Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats.

Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3 and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation.

Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux.

Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N11-ATG), compared to those of odcA/orf419 (CAT-N11-ATG) and odcC (CAT-N11-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.

The effect of macrophage polarization on the expression of the oxytocin signalling system in enteric neurons.

BACKGROUND: The aim of the current study was to investigate the effect of macrophage polarization on the expression of oxytocin (OT) and the oxytocin receptor (OTR) in enteric neurons. METHODS: In this study, we used a classic colitis model and D-mannose model to observe the correlation between macrophage polarization and OT signalling system. In order to further demonstrate the effect of macrophages, we examined the expression of OT signalling system after depletion of macrophages. RESULTS: The data showed that, in vitro, following polarization of macrophages to the M1 type by LPS, the macrophage supernatant contained proinflammatory cytokines (IL-1ß, IL-6 and TNF-α) that inhibited the expression of OT and OTR in cultured enteric neurons; following macrophage polarization to the M2 type by IL4, the macrophage supernatant contained anti-inflammatory cytokines (TGF-ß) that promoted the expression of OT and OTR in cultured enteric neurons. Furthermore, M1 macrophages decreased the expression of the OT signalling system mainly through STAT3/NF-κB pathways in cultured enteric neurons; M2 macrophages increased the expression of the OT signalling system mainly through activation of Smad2/3 and inhibition of the expression of Peg3 in cultured enteric neurons. In a colitis model, we demonstrated that macrophages were polarized to the M1 type during the inflammatory phase, with significant decreased in the expression of OT and OTR. When macrophages were polarized to the M2 type during the recovery phase, OT and OTR expression increased significantly. In addition, we found that D-mannose increased the expression of OT and OTR through polarization of macrophages to the M2 type. CONCLUSIONS: This is the first study to demonstrate that macrophage polarization differentially regulates the expression of OT and OTR in enteric neurons.

Chitiniphilus eburneus sp. nov., a novel chitinolytic bacterium isolated from sludge.

A novel Gram-stain-negative, curved rod-shaped, motile and non-endospore-forming strain, designated HX-2-15T, was isolated from activated sludge of agricultural chemical plant in Nanjing, Jiangsu province, PR China (32° 03' N, 118° 46' E) . Growth was observed at 15-37 °C (optimum between 25 and 30 °C), at pH 6.0-8.0 (optimum at pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum at 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain showed closest affiliation to Chitiniphilus shinanonensis SAY3T, with a sequence similarity of 99.0 %. The predominant cellular fatty acids were C16:0, C17:0 cyclo and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The major quinone was ubiquinone Q-8 . The polar lipid profile was composed of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified lipid and one unidentified aminophosphoglycolipid . The genomic DNA G+C content of the strain was 63.6 mol%. The ANI and dDDH values obtained between the genomes of HX-2-15T and C. shinanonensis SAY3T were 85.3 and 29.3 % respectively. On the basis of data from phenotypic, chemotaxonomic and genotypic analysis, strain HX-2-15T represents a novel species of the genus Chitiniphilus, for which the name Chitiniphilus eburneus sp. nov. is proposed. The type strain is HX-2-15T (=KCTC 72286T=CCTCC AB 2019178T).

Pedobacter puniceum sp. nov. Isolated from Sludge.

Strain HX-22-1T was isolated from the sludge collected from the outlet of the biochemical treatment facility of an agricultural chemical factory in Nanjing city, Jiangsu province, PR China. Strain HX-22-1T is Gram-staining-negative, rod-shaped, non-spore-forming and non-flagellated. The 16S rRNA gene-based phylogenetic analysis indicates that the strain HX-22-1T belongs to the genus Pedobacter, closely related to Pedobacter glucosidilyticus KCTC 22438T (98.63% similarity). The genomic DNA G+C content of the strain was 34.4 mol%. Strain HX-22-1T was able to grow at 16-37 °C (optimum at 30 °C), at pH 6.0-8.0 (optimum at pH 7.0), and with 0-1% (w/v) NaCl (optimum at 0). Predominant fatty acid constituents were iso-C15:0 and summed feature 3 (iso-C16:1ω7c and/or C16:1ω6c). The predominant respiratory ubiquinone was MK-7. The polar lipid profile is composed of phosphatidylethanolamine (PE), aminophospholipid (APL), aminolipid (AL), and phospholipids (PL). The ANI and dDDH values obtained between the genomes of HX-22-1T and P. glucosidilyticus KCTC 22438T were 89.6 and 38.8%, respectively. On the basis of data from phenotypic, chemotaxonomic, and genotypic analysis, strain HX-22-1T represents a novel species of the genus Pedobacter, for which the name Pedobacter puniceum sp. nov. is proposed. The type strain is HX-22-1T (= KCTC 72655T = CCTCC AB 2019348T).

Crenobacter caeni sp. nov. Isolated from Sludge.

Strain HX-7-9T was isolated from the activated sludge collected from the outlet of the biochemical treatment facility of agricultural chemical plant in Nanjing, Jiangsu province, PR China. Strain HX-7-9T is Gram staining-negative, rod-shaped, non-spore-forming and flagellated. The 16S rRNA gene-based phylogenetic analysis indicate that strain HX-7-9T belongs to the genus Crenobacter, moderately related to Crenobacter luteus YIM-78141T (94.8% similarity). The genomic DNA G+C content of the strain was 67.5 mol%. Strain HX-7-9T was able to grow at 16-45 °C (optimum at 37 °C), at pH 6.0-8.0 (optimum at pH 7.0) and with 0-1% (w/v) NaCl (optimum at 0). Predominant fatty acid constituents were C16:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The respiratory ubiquinone was Q-8. The polar lipid profile is composed of diphosphatidylglycerol (DPG), phosphatidylmonomethylethanolamine (PME), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and aminophospholipid (APL). The ANI and dDDH values obtained between the genomes of HX-7-9T and C. luteus YIM-78141T were 79.8 and 19.1%, respectively. On the basis of data from phenotypic, chemotaxonomic and genotypic analysis, strain HX-7-9T represents a novel species of the genus Crenobacter, for which the name Crenobacter caeni sp. nov. is proposed. The type strain is HX-7-9T (= KCTC 72654T = CCTCC AB 2019349T).

Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China.

A Gram-stain-negative, facultative aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, designated strain NAU-18T was isolated from an oil-contaminated soil in China. Strain NAU-18T could grow at 10-42 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum, 0.5% NaCl in R2A). The predominant fatty acids were C18:1ω7c (71.2%) and Summed feature 2 (5.1%), representing 76.3% of the total fatty acids. The major respiratory quinones were Q9 and Q10. The DNA G + C content of strain NAU-18T was 61.4 mol% based on its draft genome sequence. Genome annotation of strain NAU-18T predicted the presence of 6668 genes, of which 6588 are coding proteins and 80 are RNA genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NAU-18T was a member of the genus Rhizobium and showed 96.93% (with 93.2% coverage) and 96.81% (with 100% coverage) identities with those of Neorhizobium alkalisoli CCBAU 01393T and Rhizobium oryzicola ZYY136T, respectively. In the phylogenetic analysis, strain NAU-18T and R. oryzicola ZYY136T are consistently placed in the same branch. Strain NAU-18T represents a novel species within the genus Rhizobium, for which the name Rhizobium terrae sp. nov. is proposed, with the type strain NAU-18T (=KCTC 62418T = CCTCC AB 2018075T).

The Properties of 5-Methyltetrahydrofolate Dehydrogenase (MetF1) and Its Role in the Tetrahydrofolate-Dependent Dicamba Demethylation System in Rhizorhabdus dicambivorans Ndbn-20.

The herbicide dicamba is initially degraded via the tetrahydrofolate (THF)-dependent demethylation system in Rhizorhabdus dicambivorans Ndbn-20. Two THF-dependent dicamba methyltransferase gene clusters, scaffold 50 and scaffold 66, were found in the genome of strain Ndbn-20. Each cluster contains a dicamba methyltransferase gene and three THF metabolism-related genes, namely, metF (coding for 5,10-CH2-THF reductase), folD (coding for 5,10-CH2-THF dehydrogenase-5,10-methenyl-THF cyclohydrolase), and purU (coding for 10-formyl-THF deformylase). In this study, reverse transcription-PCR (RT-PCR) results showed that only genes in scaffold 66, not those in scaffold 50, were transcribed in dicamba-cultured cells. The metF gene of scaffold 66 (metF1) was expressed in Escherichia coli BL21(DE3), and the product was purified as a His6-tagged protein. Purified MetF1 was found to be a monomer and exhibited 5-CH3-THF dehydrogenase activity in vitro The kcat and Km for 5-CH3-THF were 0.23 s-1 and 16.48 µM, respectively. However, 5,10-CH2-THF reductase activity was not detected for MetF1 under the conditions tested. Gene disruption results showed that metF1 is essential for dicamba degradation, whereas folD1 is dispensable.IMPORTANCE There are several THF-dependent methyltransferase genes and THF-metabolic genes in the genome of R. dicambivorans Ndbn-20; however, which genes are involved in dicamba demethylation and the mechanism underlying THF regeneration remain unknown. This study revealed that scaffold 66 is responsible for dicamba demethylation and that MetF1 physiologically catalyzes the dehydrogenation of 5-CH3-THF to 5,10-CH2-THF in the THF-dependent dicamba demethylation system in R. dicambivorans Ndbn-20. Furthermore, the results showed that MetF1 differs from previously characterized MetF in phylogenesis, biochemical properties, and catalytic activity; e.g., MetF1 in vitro did not show 5,10-CH2-THF reductase activity, which is the physiological function of Escherichia coli MetF. This study provides new insights into the mechanism of the THF-dependent methyltransferase system.

Protective roles of hepatic GABA signaling in acute liver injury of rats.

γ-Aminobutyric acid (GABA) is produced by various cells through the catalytic activity of glutamic acid decarboxylase (GAD). Activation of type-A GABA receptor (GABAAR) inhibits stem cell proliferation but protects differentiated cells from injures. The present study investigated hepatic GABA signaling system and the role of this system in liver physiology and pathophysiology. RT-PCR and immunoblot assays identified GAD and GABAAR subunits in rat livers and in HepG2 and Clone 9 hepatocytes. Patch-clamp recording detected GABA-induced currents in Clone 9 hepatocytes and depolarization in WITT cholangiocytes. The function of hepatic GABA signaling system in rats was examined using models of d-galactosamine (GalN)-induced acute hepatocytic injury in vivo and in vitro. The expression of GAD increased whereas GABAAR subunits decreased in the liver of GalN-treated rats. Remarkably, treating rats with GABA or the GABAAR agonist muscimol, but not the GABABR agonist baclofen, protected hepatocytes against GalN toxicity and improved liver function. In addition, muscimol treatment decreased the formation of pseudobile ductules and the enlargement of hepatocytic canaliculi in GalN-treated rats. Our results revealed that a complex GABA signaling system exists in the rat liver. Activation of this intrahepatic GABAergic system protected the liver against toxic injury.NEW & NOTEWORTHY Auto- and paracrine GABAergic signaling systems exist in the rat hepatocytes and cholangiocytes. Activation of GABA signaling protects liver function from d-galactosamine injury by reducing toxic impairment of hepatocytes and by decreasing cholangiocyte proliferation.

Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost.

Strain Ndbn-20T, a Gram-staining-negative, non-spore-forming bacterium, was isolated from compost of plant litter. The strain was able to degrade dicamba. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Ndbn-20Trepresented a member of the family Sphingomonadaceae of the Alphaproteobacteria and showed high sequence similarities to Rhizorhabdusargentea SP1T (98.8 %), Sphingomonaswittichii RW1T (97.9 %), Sphingomonasstarnbergensis 382T (97.7 %) and Sphingomonashistidinilytica UM2T (97.7 %). However, the strain showed low DNA sequence relatedness with R. argentea SP1T (45.6±1.9 %), S. wittichii RW1T (33.5±2.3 %), S.histidinilytica UM2T (39.4±3.6 %) and S. starnbergensis382T (42.1±4.1 %). Ndbn-20T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine, and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), C17 : 1ω6c, C16 : 0 and C14 : 02-OH as the major fatty acids (>5 % of the total). The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, glycolipid, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylglycerol. The DNA G+C content was 65.4 mol%. Based on a polyphasic taxonomic analysis, strain Ndbn-20T is proposed to represent a novel species of the genus Rhizorhabdus, with the proposed name of Rhizorhabdus dicambivorans sp. nov. The type strain is Ndbn-20T (=CCTCC AB 2016143=KACC 18661).

A novel amidohydrolase (DmhA) from Sphingomonas sp. that can hydrolyze the organophosphorus pesticide dimethoate to dimethoate carboxylic acid and methylamine.

OBJECTIVES: To characterize a novel dimethoate amidohydrolase from Sphingomonas sp. DC-6. RESULTS: A gene, dmhA, encoding the dimethoate amidohydrolase responsible for transforming dimethoate to dimethoate carboxylic acid and methylamine, was cloned from Sphingomonas sp. DC-6. Sequence analysis and molecular modeling indicate that DmhA shares 31-57 % amino acid sequence identities with other functionally confirmed amidohydrolase. DmhA was expressed in Escherichia coli BL21 (DE3) and purified by Ni-NTA affinity chromatography. The purified DmhA could hydrolyze 4-acetaminophenol, dimethoate and propanil. DmhA activity was optimal at 30 °C and pH 7.5. Hg(2+), Zn(2+), Cu(2+), Cd(2+), Tween 80, Triton X-100 or SDS strongly inhibited its activity. The K m and k cat values of DmhA for dimethoate are 0.02 mM and 1.2 s(-1), respectively. CONCLUSIONS: DmhA was confirmed to be a novel dimethoate amidohydrolase which could eliminate the toxicity of dimethoate, providing a novel gene resource for the development of pesticide-degrading enzyme preparation and mechanistic study of dimethoate hydrolysis.

Tahibacter caeni sp. nov., isolated from activated sludge.

A Gram-reaction-negative, aerobic, rod-shaped, non-spore-forming, non-motile bacterial strain, designated BUT-6(T), was isolated from activated sludge of a wastewater-treatment facility. The strain grew at 15-35 °C (optimum 30 °C), pH 4.0-10.0 (optimum pH 7.0) and 0-3.0 % (w/v) NaCl (optimum 1.0 %). Phylogenetic analysis based on 16S rRNA sequences showed that strain BUT-6(T) was most closely related to Tahibacter aquaticus PYM5-11(T) (98.6 % similarity). However, the DNA-DNA relatedness between strain BUT-6(T) and T. aquaticus PYM5-11(T) was 47.1 %. The major fatty acids (>10 % of total fatty acids) of strain BUT-6(T) were iso-C15 : 0, iso-C17 : 1ω9c and iso-C17 : 0. The major respiratory quinone was ubiquinone Q-8. The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and unidentified phospholipids. The DNA G+C content of strain BUT-6(T) was 71.7 mol%. On the basis of the data from the polyphasic taxonomic study presented, strain BUT-6(T) is considered to represent a novel species of the genus Tahibacter, for which the name Tahibacter caeni sp. nov. is proposed. The type strain is BUT-6(T) ( = CCTCC AB 2013266(T) = KACC 17139(T)).

Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory.

A novel aerobic, Gram-stain-negative, motile bacterium, designated strain BUT-10(T), was isolated from the sludge of a pesticide manufacturing factory in Kunshan, China. Cells were rod-shaped (0.4-0.45×0.9-1.4 µm) and colonies were white, circular with entire edges and had a smooth surface. The strain grew at 25-37 °C, at pH 6.0-8.0 and with 0-0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BUT-10(T) was a member of the genus Phenylobacterium, and showed highest sequence similarities to Phenylobacterium muchangponense A8(T) (97.49 %), Phenylobacterium immobile DSM 1986(T) (97.14 %) and Phenylobacterium lituiforme FaiI3(T) (96.34 %). Major fatty acids (>5 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 71.85 mol%. Strain BUT-10(T) showed low DNA-DNA relatedness with P. muchangponense A8(T) (15.7±2.9 %) and P. immobile DSM 1986(T) (12.8±1.1 %). On the basis of the phenotypic, phylogenetic and genotypic data, strain BUT-10(T) is considered to represent a novel species of the genus Phenylobacterium, for which the name Phenylobacterium kunshanense sp. nov. is proposed. The type strain is BUT-10(T) ( = CCTCC AB 2013085(T) = KCTC 42014(T)).

Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory.

Strain BUT-8(T), a Gram-stain-negative, non-motile and rod-shaped aerobic bacterium, was isolated from the activated sludge of a herbicide-manufacturing wastewater treatment facility. Comparative 16S rRNA gene sequence analysis revealed that strain BUT-8(T) clustered with species of the genus Lysobacter and was closely related to Lysobacter ruishenii DSM 22393(T) (98.3 %) and Lysobacter daejeonensis KACC 11406(T) (98.7 %). The DNA G+C content of the genomic DNA was 70.6 mol%. The major respiratory quinone was ubiquinone-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 010-methyl). The DNA-DNA relatedness between strain BUT-8(T) and its closest phylogenetic neighbours was below 70 %. Phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain BUT-8(T) belongs to the genus Lysobacter and represents a novel species for which the name Lysobacter caeni sp. nov. is proposed. The type strain is BUT-8(T) ( = CCTCC AB 2013087(T) = KACC 17141(T)).

Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil.

An aerobic, Gram-stain negative, pale, rod-shaped, nitrogen-fixing bacterial strain, DDT-3(T), was isolated from dichlorodiphenyltrichloroethane-contaminated soil in Liyang, PR China. Strain DDT-3(T) grew at temperatures ranging from 20 to 40 °C (optimum 30-37 °C) and a pH of between 5.0 and 10.0 (optimum pH 7.0-8.0). The G+C content of the total DNA was 70.1 mol%. The 16S rRNA gene sequence of strain DDT-3(T) showed the highest similarity to that of Pseudoxanthobacter soli CC4(T) (99.6%), followed by Kaistia dalseonensis B6-8(T) (93.3%), Kaistia soli 5YN9-8(T) (93.0%) and Amorphus orientalis YIM D10(T) (93.0%). Strain DDT-3(T) showed less than 92.6 % similarity with other species of the family Xanthobacteraceae. The major cellular fatty acids of strain DDT-3(T) were C19:0 cyclo ω8c (42.6%), C16:0 (33.2%) and C18:1ω7c (10.0%). The only respiratory quinone was ubiquinone Q-10. The characteristic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major polar lipids were glycolipid, lipid, phosphatidylcholine, aminolipid, phosphatidylmethylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile consisted of major amounts of putrescine (92.9%) and minor amounts of spermidine (5.0%) and spermine (2.1%). These chemotaxonomic data support the affiliation of strain DDT-3(T) with the genus Pseudoxanthobacter. The DNA-DNA hybridization value between strain DDT-3(T) and strain CC4(T) was 47.8% (reciprocal 44.3%). DNA-DNA hybridization data as well as the biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain DDT-3(T) and strain CC4(T). Strain DDT-3(T), therefore, represents a novel species of the genus Pseudoxanthobacter, for which the name Pseudoxanthobacter liyangensis sp. nov. is proposed. The type strain is DDT-3(T) ( = KACC 16601(T) = CCTCC AB 2013167(T)).

Protective effect of oxytocin on vincristine-induced gastrointestinal dysmotility in mice.

Aims: Vincristine (VCR), an antineoplastic drug, induces peripheral neuropathy characterized by nerve damage, limiting its use and reducing the quality of life of patients. VCR causes myenteric neuron damage, inhibits gastrointestinal motility, and results in constipation or paralytic ileus in patients. Oxytocin (OT) is an endogenous neuropeptide produced by the enteric nerve system, which regulates gastrointestinal motility and exerts neuroprotective effects. This study aimed to investigate whether OT can improve VCR-induced gastrointestinal dysmotility and evaluate the underlying mechanism. Methods: Mice were injected either with saline or VCR (0.1 mg/kg/d, i. p.) for 14 days, and OT (0.1 mg/kg/d, i.p.) was applied 1 h before each VCR injection. Gastrointestinal transit and the contractile activity of the isolated colonic segments were assessed. The concentration of OT in plasma was measured using ELISA. Immunofluorescence staining was performed to analyze myenteric neurons and reactive oxygen species (ROS) levels. Furthermore, the indicators of oxidative stress were detected. The protein expressions of Nrf2, ERK1/2, P-ERK1/2, p38, and P-p38 in the colon were tested using Western blot. Results: VCR reduced gastrointestinal transit and the responses of isolated colonic segments to electrical field stimulation and decreased the amount of neurons. Furthermore, VCR reduced neuronal nitric oxide synthase and choline acetyltransferase immunopositive neurons in the colonic myenteric nerve plexus. VCR increased the concentration of OT in plasma. Exogenous OT pretreatment ameliorated the inhibition of gastrointestinal motility and the injury of myenteric neurons caused by VCR. OT pretreatment also prevented the decrease of superoxide dismutase activity, glutathione content, total antioxidative capacity, and Nrf2 expression, the increase of ROS levels, and the phosphorylation of ERK1/2 and p38 MAPK following VCR treatment. Conclusion: Our results suggest that OT pretreatment can protect enteric neurons from VCR-induced injury by inhibiting oxidative stress and MAPK pathways (ERK1/2, p38). This may be the underlying mechanism by which it alleviates gastrointestinal dysmotility.

Potential and benefits of biochar production: crop straw management and carbon emission mitigation in Shaanxi Province, China.

Shaanxi Province is an important agricultural province in western China. Its profit-oriented management of crop residues remains a concern in the agriculture sector. Aiming to accelerate the valorization of agricultural straw and offer potential solutions for profit-oriented use of crop residues in Shaanxi, this study estimated the quantity of resources and collectable amount of crop straw by using the grain-to-straw ratio, analyzed the carbon emission reduction potential considering biochar energy and soil uses with the help of a life cycle assessment (LCA) model, and calculated the economic benefits of biochar production using waste and abandoned straw in Weinan (a city of Shaanxi). The theoretical resources and collectible amount of crop straw in Shaanxi showed an overall growth trend from 1949 to 2021, reaching 1.47 × 107 and 1.26 × 107 t in 2021 respectively. In 2021, straw from corn, wheat, and other grains accounted for 94.32% of the total straw. Among the 11 cities in Shaanxi, Weinan had the largest straw resources of 2.82 × 106 t, Yulin had the largest per capita straw resources of 0.72 t/person, and Yangling had the highest resource density of 7.60 t/hm2. The total carbon emission reduction was 3.11 × 104 t under scenario A with crop straw used for power generation. The emission reduction ranged from 1.25 × 107 to 1.27 × 107 CO2e t under scenario B with biochar production for energy and soil use. By using waste and abandoned straw in Weinan for biochar production, carbon emissions could be reduced by up to 2.07 × 105 t CO2e. In terms of the economic benefit from straw pyrolysis, the actual income was estimated to range from 0.67 × 108 to 1.33 × 108 ¥/a with different carbon prices. This study sheds light on the economic and environmental benefits of agricultural straw valorization through pyrolysis in Shaanxi, and provided an important basis for promoting the agricultural straw utilization in view of its potential for carbon emission reduction.

A fast and efficient method for isolating and culturing enteric neural precursor cells from adult mouse colon.

BACKGROUND: The enteric neural precursor cells (ENPCs) are important for researching the pathogenesis of enteric nervous system (ENS)-related diseases, especially in adulthood. Because primary ENPCs are difficult to isolate and survive, easy to contaminate and low-yielding, a rapid and effective method to isolate and cultivate ENPCs from adult mice is necessary. NEW METHODS: The longitudinal muscle myenteric plexus (LMMP) was isolated from the adult mouse colon. The papain and collagenase Ⅱ were chosen to increase the yield of ENPCs. The growth and proliferation of ENPCs could be promoted by using polylysine precoated culture plates and reasonable cell seeding density. The ENPCs were identified by Nestin and the proliferative properties were verified by EDU. The transgenic Nestin-cre:tdTomato mice were used to observe the proliferation of ENPCs more intuitively in vitro. RESULTS: Our method to isolate the ENPCs from adult mouse colon was effective and high-yielding. The ENPCs were identified as Nestin positive. The Nestin-positive ENPCs could proliferate rapidly and had a tendency to differentiate into neurons and glial cells in vitro without any inducing factors. COMPARISON WITH EXISTING METHODS: Previous studies about the ENPCs focused on experiment in vivo or were limited to the embryonic mice, and had limitations of low yield and long experiment time. The ENPCs from adult mice were isolated quickly by our method, and had a high yield and purity. CONCLUSION: We described a rapid, efficient, step by step method for isolation and culture of ENPCs from the adult mouse colon, which was simple and obtained high yield of ENPCs.

[Temporal and Spatial Distribution, Utilization Status, and Carbon Emission Reduction Potential of Straw Resources in China].

Based on the crop yield data of China and each region from 1981 to 2020 (excluding data from Hong Kong, Macao, and Taiwan), by using the grain-straw ratio method, this study estimated the total amount of crop straw and collectable amount of crops, including corn, rice, wheat, other cereals, cotton, rapeseeds, peanuts, beans, tubers, sesame, fiber crops, sugarcane, and beetroots, and the spatial and temporal distribution characteristics of resource density and per capita resources of crop straw were analyzed. This study analyzed the current utilization mode, development, and change of crop straw in China. Finally, we used the life circle assessment (LCA) method to estimate the carbon emission reduction potential of biochar prepared from crop straw. The main findings were:from 1981 to 2020, the temporal distribution trend of theoretical crop straw resources and collectable straw resources in China generally showed a steady growth trend, and the two increased from 3.33×108 t and 3.04×108 t in 1981 to the highest values of 7.70×108 t and 6.63×108 t in 2020, with a net increase of 4.37×108 t and 3.59×108 t, respectively. The net increase in rice, wheat, and corn straw resources was 3.69×108t, accounting for between 77% and 85% of the total crop straw and always occupying the main position of straw resources in China. The proportion of wheat straw in the total amount of straw was maintained at approximately 20%, rice straw resources decreased from 44% to 28.4%, and corn straw increased from 19.9% to 34.2% from 1981 to 2020. In 2020, the total theoretical resources of crop straw in China were 7.72×108 t, and the source structures were:rice 28.4%, wheat 21.45%, corn 31.45%, other cereals 1.4%, beans 3.4%, tubers 0.82%, cotton 2.28%, peanuts 2.97%, rapeseeds 3.4%, sesame 0.12%, fiber crops 0.06%, beetroots 0.67%, and sugarcane 0.84%. As to the spatial distribution of crop straw resources in China in 2020, the locations with straw resources ≥ 60 million tons included Heilongjiang, Henan, and Shandong, of which Henan had as much as 88.56 million tons; those with between 40 million and 60 million tons included Hebei, Inner Mongolia, Jiangsu, and Anhui; those with between 20 million and 40 million tons included Liaoning, Jilin, Jiangxi, Hubei, Hunan, Sichuan, Yunnan, and Xinjiang; and the straw resources in the rest of the region were below 20 million tons. Rice straw was mostly distributed in the middle and lower reaches of the Yangtze River and the Northeast region, of which the amount of Heilongjiang rice straw was the largest, with 31.86 million tons; wheat straw was mainly distributed in North China, with Henan having the most abundant resources (48.04 million tons). Corn straw was mainly distributed in Northeast China and North China, of which Heilongjiang and Inner Mongolia corn straw resources were relatively rich, with 33.18 million tons and 29.90 million tons, respectively. Crop straw resource density and per capita resources were shared in 2020 in China. The average density of crop straw resources in China was 4.61 t·hm-2, and the average densities of crop straw resources in various agricultural areas were 5.39 t·hm-2 in Northeast China, 5.42 t·hm-2 in North China, 4.45 t·hm-2 in the Mengxin Region, 4.44 t·hm-2 in the middle and lower reaches of the Yangtze River, 3.92 t·hm-2in Tibet, 3.40 t·hm-2 in the Loess Plateau, 3.08 t·hm-2 in South China, and 2.91 t·hm-2 in Southwest China. The average per capita share of straw resources was 0.55 t. The average values of per capita straw resources in each region were:1.46 t in the Northeast area, 1.20 t in the Mengxin Region, 0.47 t in North China, 0.44 t in the middle and lower reaches of the Yangtze River, 0.40 t in the Loess Plateau, 0.37 t in the Southwest area, 0.33 t in the Qinghai-Tibet area, and 0.20 t in the South China area. The utilization of crop straw in China was diversified. Fertilizer and feed were the main utilizations, accounting for 62.1% and 15.4%, respectively. In 2020, collectable crop straw resources for the preparation of biochar totaled 2.04×108 t in China. Renewable energy replaced fossil fuels in the process of preparing biochar, which could reduce CO2e(CO2e:CO2 equivalent) emissions by 1.45×108 t. Biochar could sequester approximately 4.63×108 t of CO2e; biochar application was able to reduce chemical fertilizer application to achieve a CO2 emission reduction of 8.58×105 t; and biochar application could promote crop yield in order to reduce CO2e emissions by approximately 7.77×106 t. The inhibition of N2, respectively. In the process of biochar preparation and application, the total greenhouse gas emission was 3.32×107 t, and the net greenhouse effect emission reduction reached 5.86×108 t, i.e., it could sequester 0.88 t CO2e per ton of raw materials. The net greenhouse gas emission reduction of unused straw was 6.73×107 t in 2020. With the continuous harvest of grain crops in China, the potential of biochar preparation and carbon sequestration will increase yearly. Using crop straw to prepare biochar has great potential and will be one of the most effective ways to achieve carbon emission reduction in agriculture. It is suggested that government departments should pay attention to the preparation of biochar, support the field experiments of biochar application effects after applying soil on policy and funds, and then introduce relevant biochar standards to ensure the scientific application of biochar prepared by crop straw according to local conditions, so as to achieve the dual benefits of carbon emission reduction and soil remediation and yield increase.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation.

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.