A Novel Degradation Mechanism for Pyridine Derivatives in Alcaligenes faecalis JQ135

DipR, a GntR/FadR-family transcriptional repressor: regulatory mechanism and widespread distribution of the dip cluster for dipicolinic acid catabolism in bacteria

Dipicolinic acid is an essential component of bacterial spores for stress resistance, which is released into the environment after spore germination. In a previous study, a dip gene cluster was found to be responsible for the catabolism of dipicolinic acid in Alcaligenes faecalis JQ135. However, the transcriptional regulatory mechanism remains unclear. The present study characterized the new GntR/FadR family transcriptional factor DipR, showing that the dip cluster is transcribed as the six transcriptional units, dipR, dipA, dipBC, dipDEFG, dipH and dipJKLM. The purified DipR protein has six binding sites sharing the 6-bp conserved motif sequence 5'-GWATAC-3'. Site-directed mutations indicated that these motif sequences are essential for DipR binding. Moreover, the four key amino acid residues R63, R67, H196 and H218 of DipR, examined by site-directed mutagenesis, played crucial roles in DipR regulation. Bioinformatics analysis showed that dip clusters including dipR genes are widely distributed in bacteria, are taxon-related, and co-evolved with their hosts. This paper provides new insights into the transcriptional regulatory mechanism of dipicolinic acid degradation by DipR in bacteria.

Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16

IMPORTANCE

Fusaric acid (FA) is an important virulence factor produced by several Fusarium species. These fungi are responsible for wilt and rot diseases in a diverse range of crops. FA is toxic for animals, humans and soil-borne microorganisms. This mycotoxin reduces the survival and competition abilities of bacterial species able to antagonize Fusarium spp., due to its negative effects on viability and the production of antibiotics effective against these fungi. FA biodegradation is not a common characteristic among bacteria, and the determinants of FA catabolism have not been identified so far in any microorganism. In this study, we identified genes, enzymes, and metabolic pathways involved in the degradation of FA in the soil bacterium Burkholderia ambifaria T16. Our results provide insights into the catabolism of a pyridine-derivative involved in plant pathogenesis by a rhizosphere bacterium.

Bacterial Endophytes from Moringa oleifera Leaves as a Promising Source for Bioactive Compounds

Bacterial endophytes reside within the tissues of living plant species without causing any harm or disease to their hosts. Bacterial endophytes have produced a variety of bioactive compounds that can be used for different biomedical applications. In the current study, two bacterial endophytes were isolated from healthy Moringa oleifera leaves, and identified genetically as Stenotrophomonas maltophilia and Alcaligenes faecalis. Phytochemical results illustrated that A. faecalis produced phenolics at 547.2 mg/g, tannins at 156.7 µg/g, flavonoids at 32.8 µg/g, and alkaloids at 111.2 µg/g compared to S. maltophilia, which produced phenolics at 299.5 mg/g, tannins at 78.2 µg/g, flavonoids at 12.4 µg/g, and alkaloids at 29.4 µg/g. GC-MS analysis indicated that A. faecalis extract has 24 bioactive compounds, including 9 major compounds, namely octadecanoic acid, hexadecanoic acid, linoleic acid ethyl ester, octadecenoic acid, methyl ester, methyl stearate, nonacosane, indolizine, palmitoleic acid, and heptacosane. On the other hand, S. maltophilia extract has 11 bioactive compounds, including 8 major compounds, namely oleic acid, octadecanoic acid, hexadecanoic acid, cis-2-phenyl-1, 3-dioxolane-4-methyl, ergotamine, diisooctyl phthalate, diethyl phthalate, and pentadecanoic acid. To check the safety of these extracts, the cytotoxicity of Ethyl acetate (EA) extracts of S. maltophilia and A. faecalis were evaluated against the Vero normal cell line, and the results confirmed that these extracts are safe to use. Moreover, results revealed that EA extracts of S. maltophilia and A. faecalis exhibited anticancer activity against the cancerous MCF7 cell line, where IC50 was 202.4 and 119.7 µg/mL, respectively. Furthermore, EA extracts of S. maltophilia had antibacterial and antifungal activity against Gram-positive and Gram-negative bacteria, and unicellular fungi. Likewise, the EA extract of A. faecalis exhibited antibacterial and antifungal activity against Gram-positive bacteria, as well as unicellular fungi, but did not show any activity against Gram-negative bacteria. Also, EA extracts of S. maltophilia and A. faecalis exhibited moderate antioxidant activity where IC50 were 146.2 and 147.6 µg/mL, respectively. In conclusion, the two isolated endophytic bacteria S. maltophilia and A. faecalis have promising bioactive compounds that have antibacterial, antioxidant, and anticancer activities.

Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies

3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.

One-Pot Biosynthesis of l-Aspartate from Maleic Anhydride via a Thermostable Dual-Enzyme System under High Temperature

l-Aspartate is an important chemical in the food and pharmaceutical industries. Herein, a dual-enzyme system was constructed to synthesize l-aspartate from maleic anhydride at 50 °C, which can reduce the byproduct production. Maleate transformed from maleic anhydride in the solution was converted into l-aspartate via fumarate catalyzed by maleate isomerase (MaiA) and thermostable aspartase (AspB), respectively. Because MaiA is a rate-limiting enzyme, enzyme activities of various MaiAs were compared, and the efficient and thermostable maleate isomerase AaMaiA from Alicyclobacillus acidoterrestris was chosen. The K_cat/K_m value of AaMaiA was 264.4 mM^-1 min^-1. AaMaiA and AspB were coexpressed in E. coli to produce l-aspartate. To improve the l-aspartate production rate, the ribosome binding site (RBS) sequence located upstream of AaMaiA was optimized and the Tat signal peptide was fused with AaMaiA. The conversion rate was 96% within 60 min, and the intermediate was not detected, the possible reason of which is that high temperature inhibits the activity of bacterial endogenous enzymes, but functional enzymes remain active. Cells from fermentation produced 243.6 g/L (1.83 M) of l-aspartate with a 2 M substrate. Our study revealed an effective method to produce l-aspartate without using gene knockout and provided a strategy for l-aspartate production in the industrial field.

Structural characteristics and microbial function of biofilm in membrane-aerated biofilm reactor for the biodegradation of volatile pyridine

In order to avoid the serious air pollution caused by the volatilization of high recalcitrant pyridine, membrane-aerated biofilm reactor (MABR) with bubble-free aeration was used in this study, with the structural characteristics and microbial function of biofilm emphasized. The results showed that as high as 0.6 kg·m^-3·d^-1 pyridine could be completely removed in MABR. High pyridine loading thickened the biofilm, but without obvious detachment observed. The distinct stratification of microbes and extracellular polymeric substances were shaped by elevated pyridine load, enhancing the structural heterogeneity of biofilm. The increased tryptophan-like substances as well as α-helix and β-sheet proportion in proteins stabilized the biofilm structure against high influent loading. Based on the identified intermediates, possible pyridine biodegradation pathways were proposed. Multi-omics analyses revealed that the metabolic pathways with initial hydroxylation and reduction reaction was enhanced at high pyridine loading. The functional genes were mainly associated with Pseudomonas and Delftia, might responsible for pyridine biodegradation. The results shed light on the effective treatment of wastewater containing recalcitrant pollutants such as pyridine via MABR.

PicR as a MarR Family Transcriptional Repressor Multiply Controls the Transcription of Picolinic Acid Degradation Gene Cluster pic in Alcaligenes faecalis JQ135

Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, pic, that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the pic cluster remains known. This study showed that the entire pic cluster was composed of 17 genes and transcribed as four operons: picR, picCDEF, picB4B3B2B1, and picT1A1A2A3T2T3MN. Deletion of picR, encoding a putative MarR-type regulator, greatly shortened the lag phase of PA degradation. An electrophoretic mobility shift assay and DNase I footprinting showed that PicR has one binding site in the picR-picC intergenic region and two binding sites in the picB-picT1 intergenic region. The DNA sequences of the three binding sites have the palindromic characteristics of TCAG-N4-CTNN: the space consists of four nonspecific bases, and the four palindromic bases on the left and the first two palindromic bases on the right are strictly conserved, while the last two bases on the right vary among the three binding sites. An in vivo β-galactosidase activity reporter assay indicated that 6-hydroxypicolinic acid but not PA acted as a ligand of PicR, preventing PicR from binding to promoter regions and thus derepressing the transcription of the pic cluster. This study revealed the negative transcriptional regulation mechanism of PA degradation by PicR in A. faecalis JQ135 and provides new insights into the structure and function of the MarR-type regulator. IMPORTANCE The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha-, Beta-, and Gammaproteobacteria. Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains. This study revealed that PicR binds to three sites of the promoter regions of the pic cluster to multiply regulate the transcription of the pic cluster, which enables A. faecalis JQ135 to efficiently utilize PA. Furthermore, the study also found a unique palindrome sequence for binding of the MarR-type regulator. This study enhanced our understanding of microbial catabolism of environmental toxic pyridine derivatives.

Genome mining of Burkholderia ambifaria strain T16, a rhizobacterium able to produce antimicrobial compounds and degrade the mycotoxin fusaric acid

Burkholderia ambifaria T16 is a bacterium isolated from the rhizosphere of barley plants that showed a remarkable antifungal activity. This strain was also able to degrade fusaric acid (5-Butylpyridine-2-carboxylic acid) and detoxify this mycotoxin in inoculated barley seedlings. Genes and enzymes responsible for fusaric acid degradation have an important biotechnological potential in the control of fungal diseases caused by fusaric acid producers, or in the biodegradation/bio catalysis processes of pyridine derivatives. In this study, the complete genome of B. ambifaria T16 was sequenced and analyzed to identify genes involved in survival and competition in the rhizosphere, plant growth promotion, fungal growth inhibition, and degradation of aromatic compounds. The genomic analysis revealed the presence of several operons for the biosynthesis of antimicrobial compounds, such as pyrrolnitrin, ornibactin, occidiofungin and the membrane-associated AFC-BC11. These compounds were also detected in bacterial culture supernatants by mass spectrometry analysis. In addition, this strain has multiple genes contributing to its plant growth-promoting profile, including those for acetoin, 2,3-butanediol and indole-3-acetic acid production, siderophores biosynthesis, and solubilisation of organic and inorganic phosphate. A pan-genomic analysis demonstrated that the genome of strain T16 possesses large gene clusters that are absent in the genomes of B. ambifaria reference strains. According to predictions, most of these clusters would be involved in aromatic compounds degradation. One genomic region, encoding flavin-dependent monooxygenases of unknown function, is proposed as a candidate responsible for fusaric acid degradation.

The TetR Family Repressor HpaR Negatively Regulates the Catabolism of 5-Hydroxypicolinic Acid in Alcaligenes faecalis JQ135 by Binding to Two Unique DNA Sequences in the Promoter of hpa Operon

5-Hydroxypicolinic acid (5HPA), an important natural pyridine derivative, is microbially degraded in the environment. Previously, a gene cluster hpa responsible for 5HPA degradation has been identified in Alcaligenes faecalis JQ135. However, the transcription regulation mechanism of the hpa cluster is still unknown. In this study, the transcription start site and promoter of hpa operon was identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR, whereas the transcription of hpaR itself was not regulated by HpaR. Electrophoretic mobility shift assay and DNase I footprinting revealed that HpaR bound to two DNA sequences, covering -35 region and -10 region, respectively, in the promoter region of hpa operon. Interestingly, the two binding sequences are partial-palindromic with 3-4 mismatches, and are complementary with each other. 5HPA acted as a ligand of HpaR preventing HpaR from binding to promoter region thus derepressing the transcription of hpa operon. The study revealed that HpaR binds to two unique complementary sequences of the promoter of hpa operon to negatively regulate the catabolism of 5HPA. IMPORTANCE This study revealed that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR. The binding of HpaR to the promoter of hpa operon has the following unique features: (1) HpaR has two independent binding sites in the promoter of the hpa operon, covering -35 region and -10 region, respectively. (2) the palindrome sequences of the two binding sites are complementary with each other. (3) both of the two binding sites include a 10-nt partial palindrome sequences with 3-4 mismatches. This study provides new insights into the binding features of the TetR family regulator with DNA sequences.

Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N2 and MocR-like Transcriptional Regulator DnfR in Alcaligenes faecalis JQ135

Ammonia oxidation is an important process of both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH₃→NH₂OH→N₂) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes and its genetic regulation remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N₂ via NH₂OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N₂ in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N₂O and trace amounts of N₂ with nitrite as sole nitrogen source. Deletion of genes nirK and nosZ that are essential for denitrification did not impair the capability of JQ135 to oxidize ammonia to N₂ (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 5'-TGGTCTGT-3' in the promotor region. Bioinformatic survey showed that homologs to dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that besides A. ammonioxydans, Dirammox also occurs in other bacteria, and is regulated by the MocR-family transcriptional regulator DnfR. Importance Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previous known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation (Anammox), and complete ammonia oxidation (Comammox)) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N₂ (Dirammox), has been identified in the heterotrophic bacterium Alcaligenes ammonioxydans HO-1. This paper shows that in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by dnf genes, which are independent of the denitrification pathway. Bioinformatic survey suggests that homologs to dnf genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N₂.

Characterization of a new heterotrophic nitrification bacterium Pseudomonas sp. strain JQ170 and functional identification of nap gene in nitrite production

Heterotrophic nitrification bacteria play a critical role in nitrogen cycling and pollution removal. However, the underlying nitrification mechanisms are diverse and have rarely been investigated at the genetic level. In this study, the new heterotrophic nitrifier Pseudomonas sp. strain JQ170 was isolated. Strain JQ170 can utilize ammonia (NH₄⁺-N), nitrite (NO₂^--N), or nitrate (NO₃^--N) as sole nitrogen sources, preferring NH₄⁺-N. A ratio of 96.4% of 1.0 mM NH₄⁺-N was removed in 24 h. The optimum pH, temperature, and carbon source for NH₄⁺-N removal were pH 7.0, 30 °C, and citrate, at a C/N ratio of 9-18, respectively. During the NH₄⁺-N removal process, only NO₂^--N but neither hydroxylamine, NO₃^--N, nor gaseous nitrogen were detected. A random transposon insertion mutagenesis library of strain JQ170 was constructed. Two NO₂^--N-production deficient mutants were screened and transposon insertion sites were located in nap genes (which encode periplasmic NO₃^--N reductase Nap). Further gene knockout and complementation of the napA gene confirmed nap as essential for NO₂^--N production. The following nitrification processes in strain JQ170 is proposed: NH₄⁺-N to NO₃^--N in the cytoplasm; then NO₃^--N to NO₂^--N in the periplasmic space by Nap; finally, NO₂^--N secreted out of cells. Overall, this paper provides new insight towards understanding heterotrophic nitrification at the genetic level.

Performance and microbial community analysis of bioaugmented activated sludge for nitrogen-containing organic pollutants removal

Nitrogen-containing organic pollutants (quinoline, pyridine and indole) are widely distributed in coking wastewater, and bioaugmentation with specific microorganisms may enhance the removal of these recalcitrant pollutants. The bioaugmented system (group B) was constructed through inoculation of two aromatics-degrading bacteria, Comamonas sp. Z1 (quinoline degrader) and Acinetobacter sp. JW (indole degrader), into the activated sludge for treatment of quinoline, indole and pyridine, and the non-bioaugmented activated sludge was used as the control (group C). Both groups maintained high efficiencies (> 94%) for removal of nitrogen-containing organic pollutants and chemical oxygen demand (COD) during the long-term operation, and group B was highly effective at the starting period and the operation stage fed with raw wastewater. High-throughput sequencing analysis indicated that nitrogen-containing organic pollutants could shape the microbial community structure, and communities of bioaugmented group B were clearly separated from those of non-bioaugmented group C as observed in non-metric multidimensional scaling (NMDS) plot. Although the inoculants did not remain their dominance in group B, bioaugmentation could induce the formation of effective microbial community, and the indigenous microbes might play the key role in removal of nitrogen-containing organic pollutants, including Dokdonella, Comamonas and Pseudoxanthomonas. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis suggested that bioaugmentation could facilitate the enrichment of functional genes related to xenobiotics biodegradation and metabolism, probably leading to the improved performance in group B. This study indicated that bioaugmentation could promote the removal of nitrogen-containing organic pollutants, which should be an effective strategy for wastewater treatment.

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.

Pigmentiphaga sp. Strain D-2 Uses a Novel Amidase To Initiate the Catabolism of the Neonicotinoid Insecticide Acetamiprid

Acetamiprid, a chloronicotinyl neonicotinoid insecticide, is among the most commonly used insecticides worldwide, and its environmental fate has caused considerable concern. The compound 1-(6-chloropyridin-3-yl)-N-methylmethanamine (IM 1-4) has been reported to be the main intermediate during acetamiprid catabolism in microorganisms, honeybees, and spinach. However, the molecular mechanism underlying the hydrolysis of acetamiprid to IM 1-4 has not yet been elucidated. In this study, a novel amidase (AceAB) that initially hydrolyzes the C-N bond of acetamiprid to generate IM 1-4 was purified and characterized from the acetamiprid-degrading strain Pigmentiphaga sp. strain D-2. Based on peptide profiling of the purified AceAB and the draft genome sequence of strain D-2, aceA (372 bp) and aceB (2,295 bp), encoding the α and β subunits of AceAB, respectively, were cloned and found to be necessary for acetamiprid hydrolysis in strain D-2. The characteristics of AceAB were also systematically investigated. Though AceA and AceB showed 35% to 56% identity to the α and β subunits of the N,N-dimethylformamidase from Paracoccus aminophilus, AceAB was specific for the hydrolysis of acetamiprid and showed no activities to N,N-dimethylformamide or its structural analogs.IMPORTANCE Acetamiprid, among the top neonicotinoid insecticides used worldwide, is one of the most important commercial insecticides. Due to its extensive use, the environmental fate of acetamiprid, especially its microbial degradation, has caused considerable concern. Although the catabolic pathways of acetamiprid in microorganisms have been extensively studied, the molecular mechanisms underlying acetamiprid biodegradation (except for a nitrile hydratase) remain largely unknown, and the enzyme responsible for the biotransformation of acetamiprid into its main intermediate, IM 1-4, have not yet been elucidated. The amidase AceAB and its encoding genes, aceA and aceB, characterized in this study, were found to be necessary and specific for the initial hydrolysis of the C-N bond of acetamiprid to generate IM 1-4 in Pigmentiphaga sp. strain D-2. The finding of the novel amidase AceAB will greatly enhance our understanding of the microbial catabolism of the widely used insecticide acetamiprid at the molecular level.

Enhanced biodegradation of styrene vapors in the biotrickling filter inoculated with biosurfactant-generating bacteria under H2O2 stimulation

Biotrickling filters (BTFs) applied to hydrophobic volatile organic compounds (VOCs) suffer from limited mass transfer. Phase transfer kinetic and equilibrium effects limit the biodegradation of hydrophobic VOCs especially at high concentrations. This study evaluates two strategies for overcoming the problem. First, a natural process was used to enhance the aqueous availability of styrene, a hydrophobic VOC model, by inoculating the BTF with a mixture of biosurfactant-generating bacteria. This method achieved a maximum elimination capacity (ECmax) of 139 g m^-3h^-1 in the BTF at an empty bed residence time (EBRT) of 60s. The highest concentrations of the biosurfactants surfactin and rhamnolipid were 205 and 86 mg L^-1, respectively, in this step. Sequencing 16S rRNA confirmed the presence of biosurfactant-producing bacteria capable of biodegrading styrene in the BTF including Bacillus sonorensis, Bacillus subtilis, Lysinibacillus sphaericus, Lysinibacillus fusiformis, Alcaligenes feacalis, Arthrobacter creatinolyticus, and Kocuria rosea. Second, the effect of adding H₂O₂ to the recycle liquid on the BTF performance was determined. The biodegradation and mineralization of styrene in the BTF operated at a loading rate of 266 g m^-3h^-1 and H₂O₂/styrene molar ratio of 0.05 with EBRT as short as 15 s were 94% and 53%, respectively, with the EC of 250 g m^-3h^-1. High concentrations of antioxidant enzymes (peroxidase and catalase: 56 and 7 U g_biomass^-1, respectively) were produced and biosurfactant generation was increased in this step, contributing to enhanced styrene biodegradation and mineralization. The styrene biodegradation and mineralization values in the BTF in the last day operated under similar conditions but without H₂O₂ were 11.4% and 5.3%, respectively. The bacterial population had no considerable change in the BTF after adding H₂O₂. Accordingly, stimulating the BTF inoculated with biosurfactant-generating bacteria with H₂O₂ is a promising strategy for improving the biodegradation of hydrophobic VOCs.

Identification and Characterization of a Novel pic Gene Cluster Responsible for Picolinic Acid Degradation in Alcaligenes faecalis JQ135

Picolinic acid (PA) is a natural toxic pyridine derivative. Microorganisms can degrade and utilize PA for growth. However, the full catabolic pathway of PA and its physiological and genetic foundation remain unknown. In this study, we identified a gene cluster, designated picRCEDFB4B3B2B1A1A2A3, responsible for the degradation of PA from Alcaligenes faecalis JQ135. Our results suggest that PA degradation pathway occurs as follows: PA was initially 6-hydroxylated to 6-hydroxypicolinic acid (6HPA) by PicA (a PA dehydrogenase). 6HPA was then 3-hydroxylated by PicB, a four-component 6HPA monooxygenase, to form 3,6-dihydroxypicolinic acid (3,6DHPA), which was then converted into 2,5-dihydroxypyridine (2,5DHP) by the decarboxylase PicC. 2,5DHP was further degraded to fumaric acid through PicD (2,5DHP 5,6-dioxygenase), PicE (N-formylmaleamic acid deformylase), PicF (maleamic acid amidohydrolase), and PicG (maleic acid isomerase). Homologous pic gene clusters with diverse organizations were found to be widely distributed in Alpha-, Beta-, and Gammaproteobacteria Our findings provide new insights into the microbial catabolism of environmental toxic pyridine derivatives.IMPORTANCE Picolinic acid is a common metabolite of l-tryptophan and some aromatic compounds and is an important intermediate in organic chemical synthesis. Although the microbial degradation/detoxification of picolinic acid has been studied for over 50 years, the underlying molecular mechanisms are still unknown. Here, we show that the pic gene cluster is responsible for the complete degradation of picolinic acid. The pic gene cluster was found to be widespread in other Alpha-, Beta-, and Gammaproteobacteria These findings provide a new perspective for understanding the catabolic mechanisms of picolinic acid in bacteria.

Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors

Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic determinants and the physiological response of A. aquatilis QD168 to model environmental stressors (benzene, oxidizing agents, and salt). Phylogenomic analyses, using 35 housekeeping genes, clustered A. aquatilis QD168 with four other strains of Alcaligenes spp. (A. aquatilis BU33N, A. faecalis JQ135, A. faecalis UBA3227, and A. faecalis UBA7629). Genomic sequence analyses of A. aquatilis QD168 with 25 Alcaligenes spp., using ANIb, indicated that A. aquatilis BU33N is the closest related strain, with 96.8% ANIb similarity. Strain QD168 harbors 95 genes encoding proteins of seven central catabolic pathways, as well as sixteen peripheral catabolic pathways/reactions for aromatic compounds. A. aquatilis QD168 was able to grow on 3-hydroxybenzoate, 4-hydroxybenzoate, benzoate, benzene, 3-hydroxycinnamate, cinnamate, anthranilate, benzamide, 4-aminobenzoate, nicotinate, toluene, biphenyl and tryptophan, as sole carbon or nitrogen source. Benzene degradation was further analyzed by growth, metabolite identification and gene expression analyses. Benzene strongly induced the expression of the genes encoding phenol hydroxylase (dmpP) and catechol 1,2-dioxygenase (catA). Additionally, 30 genes encoding transcriptional regulators, scavenging enzymes, oxidative damage repair systems and isozymes involved in oxidative stress response were identified. Oxidative stress response of strain QD168 to hydrogen peroxide and paraquat was characterized, demonstrating that A. aquatilis QD168 is notably more resistant to paraquat than to H₂O₂. Genetic determinants (47 genes) for osmoprotective responses were identified, correlating with observed high halotolerance by strain QD168. The physiological adaptation of A. aquatilis QD168 to environmental stressors such as pollutants, oxidative stress and salinity may be exploited for bioremediation of oil-polluted saline sites.

Novel 3,6-Dihydroxypicolinic Acid Decarboxylase-Mediated Picolinic Acid Catabolism in Alcaligenes faecalis JQ135

Picolinic acid (PA), a typical C-2-carboxylated pyridine derivative, is a metabolite of l-tryptophan and many other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize PA for growth. However, the precise mechanism of PA metabolism remains unknown. Alcaligenes faecalis strain JQ135 utilizes PA as its carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA), with no further degradation. A novel decarboxylase, PicC, was identified to be responsible for the decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. Although, PicC belonged to the amidohydrolase 2 family, it shows low similarity (<45%) compared to other reported amidohydrolase 2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated that picC was essential for PA degradation. The PicC was Zn²⁺-dependent nonoxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. The K_m and k _cat toward 3,6DHPA were observed to be 13.44 μM and 4.77 s^-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity. This study provides new insights into the microbial metabolism of PA at molecular level.IMPORTANCE Picolinic acid is a natural toxic pyridine derived from l-tryptophan metabolism and other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6-dihydroxypicolinic acid was an intermediate in picolinic acid catabolism and further identified and characterized a novel amidohydrolase 2 family decarboxylase PicC. PicC was also shown to catalyze the decarboxylation of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding picolinic acid degradation and its underlying molecular mechanism.

Mechanism of 6-Hydroxynicotinate 3-Monooxygenase, a Flavin-Dependent Decarboxylative Hydroxylase Involved in Bacterial Nicotinic Acid Degradation

6-Hydroxynicotinate 3-monooxygenase (NicC) is a Group A FAD-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of 6-hydroxynicotinic acid (6-HNA) to 2,5-dihydroxypyridine (2,5-DHP) with concomitant oxidation of NADH in nicotinic acid degradation by aerobic bacteria. Two mechanisms for the decarboxylative hydroxylation half-reaction have been proposed [Hicks, K., et al. (2016) Biochemistry 55, 3432-3446]. Results with Bordetella bronchiseptica RB50 NicC here show that a homocyclic analogue of 6-HNA, 4-hydroxybenzoic acid (4-HBA), is decarboxylated and hydroxylated by NicC with a 420-fold lower catalytic efficiency than is 6-HNA. The ¹³( V/ K), measured with wild-type NicC by isotope ratio mass spectrometry following the natural abundance of ¹³C in the CO₂ product, is inverse for both 6-HNA (0.9989 ± 0.0002) and 4-HBA (0.9942 ± 0.0004) and becomes negligible (0.9999 ± 0.0004) for 5-chloro-6-HNA, an analogue that is 10-fold more catalytically efficient than 6-HNA. Covalently bound 6-HNA complexes of NicC are not observed by mass spectrometry. Comparative steady-state kinetic and K_d^6HNA analyses of active site NicC variants (C202A, H211A, H302A, H47E, Y215F, and Y225F) identify Tyr215 and His47 as critical determinants both of 6-HNA binding ( K_d^Y215F/ K_d^WT > 240; K_d^H47E/ K_d^WT > 350) and in coupling rates of 2,5-DHP and NAD⁺ product formation ([2,5-DHP]/[NAD⁺] = 1.00 (WT), 0.005 (Y215F), and 0.07 (H47E)]. Results of these functional analyses are in accord with an electrophilic aromatic substitution reaction mechanism in which His47-Tyr215 may serve as the general base to catalyze substrate hydroxylation and refine the structural model for substrate binding by NicC.

Long-term operation of electroactive biofilms for enhanced ciprofloxacin removal capacity and anti-shock capabilities

Few studies have focused on the feasibility of microbial fuel cells (MFCs) for removing quinolones antibiotics and their anti-shock capabilities. After 1.5 years of operation, the removal efficiency of 10 mg/L ciprofloxacin in MFCs increased to 99.00% in 88 h. These results are in accordance with the enhanced activity of biofilms and voltage output of MFCs. Additionally, the anti-shock capacities of the biofilms in MFCs were evaluated by treating ofloxacin and enrofloxacin and operating at different temperature and salinity. These MFCs can remove 87.31% and 40.81% of ofloxacin and enrofloxacin in 72 h, respectively. Even exposed to a low temperature of 10 °C or a salinity of 3%, the MFCs can achieve greater than 50% and nearly 80% of ciprofloxacin removal efficiency, respectively. The enrichment of Alcaligenes and Chryseobacterium contributed mostly to the removal of quinolones antibiotics. This study provides scientific evidences for treating wastewater containing quinolones antibiotics using MFCs.