Metabolism Of Aromatic Compounds Research Articles

Sporosarcina hypophthalmichthys sp. nov. Isolated From Gastrointestinal Tract of Fish Hypophthalmichthys molitrix (Valenciennes, 1844).

A rod-shaped, motile, Gram-stain-positive bacterial strain RKN2T, was isolated from gut of silver carp (Hypophthalmichthys molitrix) residing in Gobindsagar reservoir, Himachal Pradesh, India. Having the greatest sequence similarity to Sporosarcina koreensis F73T (98.51%), Sporosarcina luteola Y1T (98.4%) and Sporosarcina aquimarina SW28T (98.36%), the 16S rRNA gene phylogeny confirmed the belonging of strain RKN2T to genus Sporosarcina. Digital DNA-DNA hybridization values were 21.7%, 20.6%, and 19.2%, and average nucleotide identity values were 76.42%, 80.16%, 76.51%, of strain RKN2T with Sporosarcina koreensis F73T, Sporosarcina luteola Y1T, and Sporosarcina aquimarina SW28T, respectively. The genomic analysis of strain RKN2T showed various biological properties including nitrate reduction, genes responsible for carbohydrate-active enzymes production, antimicrobial compounds, as well as potential metabolism of aromatic compounds and heavy metals. G+C composition of RKN2T genome was 52.7%. This strain can grow in temperatures between 10°C and 40°C (optimum, 28°C-30°C), NaCl concentrations up to 6.0% (w/v), and 6.0-8.0 (optimum, 6.5-7.5) pH range. MK-7 was the dominant respiratory quinone, A-4 type cell wall peptidoglycan was present with anteiso-C15:0, iso-C15: 0, and anteiso-C17:0 being the major fatty acids and Lys-Glu being main amino acids. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the strain RKN2T's three main polar lipids. The strain is a novel species under genus Sporosarcina based on polyphasic approach and the name Sporosarcina hypophthalmichthys sp. nov. is given for strain RKN2T. RKN2T is a type strain (= MCC 4365T = JCM34522T = CCM9112T).

Resolving the metabolism of monolignols and other lignin-related aromatic compounds in Xanthomonas citri

Lignin, a major plant cell wall component, has an important role in plant-defense mechanisms against pathogens and is a promising renewable carbon source to produce bio-based chemicals. However, our understanding of microbial metabolism is incomplete regarding certain lignin-related compounds like p-coumaryl and sinapyl alcohols. Here, we reveal peripheral pathways for the catabolism of the three main lignin precursors (p-coumaryl, coniferyl, and sinapyl alcohols) in the plant pathogen Xanthomonas citri. Our study demonstrates all the necessary enzymatic steps for funneling these monolignols into the tricarboxylic acid cycle, concurrently uncovering aryl aldehyde reductases that likely protect the pathogen from aldehydes toxicity. It also shows that lignin-related aromatic compounds activate transcriptional responses related to chemotaxis and flagellar-dependent motility, which might play an important role during plant infection. Together our findings provide foundational knowledge to support biotechnological advances for both plant diseases treatments and conversion of lignin-derived compounds into bio-based chemicals.

Clinical Impact of Microbiome Characteristics in Treatment-Naïve Extranodal NK/T-Cell Lymphoma Patients.

Extranodal NK/T-cell lymphoma (ENKTL) predominantly manifests in East Asia and Latin America. Despite shared intrinsic factors, such as ethnic and genetic backgrounds, the progression of ENKTL can be influenced by extrinsic factors related to changing lifestyle patterns. This study collected stool samples from newly diagnosed (ND)-ENKTL patients (n=40) and conducted whole genome shotgun sequencing. ND-ENKTL revealed reduced alpha diversity in ND-ENKTL compared to healthy controls (HCs) (p=0.008), with Enterobacteriaceae abundance significantly contributing to the beta diversity difference between ENKTL and HCs (p<0.001). Functional analysis indicated upregulated aerobic metabolism and degradation of aromatic compounds in ND-ENKTL. Enterobacteriaceae were associated not only with clinical data explaining disease status (serum CRP, stage, prognosis index of natural killer cell lymphoma (PINK), and PINK-E) but also with clinical outcomes (early relapse and short progression-free survival). The relative abundance of Enterobacteriaceae at the family level was similar between ENKTL and diffuse large B-cell lymphoma (DLBCL) (p=0.140). However, the ENKTL exhibited a higher abundance of Escherichia, in contrast to the prevalence of Enterobacter and Citrobacter in DLBCL. Linear regression analysis demonstrated a significant association between Escherichia abundance and PD-L1 levels in tissue samples (p=0.025), whereas no correlation with PD-L1 was observed for Enterobacteriaceae at the family level (p=0.571). ND-ENKTL exhibited an abundance of Enterobacteriaceae and a dominant presence of Escherichia. These microbial characteristics correlated with disease status, treatment outcomes, and PD-L1 expression, suggesting the potential of the ENKTL microbiome as a biomarker and cause of lymphomagenesis, which warrants further exploration.

Effects of Bacillus altitudinis inoculants on cigar tobacco leaf fermentation.

Microbial succession and metabolic adjustment during cigar tobacco leaf (CTL) fermentation are key factors to improve the quality and flavor of CTLs. However, the interactions in the above processes remain to be further elucidated. Bacillus altitudinis inoculants were added to the CTLs, and metagenomics and metabolomics were used to analyze the effects of the inoculants on regulating microbial succession, metabolic shift, and aroma production during fermentation. The addition of the inoculants reinforced the CTL macromolecule transformation and facilitated the aroma production efficiently, and the total aroma production was increased by 43% compared with natural fermentation. The omics analysis showed that Staphylococcus was a main contributor to fatty acid degradation, inositol phosphate metabolism, energy supply (oxidative phosphorylation), nutrient transport (ABC transporter and phosphotransferase system [PTS]), and aroma production (terpenoid backbone biosynthesis, phenylalanine metabolism, and degradation of aromatic compounds). Furthermore, Staphylococcus was positively correlated with TCA cycle intermediates (citric acid, fumaric acid, and aconitic acid), cell wall components, peptidoglycan intermediates (GlcNAc-1-P and UDP-GlcNAc), and phytic acid degradation products (inositol). The characteristics collectively showed Staphylococcus to be the most dominant in the microbial community at the genus level during microflora succession. The addition of the inoculants supplemented the nutritional components of the CTLs, enhanced the metabolic activity and diversity of bacteria such as Corynebacterium, improved their competitive advantages in the microflora succession, and facilitated the richness of microbial communities. Additionally, a metabolic shift in nicotine degradation and NAD + anabolism from Staphylococcus to Corynebacterium in fermentation with inoculants was first observed. Meanwhile, the significantly correlative differential metabolites with Staphylococcus and Corynebacterium were a metabolic complement, thus forming a completely dynamic fermentation ecosystem. The results provided evidence for CTL fermentation optimization.

Noviherbaspirillum album sp. nov., an airborne bacteria isolated from an urban area of Beijing, China.

A Gram-negative, ellipsoidal to short-rod-shaped, motile bacterium was isolated from Beijing's urban air. The isolate exhibited the closest kinship with Noviherbaspirillum aerium 122213-3T, exhibiting 98.4 % 16S rRNA gene sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that it clustered closely with N. aerium 122213-3T, thus forming a distinct phylogenetic lineage within the genus Noviherbaspirillum. The average nucleotide identity and digital DNA-DNA hybridization values between strain I16B-00201T and N. aerium 122213-3T were 84.6 and 29.4 %, respectively. The respiratory ubiquinone was ubiquinone 8. The major fatty acids (>10 %) were summed feature 3 (C16:1ω6c/C16:1ω7c, 43.3 %), summed feature 8 (C18:1ω7c/C18:1ω6c, 15.9 %) and C12:0 (11.0 %). The polyamine profile showed putrescine as the predominant compound. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unknown lipids and unknown phosphatidylaminolipids. The phenotypic, phylogenetic and chemotaxonomic results consistently supported that strain I16B-00201T represented a novel species of the genus Noviherbaspirillum, for which the name Noviherbaspirillum album sp. nov. is proposed, with I16B-00201T (=CPCC 100848T=KCTC 52095T) designated as the type strain. Its DNA G+C content is 59.4 mol%. Pan-genome analysis indicated that some Noviherbaspirillum species possess diverse nitrogen and aromatic compound metabolism pathways, suggesting their potential value in pollutant treatment.

Purification, characterization and three-dimensional structure prediction of multicopper oxidase Laccases from Trichoderma lixii FLU1 and Talaromyces pinophilus FLU12

Broad-spectrum biocatalysts enzymes, Laccases, have been implicated in the complete degradation of harmful pollutants into less-toxic compounds. In this study, two extracellularly produced Laccases were purified to homogeneity from two different Ascomycetes spp. Trichoderma lixii FLU1 (TlFLU1) and Talaromyces pinophilus FLU12 (TpFLU12). The purified enzymes are monomeric units, with a molecular mass of 44 kDa and 68.7 kDa for TlFLU1 and TpFLU12, respectively, on SDS-PAGE and zymogram. It reveals distinct properties beyond classic protein absorption at 270–280 nm, with TlFLU1's peak at 270 nm aligning with this typical range of type II Cu site (white Laccase), while TpFLU12's unique 600 nm peak signifies a type I Cu2+ site (blue Laccase), highlighting the diverse spectral fingerprints within the Laccase family. The Km and kcat values revealed that ABTS is the most suitable substrate as compared to 2,6-dimethoxyphenol, caffeic acid and guaiacol for both Laccases. The bioinformatics analysis revealed critical His, Ile, and Arg residues for copper binding at active sites, deviating from the traditional two His and a Cys motif in some Laccases. The predicted biological functions of the Laccases include oxidation–reduction, lignin metabolism, cellular metal ion homeostasis, phenylpropanoid catabolism, aromatic compound metabolism, cellulose metabolism, and biological adhesion. Additionally, investigation of degradation of polycyclic aromatic hydrocarbons (PAHs) by purified Laccases show significant reductions in residual concentrations of fluoranthene and anthracene after a 96-h incubation period. TlFLU1 Laccase achieved 39.0% and 44.9% transformation of fluoranthene and anthracene, respectively, while TpFLU12 Laccase achieved 47.2% and 50.0% transformation, respectively. The enzyme structure–function relationship study provided insights into the catalytic mechanism of these Laccases for possible biotechnological and industrial applications.

First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample.

A newly isolated bacterium Acinetobacter pittii S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO4. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of A. pittii S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in A. pittii strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.

Alteration of the gut microbiota profile in children with autism spectrum disorder in China.

Autism spectrum disorder (ASD) is associated with alterations in the gut microbiome. However, there are few studies on gut microbiota of children with ASD in China, and there is a lack of consensus on the changes of bacterial species. Autism spectrum disorder (ASD) is associated with alterations in the gut microbiome. However, there are few studies on gut microbiota of children with ASD in China, and there is a lack of consensus on the changes of bacterial species. We used 16S rRNA sequencing to analyze ASD children (2 to 12 years), HC (2 to 12 years). Our findings showed that the α-diversity, composition, and relative abundance of gut microbiota in the ASD group were significantly different from those in the HC groups. Compared with the HC group, the α-diversity in the ASD group was significantly decreased. At the genus level, the relative abundance of g_Faecalibacterium, g_Blautia, g_Eubacterium_eligens_group, g_Parasutterella, g_Lachnospiraceae_NK4A136_group and g_Veillonella in ASD group was significantly increased than that in HC groups, while the relative abundance of g_Prevotella 9 and g_Agathobacter was significantly decreased than that in HC groups. In addition, KEGG pathway analysis showed that the microbial functional abnormalities in ASD patients were mainly concentrated in metabolic pathways related to fatty acid, amino acid metabolism and aromatic compound metabolism, and were partially involved in neurotransmitter metabolism. This study revealed the characteristics of gut microbiota of Chinese children with ASD and provided further evidence of gut microbial dysbiosis in ASD.

Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China.

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35°C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Molybdenum - a scoping review for Nordic Nutrition Recommendations 2023.

Molybdenum is an essential element in the form of the molybdenum cofactor (Moco). In humans, Moco is required for four enzymes: xanthine oxidase (XO), aldehyde oxidase, sulfite oxidase (SO), and mitochondrial amidoxime-reducing component (mARC). The enzymes are involved in the oxidation of purines to uric acid, metabolism of aromatic aldehydes and heterocyclic compounds, and in the catabolism of sulfur amino acids. Molybdenum cofactor deficiency is a rare autosomal recessive syndrome due to a defective synthesis of Moco, resulting in a deficiency of all the molybdoenzymes. There are no reports on clinical signs of dietary molybdenum deficiency in otherwise healthy humans. Water-soluble molybdate is efficiently absorbed from the digestive tract. The body retention is regulated by urinary excretion. Plasma molybdenum reflects long-term intake and 24-h urinary excretion is related to recent intake. There are no biochemical markers of molybdenum status. Cereal products are the main contributors to molybdenum dietary intake, estimated to 100-170 μg/day in Nordic studies. Little data are available on molybdenum toxicity in humans. A tolerable upper intake level of molybdenum has been based on reproductive toxicity in rats, but the effects have not been reproduced in more recent studies. The U.S. Institute of Medicine (IOM, present National Academy of Sciences, Engineering, and Medicine; NASEM) established a Recommended Dietary Allowance of 45 μg/day in adult men and women in 2001, based on a small study reporting urinary excretion in balance with intake at 22 μg/day. The European Food Safety Authority (EFSA) considered in 2013 the evidence to be insufficient to derive an Average Requirement and a Population Reference Intake, but proposed an Adequate Intake of 65 μg/day for adults.

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.

Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.

Upcycling of PET oligomers from chemical recycling processes to PHA by microbial co-cultivation

Polyethylene terephthalate (PET) is the most widely consumed polyester plastic and can be recycled by many chemical processes, of which glycolysis is most cost-effective and commercially viable. However, PET glycolysis produces oligomers due to incomplete depolymerization, which are undesirable by-products and require proper disposal. In this study, the PET oligomers from chemical recycling processes were completely bio-depolymerized into monomers and then used for the biosynthesis of biodegradable plastics polyhydroxyalkanoates (PHA) by co-cultivation of two engineered microorganisms Escherichia coli BL21 (DE3)-LCCICCG and Pseudomonas putida KT2440-ΔRDt-ΔZP46C-M. E. coli BL21 (DE3)-LCCICCG was used to secrete the PET hydrolase LCCICCG into the medium to directly depolymerize PET oligomers. P. putida KT2440-ΔRDt-ΔZP46C-M that mastered the metabolism of aromatic compounds was engineered to accelerate the hydrolysis of intermediate products mono-2-(hydroxyethyl) terephthalate (MHET) by expressing IsMHETase, and biosynthesize PHA using ultimate products terephthalate and ethylene glycol depolymerized from the PET oligomers. The population ratios of the two microorganisms during the co-cultivation were characterized by fluorescent reporter system, and revealed the collaboration of the two microorganisms to bio-depolymerize and bioconversion of PET oligomers in a single process. This study provides a biological strategy for the upcycling of PET oligomers and promotes the plastic circular economy.

Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification.

Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.

A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips

Insects have a limited host range due to genomic adaptation. Thysanoptera, commonly known as thrips, occupies distinct feeding habitats, but there is a lack of comparative genomic analyses and limited genomic resources available. In this study, the chromosome-level genome of Stenchaetothrips biformis, an oligophagous pest of rice, is assembled using multiple sequencing technologies, including PacBio, Illumina short-reads, and Hi-C technology. A 338.86 Mb genome is obtained, consisting of 1269 contigs with a contig N50 size of 381 kb and a scaffold N50 size of 18.21 Mb. Thereafter, 17,167 protein-coding genes and 36.25% repetitive elements are annotated. Comparative genomic analyses with two other polyphagous thrips, revealing contracted chemosensory-related and expanded stress response and detoxification gene families in S. biformis, potentially facilitating rice adaptation. In the polyphagous thrips species Frankliniella occidentalis and Thrips palmi, expanded gene families are enriched in metabolism of aromatic and anthocyanin-containing compounds, immunity against viruses, and detoxification enzymes. These expansion gene families play crucial roles not only in adapting to hosts but also in development of pesticide resistance, as evidenced by transcriptome results after insecticides treatment. This study provides a chromosome-level genome assembly and lays the foundation for further studies on thrips evolution and pest management.

Decolorization of p-nitrophenol and draft genome sequence of Pseudomonas sp. strain PNPG3: A preliminary report

Aim: To study decolorization (with concomitant depletion) of p-nitrophenol by a bacterial strain designated as PNPG3 and determination of draft genome sequence of the strain to understand its potential. Methodology: A comparative study of PNP’s decolorization (with concomitant removal) in three different test conditions was undertaken. The experiment was carried out in one-liter volume Schott Duran bottles. Genomic DNA was extracted and draft genome sequence was determined using Illumina HiSeqX platform. Raw reads were assembled and subjected to subsystem classification using several bioinformatics tools (RAST, PATRIC, and NCBI’s PGAP pipelines). The genome sequence was deposited at the NCBI Genome database and the strain PNPG3 was also deposited at MTCC, IMTECH, Chandigarh. Results: The bacterial strain PNPG3 could carry out decolorization with concomitant removal of PNP in all three sets of experiments, including one set, where only distilled water was used. The best decolorization (with concomitant PNP removal) capacity was recorded for set D (with Minimal Medium, MM; PNP, and free cells) followed by set E (MM, PNP, and immobilized cells) and set B (distilled water, PNP and free cells) conditions. The size of the draft genome sequence of the strain PNPG3 was 6,566,321 bp, with 62.26% GC contents. The genome had 6210 protein-coding sequences and 66 tRNA genes. The predictive presence of different types of proteases and siderophore receptors indicated its possible potential for industrial applications and plant growth-promoting activities. Interpretation: The bacterium Pseudomonas sp. strain PNPG3 has the capacity to decolorize p-nitrophenol even in presence of distilled water and it remains viable for up to twelve days. The genome sequence revealed that the strain harbored genes responsible for the metabolism of aromatic compounds, chemotaxis, protease, and siderophore receptors indicating the versatile nature of the strain. Key words: Decolorization, P-nitrophenol, Pseudomonas sp., RAST, Xenobiotic

Analysis of bacterioplankton genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium.

Hamilton Harbour is an impaired embayment of Lake Ontario that experiences seasonal algal blooms despite decades of remedial efforts. To study the harbour's cyanobacterial and heterotrophic bacterial communities, we extracted and sequenced community DNA from surface water samples collected biweekly from different sites during summer and fall. Assembled contigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobacteria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer. Microcystis aeruginosa and Limnoraphis robusta were most abundant throughout the sampling period, expanding the documented diversity of Cyanobacteria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism, and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism was consistent, suggesting that these genes remained essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing Cyanobacteria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.

Impacts of dibutyl phthalate on bacterial community composition and carbon and nitrogen metabolic pathways in a municipal wastewater treatment system

Dibutyl phthalate (DBP) is a typical toxic and hazardous pollutant in pharmaceutical wastewater, affecting the metabolism of microbial flora, leading to decreased treatment efficiency, and deteriorated effluent quality in municipal wastewater treatment plants (WWTPs). This study conducted a long-term experiment with 6 operational stages in a pilot-scale A2O-MBR system, analyzing the effect of DBP on the bacterial community and their carbon and nitrogen metabolic pathways. 16S rRNA gene amplicon sequencing analysis and principal components analysis (PCA) showed that DBP at 8 mg/L significantly influenced the structure of bacterial community (P < 0.05), resulting in reduced bacterial community diversity. Metagenomic analysis was used to explore the embedded carbon and nitrogen metabolic pathways. At the presence of DBP, the metabolism of saccharides, lipids, and aromatic compounds were blocked owing to the vanishment of key enzyme (such as acetylaminohexosyltransferase (EC 2.4.1.92) and UDP-sugar pyro phosphorylase (EC 2.7.7.64)) encoding genes, resulting in weakened carbon metabolism, and thus reduced COD removal performance. The resultant deficiency of the genes such as those encoding hydroxyproline dehydrogenase (EC 1.5.5.3) gave rise to interrupted metabolic pathways of amino acid (arginine, proline, tyrosine, and tryptophan), resulting in declined function of nitrogen metabolism and thus reduced TN removal efficiency. The uncovery of the mechanisms by which DBP affects wastewater treatment system efficiency and microbial metabolism is of theoretical importance for the efficient operation of municipal and pharmaceutical wastewater treatment systems.

Pyrethroids exposure alters the community and function of the internal microbiota in Aedes albopictus

Large amounts of insecticides bring selection pressure and then develop insecticide resistance in Aedes albopictus. This study demonstrated for the first time the effect of pyrethroid exposure on the internal microbiota in Ae. albopictus. 36, 48, 57 strains of virgin adult Ae. albopictus were exposed to the pyrethroids deltamethrin (Dme group), β-cypermethrin (Bcy group), and cis-permethrin (Cper group), respectively, with n-hexane exposure (Hex group) as the controls (n = 36). The internal microbiota community and functions were analyzed based on the metagenomic analysis. The analysis of similarity (ANOSIM) results showed that the Hex/Bcy (p = 0.001), Hex/Cper (p = 0.006), Hex/Dme (p = 0.001) groups were well separated, and the internal microbes of Ae. albopictus vary in the composition and functions depending on the type of pyrethroid insecticide they are applied. Four short chain fatty acid-producing genera, Butyricimonas, Prevotellaceae, Anaerococcus, Pseudorhodobacter were specifically absent in the pyrethroid-exposed mosquitoes. Morganella and Streptomyces were significantly enriched in cis-permethrin-exposed mosquitoes. Wolbachia and Chryseobacterium showed significant enrichment in β-cypermethrin-exposed mosquitoes. Pseudomonas was significantly abundant in deltamethrin-exposed mosquitoes. The significant proliferation of these bacteria may be closely related to insecticide metabolism. Our study recapitulated a specifically enhanced metabolic networks relevant to the exposure to cis-permethrin and β-cypermethrin, respectively. Benzaldehyde dehydrogenase (EC 1.2.1.28), key enzyme in aromatic compounds metabolism, was detected enhanced in cis-permethrin and β-cypermethrin exposed mosquitoes. The internal microbiota metabolism of aromatic compounds may be important influencing factors for pyrethroid resistance. Future work will be needed to elucidate the specific mechanisms by which mosquito microbiota influences host resistance and vector ability.

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

Metagenomics Reveals the Microbiome Multifunctionalities of Environmental Importance From Termite Mound Soils.

The ecological deterioration caused by the continuous and excessive use of synthetic inputs in agriculture has prompted the search for environmentally favorable resources for crop production. Many have advocated for the use of soils from termite mounds to improve soil and plant health; therefore, the purpose of this study was to characterize the microbiome multifunctionalities that are important for plant health and growth in termite mound soil. The metagenomics of soil from termite mounds revealed taxonomic groups with functional potentials associated with promoting the growth and health of plants in nutrient-poor, virtually dry environments. Analysis of microorganisms revealed that Proteobacteria dominated the soil of termite colonies, while Actinobacteria ranked second. The predominance of Proteobacteria and Actinobacteria, the well-known antibiotic-producing populations, indicates that the termite mound soil microbiome possesses metabolic resistance to biotic stresses. Functions recognized for diverse proteins and genes unveiled that a multi-functional microbiome carry out numerous metabolic functions including virulence, disease, defense, aromatic compound and iron metabolism, secondary metabolite synthesis, and stress response. The abundance of genes in termite mound soils associated with these prominent functions could unquestionably validate the enhancement of plants in abiotic and biotically stressed environments. This study reveals opportunities to revisit the multifunctionalities of termite mound soils in order to establish a connection between taxonomic diversity, targeted functions, and genes that could improve plant yield and health in unfavorable soil conditions.