages reached 96 and 91 % over a 36-h incubation period. The present study indicates that the protoplast-fusion technique may have possible applications in environmental pollution control.

Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols

Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use nonionic surfactants (alkylphenol polyethoxylates) and estrogen-like compounds (4-t-octylphenol and 4-nonylphenol) as a sole carbon source. This is the first report on the genome sequence of P. nitroreducens.

Analysis of bacterial degradation pathways for long-chain alkylphenols involving phenol hydroxylase, alkylphenol monooxygenase and catechol dioxygenase genes

Eighteen 4-t-octylphenol-degrading bacteria were isolated and screened for the presence of degradative genes by polymerase chain reaction method using four designed primer sets. The primer sets were designed to amplify specific fragments from multicomponent phenol hydroxylase, single component monooxygenase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase genes. Seventeen of the 18 isolates exhibited the presence of a 232 bp amplicon that shared 61-92% identity to known multicomponent phenol hydroxylase gene sequences from short and/or medium-chain alkylphenol-degrading strains. Twelve of the 18 isolates were positive for a 324 bp region that exhibited 78-95% identity to the closest published catechol 1,2-dioxygenase gene sequences. The two strains, Pseudomonas putida TX2 and Pseudomonas sp. TX1, contained catechol 1,2-dioxygenase genes also have catechol 2,3-dioxygenase genes. Our result revealed that most of the isolated bacteria are able to degrade long-chain alkylphenols via multicomponent phenol hydroxylase and the ortho-cleavage pathway.