Sphingobium phenoxybenzoativorans sp. nov., a 2-phenoxybenzoic-acid-degrading bacterium

Comparative evaluation of trimethylated α-, β-, and γ-cyclodextrins as optimal dispersants for ready biodegradability testing of poorly water-soluble substances

We investigated whether various modified cyclodextrins (CDs) and emulsifiers could be applied as dispersing agents in ready biodegradability tests of poorly water-soluble substances. Trimethylated α-, β-, and γ-CDs and partially methylated β-CD were not biodegraded in the test period but accelerated the biodegradation of octabenzone and anthraquinone. The process by which trimethylated α-, β-, and γ-CDs enhance the biodegradation of test substances has been partially uncovered. These CDs create inclusion complexes with the substances, which then coalesce into larger aggregates. These aggregates disperse throughout the testing medium and attach to clusters of activated sludge, known as flocs. This close contact with the sludge speeds up the breakdown of the hydrophobic substances being tested.

Microbial consortia degrade several widely used organic UV filters, but a number of hydrophobic filters remain recalcitrant to biodegradation

Organic UV filters are important ingredients in many personal care products, including sunscreens. Evaluating the biodegradability of organic UV filters is key to estimate their recalcitrance and environmental fate and thus central to their overall environmental risk assessment. In order to further understand the degradation process, the aim was to investigate whether specific consortia could degrade certain UV filters. Several bacterial strains were isolated from enrichment cultures actively degrading octocrylene (OC), butyl methoxydibenzoylmethane (BM), homosalate (HS), and 2-ethylhexyl salicylate (ES) and were utilized to construct an in-house consortium. This synthetic consortium contained 27 bacterial strains and degraded OC, BM, HS, and ES 60-80% after 12 days, but not benzophenone-3 (BP3), methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (EHT), or diethylamino hydroxybenzoyl hexyl benzoate (DHHB). Furthermore, several commercial microbial mixtures from Greencell were tested to assess their degradation activity toward the same organic UV filters. ES and HS were degraded by some of the commercial consortia, but to a lesser extent. The rest of the tested UV filters were not degraded by any of the commercial bacterial mixes. These results confirm that some organic UV filters are recalcitrant to biodegradation, while others are degraded by a specific set of microorganisms.

Metagenomic analysis of ready biodegradability tests to ascertain the relationship between microbiota and the biodegradability of test chemicals

Ready biodegradability tests conducted in accordance with the Organisation for Economic Co-operation and Development guidelines (test 301C or test 301F) are performed using activated sludge (AS) prepared by the Chemicals Evaluation and Research Institute (AS-CERI) or that taken from a sewage treatment plant (AS-STP). It had been reported that AS-CERI had lower activity than AS-STP in biodegrading test chemicals, and that biodegradation was accelerated by increasing the volume of the test medium. However, these phenomena have not been clarified from the perspective of the microbiota. In this study, using metagenomic analysis, we first showed that the microbiota of AS-CERI was biased in its distribution of phyla, less diverse, and had greater lot-to-lot variability than that of AS-STP. Second, after cultivation for a long period of time, the microbiota of AS-STP and AS-CERI became more similar to each other in terms of community structure. Third, determining degraders of test substances when each substance was actively biodegraded was found to be an effective approach. Finally, we clarified experimentally that a large volume of test medium increased the number of species that could degrade test substances in the condition where the initial concentrations of each substance and AS-STP were kept constant.

Bacterial degradation of bisphenol analogues: an overview

Bisphenol A (BPA) is one of the most produced synthetic monomers in the world and is widespread in the environment. BPA was replaced by bisphenol analogues (BP) because of its adverse effects on life. Bacteria can degrade BPA and other bisphenol analogues (BP), diminishing their environmental concentrations. This study aimed to summarize the knowledge and contribute to future studies. In this review, we surveyed papers on bacterial degradation of twelve different bisphenol analogues published between 1987 and June 2022. A total of 102 original papers from PubMed and Google Scholar were selected for this review. Most of the studies (94.1%, n = 96) on bacterial degradation of bisphenol analogues focused on BPA, and then on bisphenol F (BPF), and bisphenol S (BPS). The number of studies on bacterial degradation of bisphenol analogues increased more than six times from 2000 (n = 2) to 2021 (n = 13). Indigenous microorganisms and the genera Sphingomonas, Sphingobium, and Cupriavidus could degrade several BP. However, few studies focussed on Cupriavidus. The acknowledgement of various aspects of BP bacterial biodegradation is vital for choosing the most suitable microorganisms for the bioremediation of a single BP or a mixture of BP.

Isolation and Characterization of a Topramezone-Resistant 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19

Topramezone is a 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor. Due to its broad-spectrum, high efficiency, and low toxicity, topramezone is a candidate herbicide for the construction of genetically modified (GM) herbicide-resistant crops. In the present study, we screened a topramezone-resistant isolate Sphingobium sp. TPM-19 and cloned a topramezone-resistant HPPD gene (SphppD) from this isolate. SpHPPD shared the highest similarity (53%) with an HPPD from Vibrio vulnificus CMCP6. SpHPPD was synthesized in Escherichia coli BL21(DE3) and purified to homogeneity using Co²⁺-affinity chromatography. SpHPPD was found to be a monomer. The K_m and k_cat of SpHPPD for 4-hydroxyphenylpyruvate (4-HPP) were 82.8 μM and 15.0 s^-1, respectively. SpHPPD showed high resistance to topramezone with half maximal inhibitory concentration (IC₅₀) and K_i values of 5.2 and 2.5 μM, respectively. Additionally, SpHPPD also showed high resistance to isoxaflutole (DKN) (IC₅₀: 8.7 μM; K_i: 6.0 μM) and mesotrione (IC₅₀: 4.2 μM; K_i: 1.3 μM) and moderate resistance to tembotrione (IC₅₀: 2.5 μM; K_i: 1.0 μM). The introduction of the SphppD gene into Arabidopsis thaliana enhanced obvious resistance against topramezone. In conclusion, this study provides a novel topramezone-resistant HPPD gene for the genetic engineering of GM herbicide-resistant crops.

Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater

A Gram-negative, aerobic, slightly yellow-pigmented bacterium, designated as SKLS-A10^T, was isolated from groundwater sample of the 'Siklós' petroleum hydrocarbon contaminated site (Hungary). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SKLS-A10^T formed a distinct phyletic lineage within the genus Sphingobium. It shared the highest 16S rRNA gene homology with Sphingobium abikonense DSM 23268^T (97.29 %), followed by Sphingobium lactosutens DSM 23389^T (97.23 %), Sphingobium phenoxybenzoativorans KCTC 42448^T (97.16 %) and Sphingobium subterraneum NBRC 109814^T (96.74 %). The predominant fatty acids (>5 % of the total) are C18 : 1ω7c, C14 : 0 2-OH, C16 : 1ω7c/iso C15 : 0 2-OH, C17 : 1ω6c and C16 : 0. The major ubiquinone is Q-10. The predominant polyamine is spermidine. The major polar lipids are sphingoglycolipid and diphosphatidylglycerol. The DNA G+C content of strain SKLS-A10^T is 65.9 mol%. On the basis of evidence from this taxonomic study using a polyphasic approach, strain SKLS-A10^T represents a novel species of the genus Sphingobium for which the name Sphingobiumaquiterrae sp. nov. is proposed. The type strain is SKLS-A10^T (=DSM 106441^T=NCAIM B. 02634^T).

Microbial community structure in aerobic and fluffy granules formed in a sequencing batch reactor supplied with 4-chlorophenol at different settling times

Toxic compounds, such as 4-chlorophenol (4-CP), which is a common pollutant in wastewater, are removed efficiently from sequencing batch reactors (SBRs) by microorganisms. The bacterial community in aerobic granules formed during the removal of 4-CP in a SBR was monitored for 63days. The SBR reactor was operated with a constant filling and withdrawal time of 7 and 8min and decreasing settling time (30, 5, 3 and 2min) to induce the formation of aerobic granules. During the acclimation period lasting 15days (30min settling time) had a strong effect on the bacterial community. From day 18 onwards, Sphingobium and Comamonadaceae were detected. Rhizobiaceae were dominant from day 24 to day 28 when stable aerobic granules were formed. At day 35, fluffy granules were formed, but the bacterial community structure did not change, despite the changes in the reactor operation to inhibit filamentous bacteria growth. This is the first report on changes in the bacterial community structure of aerobic and fluffy granules during granulation process in a reactor fed with 4-CP and the prediction of its metabolic pathways.

Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov., isolated from a freshwater green alga Paulinella chromatophora

Two Gram-stain-negative, aerobic, catalase- and oxidase-positive, yellow-pigmented bacteria, designated strains Pch-B^T and Pch-E^T, were isolated from a green alga Paulinella chromatophora. Both strains were motile short rods with a flagellum and optimally grew at pH 6.0-7.0, 25-30 °C and 0-1 % NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, C16 : 0, C14 : 0 2-OH and summed features 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, two sphingoglycolipids and phosphatidylcholine as the major polar lipids. DNA G+C contents of strains Pch-B^T and Pch-E^T were 61.4 and 63.9 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains Pch-B^T and Pch-E^T formed a phylogenic lineage with Sphingobium limneticum 301^T. Strains Pch-B^T and Pch-E^T had a 99.86 % 16S rRNA gene sequence similarity and their DNA-DNA hybridization (DDH) relatedness value was 40.6 %. Strains Pch-B^T and Pch-E^T were most closely related to S. limneticum 301^T with 99.93 and 99.76 % 16S rRNA gene sequence similarities, respectively and the DDH values between strains Pch-B^T and Pch-E^T and the type strain of S. limneticum were 43.3 and 32.1 %, respectively. In conclusion, strains Pch-B^T and Pch-E^T represent novel species of the genus Sphingobium, for which the names Sphingobiumpaulinellae sp. nov. and Sphingobium algicola sp. nov. are proposed, respectively. The type strains of S. paulinellae and S. algicola are Pch-B^T (=KACC 19283^T=JCM 32054^T) and Pch-E^T (=KACC 19284^T=JCM 32055^T), respectively.

Degradation of Diphenyl Ether in Sphingobium phenoxybenzoativorans SC_3 Is Initiated by a Novel Ring Cleavage Dioxygenase

Sphingobium phenoxybenzoativorans SC_3 degrades and utilizes diphenyl ether (DE) or 2-carboxy-DE as its sole carbon and energy source. In this study, we report the degradation of DE and 2-carboxy-DE initiated by a novel ring cleavage angular dioxygenase (diphenyl ether dioxygenase [Dpe]) in the strain. Dpe functions at the angular carbon and its adjacent carbon (C-1a, C-2) of a benzene ring in DE (or the 2-carboxybenzene ring in 2-carboxy-DE) and cleaves the C-1a-C-2 bond (decarboxylation occurs simultaneously for 2-carboxy-DE), yielding 2,4-hexadienal phenyl ester, which is subsequently hydrolyzed to muconic acid semialdehyde and phenol. Dpe is a type IV Rieske non-heme iron oxygenase (RHO) and consists of three components: a hetero-oligomer oxygenase, a [2Fe-2S]-type ferredoxin, and a glutathione reductase (GR)-type reductase. Genetic analyses revealed that dpeA1A2 plays an essential role in the degradation and utilization of DE and 2-carboxy-DE in S. phenoxybenzoativorans SC_3. Enzymatic study showed that transformation of 1 molecule of DE needs two molecules of oxygen and two molecules of NADH, supporting the assumption that the cleavage of DE catalyzed by Dpe is a continuous two-step dioxygenation process: DE is dioxygenated at C-1a and C-2 to form a hemiacetal-like intermediate, which is further deoxygenated, resulting in the cleavage of the C-1a-C-2 bond to form one molecule of 2,4-hexadienal phenyl ester and two molecules of H₂O. This study extends our knowledge of the mode and mechanism of ring cleavage of aromatic compounds.IMPORTANCE Benzene ring cleavage, catalyzed by dioxygenase, is the key and speed-limiting step in the aerobic degradation of aromatic compounds. As previously reported, in the ring cleavage of DEs, the benzene ring needs to be first dihydroxylated at a lateral position and subsequently dehydrogenated and opened through extradiol cleavage. This process requires three enzymes (two dioxygenases and one dehydrogenase). In this study, we identified a novel angular dioxygenase (Dpe) in S. phenoxybenzoativorans SC_3. Under Dpe-mediated catalysis, the benzene ring of DE is dioxygenated at the angular position (C-1a, C-2), resulting in the cleavage of the C-1a-C-2 bond to generate a novel product, 2,4-hexadienal phenyl ester. This process needs only one angular dioxygenase, Dpe. Thus, the ring cleavage catalyzed by Dpe represents a novel mechanism of benzene ring cleavage.