Pusillimonas sp. 5HP degrading 5-hydroxypicolinic acid

Efficient degradation of carbamazepine and metagenomic investigations of anodic biofilm in microbial fuel cells

Environmental contamination with carbamazepine is a considerable global problem. In this study, two-compartment microbial fuel cells (MFCs) were constructed to investigate the degradation performance of carbamazepine, and the degradation mechanism was further explored by using metagenomic analysis. The results showed that MFCs exhibited excellent carbamazepine removal performance and also generated electricity. The removal rate of carbamazepine reached 73.56% over the 72-h operation period, which was 3.09 times higher than that of the traditional anaerobic method, and the peak voltage of the MFCs could reach 416 mV. Metagenomics revealed significant differences in microbial community composition between MFCs and the traditional anaerobic method (p < 0.05), and Proteobacteria (81.57%) was predominant bacterial phyla during the degradation of carbamazepine by MFCs. Among them, the microbial communities at the genus level were mainly composed of Pseudomonas, Pusillimonas, Burkholderia, Stenotrophomonas, Methyloversatilis and Nitrospirillum. Kyoto Encyclopedia of genes and genomes (KEGG) metabolic pathway analysis showed that the number of genes related to carbon and nitrogen metabolism increased by 85.12% and 142.25%, respectively. Importantly, a greater number of genes of microbial grown on the surface of anode were assigned to denitrification and the degradation of aromatic compounds. This research provides a cost-effective method for treating wastewater contaminated with carbamazepin.

Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and C14 : 0 3OH/iso-C16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with 'Neopusillimonas minor' (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae. The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA-DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667T (=BCRC 81321T =JCM 34761T).

Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge

A novel pale white-pigmented bacterial strain designated YC-7-48^T was isolated from activated sludge in China. Cells of the strain, which grew at 15-37 °C (optimum at 30 °C) and pH 6.0-9.0 (optimum at 7.0), were Gram-stain-negative, rod-shaped and motile. Strain YC-7-48^T had 97.4-97.1% 16S rRNA gene sequence similarity to type strains of eight species in the genera Pusillimonas, Eoetvoesia, Paralcaligenes, Parapusillimonas and Paracandidimonas of the family Alcaligenaceae. Phylogenetic analysis based on 16S rRNA gene sequencing placed the strain on a separate branch in the genus Pusillimonas and showed that it exhibited 97.4, 97.3 and 96.6% similarity to Pusillimonas caeni EBR-8-1^T, Pusillimonas noertemannii BN9^T and Pusillimonas maritima 17-4A^T, respectively. The genome size of strain YC-7-48^T was 3202438 bp, with 54.3 mol% G+C content. According to the genome analysis, YC-7-48^T encodes several heavy metal resistance proteins and enzymes related to the metabolism of nicotine and aromatic compounds. The results of digital DNA-DNA hybridization and average nucleotide identity analyses based on whole genome sequences between strain YC-7-48^T and the closely related strains indicated that the strain represented a new species of the genus Pusillimonas. The chemotaxonomic results identified Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified aminolipids as the major polar lipids, and C_16:0 (27.4 %), C_17:0 cyclo (22.0 %), C_18:0 (11.7 %) and C_19:0 cyclo ω8c (9.5 %) as the major fatty acids. Thus, based on morphological, chemotaxonomic and phylogenetic characterization and genomic data, we proposed that the isolate is a representative of a novel species named Pusillimonas minor sp. nov., with the type strain YC-7-48^T (=CGMCC 1.17466^T=KACC 21349^T).

3-Hydroxypyridine Dehydrogenase HpdA Is Encoded by a Novel Four-Component Gene Cluster and Catalyzes the First Step of 3-Hydroxypyridine Catabolism in Ensifer adhaerens HP1

3-Hydroxypyridine (3HP) is an important natural pyridine derivative. Ensifer adhaerens HP1 can utilize 3HP as its sole sources of carbon, nitrogen, and energy to grow, but the genes responsible for the degradation of 3HP remain unknown. In this study, we predicted that a gene cluster, designated 3hpd, might be responsible for the degradation of 3HP. The analysis showed that the initial hydroxylation of 3HP in E. adhaerens HP1 was catalyzed by a four-component dehydrogenase (HpdA1A2A3A4) and led to the formation of 2,5-dihydroxypyridine (2,5-DHP). In addition, the SRPBCC component in HpdA existed as a separate subunit, which is different from other SRPBCC-containing molybdohydroxylases acting on N-heterocyclic aromatic compounds. Moreover, the results demonstrated that the phosphoenolpyruvate (PEP)-utilizing protein and pyruvate-phosphate dikinase were involved in the HpdA activity, and the presence of the gene cluster 3hpd was discovered in the genomes of diverse microbial strains. Our findings provide a better understanding of the microbial degradation of pyridine derivatives in nature and indicated that further research on the origin of the discovered four-component dehydrogenase with a separate SRPBCC domain and the function of PEP-utilizing protein and pyruvate-phosphate dikinase might be of great significance.IMPORTANCE 3-Hydroxypyridine is an important building block for the synthesis of drugs, herbicides, and antibiotics. Although the microbial degradation of 3-hydroxypyridine has been studied for many years, the molecular mechanisms remain unclear. Here, we show that 3hpd is responsible for the catabolism of 3-hydroxypyridine. The 3hpd gene cluster was found to be widespread in Actinobacteria, Rubrobacteria, Thermoleophilia, and Alpha-, Beta-, and Gammaproteobacteria, and the genetic organization of the 3hpd gene clusters in these bacteria shows high diversity. Our findings provide new insight into the catabolism of 3-hydroxypyridine in bacteria.

Pusillimonas maritima sp. nov., isolated from surface seawater

Two Gram-stain-negative, short rod-shaped and non-flagellated strains, designated 17-4A^T and L52-1-41, were isolated from the surface seawater of the Indian Ocean and South China Sea, respectively. The 16S rRNA genes of the two strains shared sequence similarity of 99.45 %. Strain 17-4A^T shared the highest 16S rRNA gene similarity of 98.02 % with Pusillimonas caeni EBR-8-1^T, followed by Pusillimonas noertemannii BN9^T (97.47 %), Pusillimonas soli MJ07^T (96.93 %), Parapusillimonas granuli Ch07^T (96.68 %), Pusillimonas ginsengisoli DCY25^T (96.65 %), Eoetvoesia caeni PB3-7B^T (96.63 %), Paracandidimonas caeni 24^T (96.34 %), Castellaniella defragrans 54Pin^T (96.28 %) and Pusillimonas harenae B201^T (96.05 %). L52-1-41 shared the highest 16S rRNA gene similarity of 97.74 % with Pusillimonas caeni EBR-8-1^T, followed by Pusillimonas noertemannii BN9^T (97.47 %), Pusillimonas soli MJ07^T (96.65 %), Parapusillimonas granuli Ch07^T (96.41 %), Pusillimonas ginsengisoli DCY25^T (96.37 %), Eoetvoesia caeni PB3-7B^T (96.35 %), Pusillimonas harenae B201^T (96.28 %), and Paracandidimonas caeni 24^T (96.06 %). The results of phylogenetic analyses indicated that 17-4A^T and L52-1-41 formed a stable, distinct and highly supported lineage affiliated to the genus Pusillimonas. The results of the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses indicated that they represented a single species. They featured similar genomic DNA G+C contents of 53.2-53.4 mol%. Activities of catalase and oxidase were negative for both strains. The fatty acids patterns of 17-4A^T and L52-1-41 were most similar, mostly comprised of C_16 : 0, C_17 : 0cyclo, C_18 : 0, C_18 : 1ω9c and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1  ω6c). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The respiratory quinone of the two strains was Q-8. Hence, on the basis of the phenotypic, chemotaxonomic and genotypic data presented in this study, we proposed the classification of both strains as representatives of a novel species named Pusillimonas maritima sp. nov., with the type strain 17-4A^T (=MCCC 1A12670^T=KCTC 62121^T=NBRC 113794^T), and another strain L52-1-41 (=MCCC 1A05046=KCTC 52313).

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK^®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK^®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK^® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge

A Gram-stain-negative, motile bacterium, designated strain YE3T, was isolated from activated sludge obtained from a municipal wastewater treatment plant in Daejeon Metropolitan City, Republic of Korea. The cells were oxidase- and catalase-positive, and grew under aerobic conditions at 10–40 °C (optimum, 30 °C), with 1.0–8.0 % (w/v) NaCl (1.0 %) and at pH 5.5–9.0 (pH 7.0). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YE3T was most closely related to Pusillimonas harenae KACC 14927T (98.2 % sequence similarity) and Pusillimonas ginsengisoli KCTC 22046T (98.0 %). DNA–DNA relatedness values for strain YE3T and P. harenae KACC 14927T, P. ginsengisoli KCTC 22046T and P. soli KCTC 22455T were 28.7±2.27 %, 21.3±1.16 %, and 14.0±0.67 %, respectively. The genomic G+C content of the type strain YE3T was 59.3 mol%, as determined by whole-genome sequencing. The dominant fatty acids were C16 : 0 (39.2 %) and C17 : 0cyclo (37.5 %). The major polar lipids of strain YE3T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Two aminophospholipids and four unidentified lipids were also detected. Furthermore, strain YE3T was able to oxidize thiosulfate under heterotrophic conditions. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain YE3T represents a novel species of the genus Pusillimonas , for which the name Pusillimonas thiosulfatoxidans sp. nov. is proposed. The type strain is YE3T (=KCTC 62737T=NBRC 113113T).

A Novel Degradation Mechanism for Pyridine Derivatives in Alcaligenes faecalis JQ135

5-Hydroxypicolinic acid (5HPA), a natural pyridine derivative, is microbially degraded in the environment. However, the physiological, biochemical, and genetic foundations of 5HPA metabolism remain unknown. In this study, an operon (hpa), responsible for 5HPA degradation, was cloned from Alcaligenes faecalis JQ135. HpaM was a monocomponent flavin adenine dinucleotide (FAD)-dependent monooxygenase and shared low identity (only 28 to 31%) with reported monooxygenases. HpaM catalyzed the ortho decarboxylative hydroxylation of 5HPA, generating 2,5-dihydroxypyridine (2,5DHP). The monooxygenase activity of HpaM was FAD and NADH dependent. The apparent K_m values of HpaM for 5HPA and NADH were 45.4 μM and 37.8 μM, respectively. The genes hpaX, hpaD, and hpaF were found to encode 2,5DHP dioxygenase, N-formylmaleamic acid deformylase, and maleamate amidohydrolase, respectively; however, the three genes were not essential for 5HPA degradation in A. faecalis JQ135. Furthermore, the gene maiA, which encodes a maleic acid cis-trans isomerase, was essential for the metabolism of 5HPA, nicotinic acid, and picolinic acid in A. faecalis JQ135, indicating that it might be a key gene in the metabolism of pyridine derivatives. The genes and proteins identified in this study showed a novel degradation mechanism of pyridine derivatives.IMPORTANCE Unlike the benzene ring, the uneven distribution of the electron density of the pyridine ring influences the positional reactivity and interaction with enzymes; e.g., the ortho and para oxidations are more difficult than the meta oxidations. Hydroxylation is an important oxidation process for the pyridine derivative metabolism. In previous reports, the ortho hydroxylations of pyridine derivatives were catalyzed by multicomponent molybdenum-containing monooxygenases, while the meta hydroxylations were catalyzed by monocomponent FAD-dependent monooxygenases. This study identified the new monocomponent FAD-dependent monooxygenase HpaM that catalyzed the ortho decarboxylative hydroxylation of 5HPA. In addition, we found that the maiA gene coding for maleic acid cis-trans isomerase was pivotal for the metabolism of 5HPA, nicotinic acid, and picolinic acid in A. faecalis JQ135. This study provides novel insights into the microbial metabolism of pyridine derivatives.

Identification and characterization of a new three-component nicotinic acid hydroxylase NahAB1 B2 from Pusillimonas sp. strain T2

Nicotinic acid (NA) is ubiquitous in nature and its microbial degradation mechanisms are diverse. In this study, Pusillimonas sp. strain T2 was found to be capable of utilizing NA as sole carbon and nitrogen sources. This strain could completely degrade 300 mg l^-1 NA within 3·5 h at 30°C and pH 7·0 and one of the degradation intermediate of NA was identified as 6-hydroxynicotinic acid (6HNA). The draft genome sequences of strain T2 were determined to have a total length of 3·3 M bp and 3054 proteins were predicted. The encoding genes of three-component NA hydroxylase (NahAB₁ B₂ ) genes were identified. The nahAB₁ B₂ genes were heterologously expressed in the non-NA-degrading Shinella sp. strain HZN7. The recombinant HZN7-pBBR-nahAB₁ B₂ converted NA into equimolar 6HNA, while the recombinants HZN7-pBBR-nahAB₁ (lacking component B₂ ) and HZN7-pBBR-nahAB₂ (lacking component B₁ ) could not convert NA. Cell-free extracts of HZN7-pBBR-nahAB₁ B₂ exhibited NA hydroxylase activity. After addition of an artificial electron acceptor (such as phenazine methosulphate, PMS), the NA hydroxylase activity was significantly increased. The K_m and V_max values for NA were 65·94 μmol l^-1 and 260·80 ± 5·69 mU mg^-1 , respectively, using PMS as an electron acceptor. This study provides a novel insight into the NA degradation by bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Nicotinic acid (NA) serves as a model system for the degradation of N-heterocyclic aromatic compounds and the microbial degradation mechanisms are diverse. This is the first time that a three-component hydroxylase has been identified. This study provides a novel insight into the NA degradation by bacteria.

Sequential decolorization of azo dye and mineralization of decolorization liquid coupled with bioelectricity generation using a pH self-neutralized photobioelectrochemical system operated with polarity reversion

A novel photobioelectrochemical system (PBES) was developed by acclimating algal-bacterial biofilm in both anode and cathode using Chlorella vulgaris and indigenous wastewater bacteria as inoculums. The PBES was operated in polarity reversion mode depend on dark/light alternate reaction to achieve simultaneous pH self-neutralization, azo dye degradation (Congo red) and bioelectricity generation. The anodic accumulated acidity and cathodic accumulated alkalinity were self-neutralized after polarity reversion and hence eliminate the membrane pH gradient. The Congo red was first decolored in the dark anode and the resultant decolorization liquid was subsequently mineralized after the dark anode changing to the photo-biocathode. The presence of C. vulgaris significantly enhanced the two-stage degradation of Congo red, with 93% increases in decolorization rates and 8% increases in mineralization compared to the algae-free BES. The PBES continuously generated stable voltage output over four months under repeatedly reversion of polarity. The maximum power density produced before and after polarity reversion was 78 and 61 mW/m(2), respectively. The synergy between C. vulgaris and mixed bacteria was responsible for the successful operation of the PBES which can be potentially applied to treat wastewater containing azo dye with benefits of enhanced azo dye degradation, high net power output and buffer minimization.

Selectivity of substrate binding and ionization of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

2-Methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) oxygenase (EC 1.14.12.4) from Pseudomonas sp. MA-1 is a flavin-dependent monooxygenase that catalyzes a hydroxylation and aromatic ring cleavage reaction. The functional roles of two residues, Tyr223 and Tyr82, located ~ 5 Å away from MHPC, were characterized using site-directed mutagenesis, along with ligand binding, product analysis and transient kinetic experiments. Mutation of Tyr223 resulted in enzyme variants that were impaired in their hydroxylation activity and had Kd values for substrate binding 5-10-fold greater than the wild-type enzyme. Because this residue is adjacent to the water molecule that is located next to the 3-hydroxy group of MHPC, the results indicate that the interaction between Tyr223, H2 O and the 3-hydroxyl group of MHPC are important for substrate binding and hydroxylation. By contrast, the Kd for substrate binding of Tyr82His and Tyr82Phe variants were similar to that of the wild-type enzyme. However, only ~ 40-50% of the substrate was hydroxylated in the reactions of both variants, whereas most of the substrate was hydroxylated in the wild-type enzyme reaction. In free solution, MHPC or 5-hydroxynicotinic acid exists in a mixture of monoanionic and tripolar ionic forms, whereas only the tripolar ionic form binds to the wild-type enzyme. The binding of tripolar ionic MHPC would allow efficient hydroxylation through an electrophilic aromatic substitution mechanism. For the Tyr82His and Tyr82Phe variants, both forms of substrates can bind to the enzymes, indicating that the mutation at Tyr82 abolished the selectivity of the enzyme towards the tripolar ionic form. Transient kinetic studies indicated that the hydroxylation rate constants of both Tyr82 variants are approximately two- to 2.5-fold higher than that of the wild-type enzyme. Altogether, our findings suggest that Tyr82 is important for the binding selectivity of MHPC oxygenase towards the tripolar ionic species, whereas the interaction between Tyr223 and the substrate is important for ensuring hydroxylation. These results highlight how the active site of a flavoenzyme is able to deal with the presence of multiple forms of a substrate in solution and ensure efficient hydroxylation.