Degradation Of Aromatic Compounds Research Articles

Physiological and Transcriptome Analysis on Diploid and Polyploid Populus ussuriensis Kom. under Salt Stress.

Populus ussuriensis Kom. is a valuable forest regeneration tree species in the eastern mountainous region of Northeast China. It is known that diploid P. ussuriensis (CK) performed barely satisfactorily under salt stress, but the salt stress tolerance of polyploid (i.e., triploid (T12) and tetraploid (F20)) P. ussuriensis is still unknown. In order to compare the salt stress tolerance and salt stress response mechanism between diploid and polyploid P. ussuriensis, phenotypic observation, biological and biochemistry index detections, and transcriptome sequencing (RNA-seq) were performed on CK, T12, and F20. Phenotypic observation and leaf salt injury index analysis indicated CK suffered more severe salt injury than T12 and F20. SOD and POD activity detections indicated the salt stress response capacity of T12 was stronger than that of CK and F20. MDA content, proline content and relative electric conductivity detections indicated CK suffered the most severe cell-membrane damage, and T12 exhibited the strongest osmoprotective capacity under salt stress. Transcriptome analysis indicated the DEGs of CK, T12, and F20 under salt stress were different in category and change trend, and there were abundant WRKY, NAM, MYB and AP2/ERF genes among the DEGs in CK, T12, and F20 under salt stress. GO term enrichment indicated the basic growth progresses of CK, and F20 was obviously influenced, while T12 immediately launched more salt stress response processes in 36 h after salt stress. KEGG enrichment indicated the DEGs of CK mainly involved in plant–pathogen interaction, ribosome biogenesis in eukaryotes, protein processing in endoplasmic reticulum, degradation of aromatic compounds, plant hormone signal transduction, photosynthesis, and carbon metabolism pathways. The DEGs of T12 were mainly involved in plant–pathogen interaction, cysteine and methionine metabolism, phagosomes, biosynthesis of amino acids, phenylalanine, tyrosine and tryptophan biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. The DEGs of F20 were mainly involved in plant hormone signal transduction, plant–pathogen interaction, zeatin biosynthesis, and glutathione metabolism pathways. In conclusion, triploid exhibited stronger salt stress tolerance than tetraploid and diploid P. ussuriensis (i.e., T12 > F20 > CK). The differences between the DEGs of CK, T12, and F20 probably are the key clues for discovering the salt stress response signal transduction network in P. Ussuriensis.

Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency.

Oil contamination is of great concern worldwide and needs to be properly addressed. The present work aimed to contribute to the development of bacterial consortia for oil recovery. We investigated the community structure of a landfarming-treated soil (LF2) by metagenomics to unravel the presence of hydrocarbon degraders. Moreover, we isolated Shinella zoogloeoides LFG9 and Bacillus swezeyi LFS15 from LF2 and combined them with Pseudomonas guguanensis SGPP2 isolated from an auto mechanic workshop soil to form the mixed consortium COG1. Bacterial isolates were tested for biosurfactant production. Additionally, the bioremediation potential of COG1 was studied as free and entrapped consortia by gas chromatography-mass spectrometry, in comparison to the single strains. Results revealed the presence of Actinobacteria (66.11%), Proteobacteria (32.21%), Gammaproteobacteria (5.39%), Actinomycetales (65.15%), Burkholderiales (13.92%), and Mycobacterium (32.22%) taxa, indicating the presence of hydrocarbon degraders in soil LF2. All three isolated strains were biosurfactant producers capable of degrading crude oil components within 14 days. However, Shinella zoogloeoides LFG9 performed best and was retained as candidate for further bioremediation investigation. In addition, COG1 performed better when immobilized, with entrapment effectiveness manifested by increased fatty acids and aromatic compound degradation. Attempt to improve crude oil biodegradation by adding surfactants failed as sodium dodecyl sulfate restrained the immobilized consortium performance.

Structural insights into the substrate specificity of 5-chloro-2-hydroxymuconate tautomerase CnbG

The catechol meta-cleavage pathway is widely involved in the degradation of aromatic compounds, including those halogenated aromatic hydrocarbons and their derivatives. CnbG is a kind of 4-oxalocrotonate tautomerase (4-OT) located in the catechol meta-cleavage pathway, catalyzes the ketonization of cis,cis-5-chloro-2-hydroxymuconate and cis,cis-2-hydroxymuconate to yield 5-chloro-2-oxo-3-hexene-1,6-dioate and 2-oxo-3-hexene-1,6-dioate, and contributes to the degradation of 4-chloronitrobenzene and chlorobenzene in Comamonas testosteroni CNB-1. Yet, the reason why CnbG and those 4-OTs could recognize various substrates is not well explained. Here, we determined the crystal structure of CnbG at resolution of 2.0 Å and identified that the potential substrate pocket involved in four conserved residues, residues Pro1, Arg11, Arg39 and Trp50, but not five conserved residues as those reported in other 4-OTs. We also found the four conserved residues assemble different sequence patterns in different 4-OTs, indicating their potential roles in catalysis and substrate binding. Via molecular docking, we found the 5-chloro group was clamped by two residues and extended to the solvent, indicating a substrate binding mode that could bear the substitution of different groups in the 5-position. Our work extends the knowledge of the substrate specificity of enzymes in the catechol meta-cleavage pathway.

Abstract 5637: Transformation of the gut microbiome in response to androgen deprivation and the transition to castration-resistant prostate cancer

Abstract Androgen deprivation therapy (ADT) remains the standard care for men with advanced prostate cancer. Although initially effective, many patients fail to maintain durable responses and progress to lethal castration-resistant prostate cancer. Commensal bacteria play important role in maintaining homeostasis and proper immune function. However, ADT alters gut bacterial compositions and the ramifications being investigated. In this study, we used a mouse model of Pten-deficient prostate cancer to characterize differences in bacterial composition of gut bacteria in mice with castration naïve-prostate cancer (CNPC) and gut microbiota from mice three and six weeks after treatment ADT via surgical castration representing castration-sensitive prostate cancer (CSPC) and CRPC, respectively. Fecal samples were collected and processed for 16s rRNA amplicon sequencing. ADT resulted in significant changes to biological diversity and local diversity was highest in CSPC (Shannon index, P=0.04). Community composition also differed significantly different between the groups (Adonis OTU Bray-Curtis, P=0.001, NMDS stress=0.07). Despite dissimilarities between bacterial communities among the groups, CNPC and CRPC shared a greater similarity. Taxa associated with CNPC included Unclassified S247, Prevotella L. reuteri, unclassified Rikenellaceae and unclassified Bacteroidales; taxa associated with CSPC included R. gnavus, Dorea, unclassified Desulfovibrionaceae, Dehalobacterium, A. muciniphilia, Bifidobacterium, and B. producta; and taxa associated with CRPC included Turicibacter, R. flavefaciens, L. garvieae, unclassified Peptostreptococcaceae and unclassified Bacilli. Mice with CSPC and CRPC had an increased abundance genes associated with of catabolic metabolic pathways associated with aromatic compound, steroid Benzoate, and toluene degradation as well as genes associated to pathways corresponding to methane metabolism, phosphonate and phosphinate metabolism, and nitrogen metabolism. Genes enriched in fecal taxa from CNPC and CRPC mice were associated with folate biosynthesis, galactose metabolism, amino sugar and nucleotide sugar metabolism, and carbon fixation pathways in prokaryotes. This study provides preclinical evidence to support the association between the gut microbiome and prostate cancer phenotypes associated with sensitivity to ADT. Citation Format: Chisato Wakamori, Marco A. De Velasco, Kazuko Sakai, Yurie Kura, Naomi Ando, Kazutoshi Fujita, Eri Banno, Kazuhiro Yoshimura, Masahiro Nozawa, Kazuto Nishio, Hirotsugu Uemura. Transformation of the gut microbiome in response to androgen deprivation and the transition to castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5637.

The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China

The diversity of prokaryotic communities in soil is shaped by both biotic and abiotic factors. However, little is known about the major factors shaping soil prokaryotic communities at a large scale in agroecosystems. To this end, we undertook a study to investigate the impact of maize production cropping systems, soil properties and geographic location (latitude and longitude) on soil prokaryotic communities using metagenomic techniques, across four distinct maize production regions in China. Across all study sites, the dominant prokaryotes in soil were Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Gemmatimonadetes, Acidobacteria, and Actinobacteria. Non-metric multidimensional scaling revealed that prokaryotic communities clustered into the respective maize cropping systems in which they resided. Redundancy analysis (RDA) showed that soil properties especially pH, geographic location and cropping system jointly determined the diversity of the prokaryotic communities. The functional genes of soil prokaryotes from these samples were chiefly influenced by latitude, soil pH and cropping system, as revealed by RDA analysis. The abundance of genes in some metabolic pathways, such as genes involved in microbe–microbe interactions, degradation of aromatic compounds, carbon fixation pathways in prokaryotes and microbial metabolism were markedly different across the four maize production regions. Our study indicated that the combination of soil pH, cropping system and geographic location significantly influenced the prokaryotic community and the functional genes of these microbes. This work contributes to a deeper understanding of the composition and function of the soil prokaryotic community across large-scale production systems such as maize.

Integrated Metabolomic-Transcriptomic Analysis Reveals Diverse Resource of Functional Ingredients From Persimmon Leaves of Different Varieties.

Persimmon leaves are used for making persimmon leaf tea or as functional ingredients due to their enrichment in flavonoids, the beneficial mineral contents, and favorable flavors contributed by volatile aroma compounds. The varieties/cultivars had a significant influence on the quality and flavor of persimmon leaf tea. In this study, the integrated metabolomic-transcriptomic analysis was conducted to investigate the potential in flavonoid biosynthesis, mineral absorption, and degradation of aromatic compounds from tender leaves of “Diospyros kaki. Heishi” (HS), “Diospyros kaki Thunb. Nishimurawase” (NM), and “Diospyros kaki Thunb. Taifu” (TF), using rootstock “Diospyros Lotus Linn” (DL) as the control. The metabolomic analysis showed that 382, 391, and 368 metabolites were differentially accumulated in the comparison of DL vs. HS, DL vs. NM, and DL vs. TF, respectively, and 229 common metabolites were obtained by comparative analysis. By RNA sequencing, 182,008 unigenes with 652 bp of mean length were annotated and 2,598, 3,503, and 3,333 differentially expressed genes (DEGs) were detected from the comparison of DL vs. HS, DL vs. NM, and DL vs. TF, respectively. After the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, 6, 6, and 3 DEGs [with | log2(fold change)| ≥ 1 simultaneously in the three comparisons] involved in flavonoid biosynthesis, mineral absorption, and degradation of aromatic compounds, respectively, were selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR) validation and the consistent trends of the relative expression level of each DEG with RNA sequencing (RNA-seq) data were observed. Based on the transcriptomic analysis and qRT-PCR validation, it was observed that the leaves of HS, NM, and TF had the greatest level of mineral absorption, flavonoid biosynthesis, and degradation of aromatic compounds, respectively. In addition, a positive correlation between the 15 DEGs and their metabolites was observed by the conjoint analysis. Thus, the tender leaves of HS, NM, and TF could be recommended for the production of persimmon leaf tea rich in mineral elements, flavonoid, and aroma compounds, respectively.

Monocot diet sources drive diversity of gut bacterial communities in Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae

AbstractMicrobiome research is currently gaining tremendous interest on the impact of diets and environment to influence life traits of several hosts. Full understanding of the insect ecology and characterization of gut microbial community including their natural enemies is vital for development of novel insect pest management strategies. This study examined the gut bacterial communities of Fall armyworm (FAW) Spodoptera frugiperda reared in the laboratory with three monocot plant diets (Sugarcane [M1], maize [M2] and onion [M3]) using 16S rRNA gene sequencing. The study revealed variations in the structure and community of the gut bacterial biota of FAW larvae reared with three monocot plants. Diet sources greatly altered the structure of the gut bacterial community. Three alpha diversity indices (observed species richness Chao1 and ACE) showed significant differences among the various diet groups. The principal component analysis revealed a moderate distinction in bacterial communities of the FAW larvae reared with the three monocot plants. Higher numbers of operational taxonomic units (OTUs) were observed in sugarcane diet (M1). The bacterial communities of all the larvae groups were dominated by phylum Firmicutes. A redundancy analysis (RDA) indicated that neutral detergent fibre (NDF) (p < 0.0005) was the most significant factors influencing the community distribution of gut bacteria of FAW larvae. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis predicted that chemoheterotrophy, fermentation, aerobic chemoheterotrophy and aromatic compound degradation were the prominent putative functions of FAW larvae gut bacteria communities. Chemoheterotrophy was the most dominant putative functions predicted and was higher in sugarcane diet. Furthermore, the complexity of the network structure was higher in M1 while the modularity was higher in maize diet. The different monocot diets had a considerable impact on bacterial composition in the gut of Fall armyworm larvae and their ecological and functional relevance are discussed.

Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660

BackgroundWhile the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation.ResultsTYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon.ConclusionsComputational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species.

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.

Copiotrophic Bacterial Traits Increase With Burn Severity One Year After a Wildfire

Wildfire and burn severity influence soil microbial communities during post-fire recovery. If post-fire differences in microbial communities affect soil carbon (C) pool dynamics, altered microbial communities could influence the transition of forests from C sources to C sinks during ecosystem recovery. For example, fire may change the abundance of copiotrophic and oligotrophic bacteria, influencing the kinetic rates of soil C pools due to differences in C-acquisition strategies and nutrient requirements. We assessed differences in soil bacterial communities and soil C pool kinetics 1 year after a wildfire in a mixed-conifer forest in northern California, United States. We determined whether differences in bacterial communities and soil C pools were related to copiotrophic versus oligotrophic life history strategies. Specifically, we assessed bacterial community oligotrophy versus copiotrophy based on phyla relative abundances and predicted 16S gene copy numbers. We then determined whether these life-histories were correlated with C pool kinetic rates. We further determined whether C degradation metabolic pathways predicted using PICRUSt2 were related to C pool kinetics. We found that copiotrophic bacteria exhibited greater abundance in burned areas than unburned areas, evidenced by increases in 16S rRNA gene copy number and by taxonomic classifications. Furthermore, the abundance of predicted metabolic pathways associated with fast-cycling C compounds increased with severity, including carbohydrate, alcohol, and amine degradation pathways, suggesting increased copiotrophic metabolic strategies. In contrast, the abundance of metabolic pathways of slow-cycling aromatic C compounds did not change, indicating oligotrophic metabolic strategies did not increase. The kinetic rate of the active C pool was positively related to the copiotrophic metabolic pathway of alcohol degradation, and negatively related to oligotrophic pathways like aromatic compound degradation. The links between C pool kinetics and phylum-level life-strategy classifications were ambiguous. Overall, our results suggest that metabolic life-strategies are related to soil C pool kinetics and could have short- and long-term impacts on soil C persistence during post-fire recovery. In the short-term, increased copiotrophy could increase soil C effluxviarapid cycling of labile C pools. However, over the longer-term lower prevalence of oligotrophic strategies could allow aromatic compounds associated with pyrogenic C to accumulate, increasing stable soil C stocks.

Collaborative removal of NOx and toluene in flue gas driven by aerobic denitrifying biotrickling filter

Nitrogen oxides (NOx) and volatile organic compounds (VOCs) may cause ozone formation and photochemical smog pollution, which may damage to human health and ecological environment seriously. An aerobic Denitrifying BioTrickling Filter (DBTF) for collaborative removal of nitrogen oxides (NOx) and toluene in flue gas was investigated. NOx and toluene removal efficiency were up to 90% and 95%, respectively. Mycobacterium, Comamonas and Pseudomonas were predominant bacteria; Mycobacterium, Pseudomonas, Comamonas, Microbacterium, Reyranella, Stenotrophomonas and Alicycliphilus were the core toluene oxidizing-denitrifying genera, denitrification genes (narGHI, nirK, nasB, napAB, nosZ and norC) and toluene oxidation genes (tom, E1.14.13.7, xyl, cat, todE, tes, mhp, pch, pob, pca, lig, gal) responsible for bacterial oxidation of toluene and NOx reduction, as shown by16S rDNA and metagenomic sequencing. Bacterial oxidation of toluene was coupled to NOx reduction in which toluene served as the electron donor while NOx served as the electron acceptor and thereby redox between toluene and NOx was formed, toluene was degraded through the classical aerobic aromatic compound degradation pathway. DBTF was capable of both toluene oxidation and NOx reduction by denitrification. These results show that the DBTF is achievable and open new possibilities for applying the DBTF to simultaneous removal of NOx and VOCs.

High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation

Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m−3 day−1. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.

Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing

Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, 13C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody “hog fuel” pile (53 and 62 °C zones). 13C-Lignin degradation was monitored using IR-GCMS of 13CO2, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with 13C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in 13C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.

Effector Or Substrate: Characterizing Molecular Features of 6‐HNA That Govern Enhanced Rates of NADH Oxidation and Hydroxylation by 6‐Hydroxynicotinate‐3‐Monooxygenase (NicC)

Group A flavin‐dependent monooxygenases are involved in the degradation of aromatic compounds and the biosynthesis of natural products. These enzymes catalyze the regioselective incorporation of one oxygen atom from dioxygen into their substrates. Comparison of the mechanisms through which the enzymes in this class work could assist in future bioremediation efforts and aid in lowering the costs of synthesis of hydroxylated aromatic compounds. 6‐Hydroxynicotinate 3‐monooxygenase (NicC), a member of this class of enzymes, catalyzes the decarboxylative‐hydroxylation of 6‐hydroxynicotinic acid (6‐HNA) to 2,5‐dihydroxypyridine with concomitant oxidation of NADH. Like other enzymes in its class, the binding of 6‐HNA stimulates an increase in the rate of oxidation of NADH, however the structural determinants of 6‐HNA responsible for this are unknown. Here we show by kinetic analyses of NicC variants that NicC uses Arg184 to form an ion pair with the carboxylate of 6‐HNA to stabilize the ES complex. Once 6‐HNA is bound, an electronegative atom para to the carboxylate (the 6‐oxo group in 6‐HNA) strongly increases the rate of NADH oxidation, possibly by changing the hydrogen bonding network in the active site and allowing the FAD cofactor to swing to the “out orientation”, allowing for closer contact with NADH and therefore more efficient hydride transfer. Previous work showed that NicC is able to bind its substrates (6‐HNA and 5‐chloro‐6‐HNA) via a 2‐step mechanism, where deprotonation of the pyrindolic group of the substrate governs the second step. Molecules that bind and increase the rate of NADH oxidation without turning over into products are called effectors. Thus, effectors share a common molecular characteristic that prevents them from undergoing the coupled hydroxylative pathway in NicC. Through this we sought to determine the 6‐HNA analogues that act as effectors of NicC in attempt to determine how NicC distinguishes between substrates and effectors. 6‐Chloro‐nicotinic acid, 6‐amino‐nicotinic acid and 6‐methyl nicotinic acid were found to be effectors in NicC (Fig 1). These three molecules are not likely to be ionized by deprotonation, signifying that deprotonation of the substrate could govern the coupled and uncoupled hydroxylation pathways in NicC (Scheme 1). Thus, NicC’s mechanism of controlling NADH reduction of FAD appears to be distinct from the mechanism utilized by p‐hydroxybenzoic acid hydroxylase, the quintessential group A flavin dependent monooxygenase.

Variation in Bacterial Community Structures and Functions as Indicators of Response to the Restoration of Suaeda salsa: A Case Study of the Restoration in the Beidaihe Coastal Wetland.

Microbes play an essential role in the restoration of degraded coastal wetlands. However, few studies have focused on the role of key bacteria in the restoration process. Here, Suaeda salsa was planted to recover the biodiversity in the degraded Beidaihe coastal wetland. We monitored omics and soil environmental factors to understand the complex relationship between the bacterial community and wetland health during the restoration period. After planting S. salsa in the degraded area, the soil quality was improved in the later stage of restoration (LPR). Bacterial α-diversity increased with restoration and was positively correlated with TOC. Proteobacteria is the dominant bacterial phylum during the restoration period, and Bacteroidetes, Planctomycetes, Gemmatimonadetes, and Acidobacteria were sensitive to the planting restoration. Random forest analysis picked 30 key OTUs, showing the key bacterial variation of successful restoration. The result indicated that the sum of the relative abundances of key bacterial OTUs was more than 2% in the health wetland. The β-diversity showed that the growth of S. salsa reshaped the soil bacterial community structure and function in the LPR, which recovered to the level in the control area. Putative biogeochemical functions showed that symbionts and aromatic compound degradation were dominant bacterial functions in the growth period of S. salsa. Our study proposed a new indicator to assess wetland health and the planting restoration of S. salsa increased bacteria groups with the ability of symbionts and aromatic compound degradation in the Beidaihe coastal wetland. This study expanded our knowledge of coastal wetland restoration and its ecological contributions.

Microbial electrolysis enhanced bioconversion of coal to methane compared with anaerobic digestion: Insights into differences in metabolic pathways

Coal seams are considered occurrence sites for coalbed methane (CBM) accumulation and bio-methanation and sequestration of CO2. Biological approaches for the enhancement of the methanation rate of CO2 for CBM production have attracted increasing attention. The microbial electrolysis cell (MEC) is a technology with strong potential to improve the performance of the traditional anaerobic digestion (AD) system. In this study, AD and MEC-AD systems were developed to produce biomethane from coal. The results showed that the cumulative methane production of MEC-AD was 6.05 mL/g coal, 39.08% higher compared to AD alone (4.35 mL/g coal). The CO2 concentration was lower in the MEC-AD reactor, suggesting that the CO2 from coal degradation was further converted to biomethane. Metagenomics sequencing results showed that Geobacter.sp and Methanosarcina.sp were enriched in the anodic biofilm to the greatest extent, implying that direct interspecies electron transfer at the anode may promote biomethanation. Moreover, there was significant upregulation in the gene abundances of key enzymes involved in the degradation of aromatic compounds and methanogenic metabolism in hydrolytic bacteria. In particular, the gene pilA, which controls conductive pili, was significantly upregulated. The key intermediate metabolites (benzoic acid, phenol, pentadecane, etc.) showed a higher concentration and conversion rate in MEC-AD hydrolysis compared to AD. These results suggest that the efficiency of hydrolysis and interspecies electron transfer during coal digestion are facilitated by MEC technology, achieving a significant increase in biomethane production. This study provides insights into the development of efficient and low or negative carbon technologies for enhancing biomethane production and CO2 emission reduction.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. The gut microbiome of C. fluminea was diverse, differed with environmental conditions and varied spatially among rivers, but was unrelated to host genetic variation. Microbial source tracking suggested that the gut microbiome of C. fluminea may be influenced by the presence of co-occurring native mussels. Inferred functions from 16S rRNA gene data using PICRUST2 predicted a high prevalence and diversity of degradation functions in the C. fluminea microbiome, especially the degradation of carbohydrates and aromatic compounds. Such modularity and functional diversity of the microbiome of C. fluminea may be an asset, allowing to acclimate to an extensive range of nutritional sources in invaded habitats, which could play a vital role in its invasive success.

Supporting non-noble metal composite organosilica monolithic foam for efficiently catalytic degradation of aromatic compounds

The porous monolithic materials supporting non-noble metal nanoparticles that acted as catalysts have recently gained increasing attention due to their robust activity and regenerative ability, resulting in simple chemical progress. It is crucial for the catalytic performance that the monolithic supporters have a hierarchically porous structure while the non-noble metal nanoparticles show a good control of their dimensions and oxidation states. Herein this work reports the composite organosilica monolithic (OSM) foams containing non-noble metal like Cu-, Co-, or Ni-based nanoparticles. As-prepared the supporting non-noble metal nanoparticles organosilica monolithic foams could act as monolithic catalyst, showing the efficiently catalytic performance for the degradation of aromatic compounds. These monolithic catalysts were prepared via amino-functionalization of organosilica monolith with ethylenic groups, followed by supporting non-noble metal nanoparticles through a simple reduction process. The monolithic catalyst involved Cu-based nanoparticles (Cu/OSM) were obtained via reduction of Cu 2+ using a mixture of NaBH 4 with and without the aid of polyvinylpyrrolidone K 90 (PVP), as denoted by Cu/OSM-N and Cu/OSM-P, respectively. It was demonstrated that the addition of PVP into the system caused the higher Cu content, the better distribution of the smaller Cu-based nanoparticles and a richer Cu(0) nanoparticles. Furthermore Cu/OSM-P exhibited high stability and durable activity, with approximately 95% conversion within 14 successive cycles, for the catalytic reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) with excess NaBH 4 in an aqueous solution. This catalyst also showed a remarkable catalytic performance for the degradation of other organic aromatic dyes like methylene blue (MB), methyl orange (MO), rhodamine B (RhB) and even their mixture. In addition, Co/OSM-P and Ni/OSM-P fabricated with the same method also showed high catalytic performance for reduction of 4-NP. We believe that the strategy developed in this work is very useful for the simple, low-cost, and environmentally friendly preparation of porous composite monolithic catalysts containing non-noble metal nanoparticles.

Comparative genomics reveals the evidence of aromatic hydrocarbons degradation potential in genus Roseovarius in marine environment

Aromatic compounds are eco-toxic organic pollutants widely distributed in the marine environment, and microbes of the genus Roseovarius have demonstrated high potential for bioremediation and degradation of aromatic compounds. However, rare comprehensive comparative genomic studies of the genus Roseovarius on their diversity and aromatic degrading functions are available. In this work, the whole genome of phenanthrene-degrading strain Roseovarius sp. SCSIO 43702 was sequenced and comparatively analyzed with other 44 isolated Roseovarius strains. We have detected a weak significant (ANOSIM, R = 0.3804, p = 0.01) between the phylogenetic clades and the geographic source, and found a complete phenanthrene metabolic pathway presented in most Roseovarius strains. Further, nine investigated Roseovarius strains were selected for the phenanthrene biodegradation assay, and eight marine originated strains exhibited significant higher the degrading ability (T-test, p < 0.05) than control group. Collectively, these results showed the environmental adaptation and aromatic degradation potential of the genus Roseovarius at the genomic and phenotypic levels, and provided references to evaluate applicable prospects of Roseovarius strains in aromatic bioremediation of the marine environment.

Genome sequencing of Pseudomonas aeruginosa strain M2 illuminates traits of an opportunistic pathogen of burn wounds.

Pseudomonas aeruginosa is a Gram-negative nosocomial pathogen and one of the most prevalent organisms isolated from burn wounds worldwide. Pseudomonas aeruginosa strain M2 (O5 serotype, type B flagella) is utilized for examining the murine model associated with burns. Pseudomonas aeruginosa M2 is similar in lethality to common laboratory P. aeruginosa strains when infecting CD-1 mice. Conversely, we recently showed that, relative to these strains, P. aeruginosa M2-infected mice are more susceptible to sepsis and demonstrate a 6-log reduction in LD50 from subcutaneous infection at the infection site directly after 10% total body surface area burn. To better understand this striking phenotypic difference from other P. aeruginosa strains employed in burn models, we sequenced the P. aeruginosa M2 genome. A total of 4,136,641 read pairs were obtained, providing an average genome coverage of 97.5X; subsequent assembly yielded a draft genome with 187 contigs comprising 6,360,304 bp with a G + C content of 66.45%. Genome-based phylogeny estimation of 92 P. aeruginosa strains placed P. aeruginosa M2 with P. aeruginosa-12-4-4(59), a nonairway clinical strain isolated from the blood culture of a burn patient. Phylogenomic analyses identified genes shared between P. aeruginosa M2 and P. aeruginosa 14, another strain exhibiting increased lethality in thermal tissues, as well as P. aeruginosa M2 unique genes with diverse functions like degradation of toxic aromatic compounds, iron scavenging, swarming motility and biofilm formation, defense against invasive DNA, and host assault. Predicted lateral gene transfers illuminate proteins heretofore uncharacterized for roles in P. aeruginosa biology. Our work yields a rich resource for assessing P. aeruginosa genes required for increased lethality in burn tissue seroma.