Groundwater denitrification enhanced by a hydrogel immobilized iron/solid carbon source: impact on denitrification and substrate release performance.

Encapsulating a solid carbon source and zero-valent iron (ZVI) within a hydrogel can prevent direct contact with groundwater, thereby extending the lifespan of their released active substrates. It is currently unclear whether the solid carbon source and ZVI will mutually influence each other's active substrate release process and the corresponding denitrification patterns, necessitating further investigation. In this study a hydrogel encapsulating different weight ratios of micron-sized zero-valent iron (mZVI, as ZVI) and polyhydroxybutyrate (PHB, as a solid carbon source) was synthesized. The aim was to investigate the influence of PHB on the release of dissolved iron from mZVI and denitrification mechanism. Results indicated that PHB was consumed at a higher rate than mZVI, and more mZVI active sites could be exposed after PHB consumption. Meanwhile, PHB increased the porosity of the hydrogel, allowing more active sites of mZVI to be exposed and thus releasing more dissolved iron. Furthermore, PHB enhanced the rate of microbial corrosion of mZVI, which further increased the release of dissolved iron. Higher PHB content in the hydrogel reduced the oxidation of the released dissolved iron, resulting in a microbial community dominated by heterotrophic microorganisms. Conversely, lower PHB content led to significant Fe(II) oxidation and a considerable relative abundance of mixotrophic microorganisms in the microbial community. Microorganisms with iron reduction potential were also detected. This study provides theoretical support for the precise control of mixed nutrient denitrification based on hydrogel immobilization and lays the foundation for its further practical application in groundwater.

Coupling of polyhydroxybutyrate and zero-valent iron for enhanced treatment of nitrate pollution within the Permeable Reactive Barrier and its downgradient aquifer.

Permeable Reactive Barriers (PRBs) have been utilized for mitigating nitrate pollution in groundwater systems through the use of solid carbon and iron fillers that release diverse nutrients to enhance denitrification efficiency. We conduct laboratory column tests to evaluate the effectiveness of PRBs in remediating nitrate pollution both within the PRB and in the downgradient aquifer. We use an iron-carbon hydrogel (ICH) as PRB filler, which has different weight ratios of polyhydroxybutyrate (PHB) and microscale zero-valent iron (mZVI). Results reveal that denitrification in the downgradient aquifer accounts for at least 19.5 % to 32.5 % of the total nitrate removal. In the ICH, a higher ratio of PHB to mZVI leads to higher contribution of the downgradient aquifer to nitrate removal, while a lower ratio results in smaller contribution. Microbial community analysis further reveals that heterotrophic and mixotrophic bacteria dominate in the downgradient aquifer of the PRB, and their relative abundance increases with a higher ratio of PHB to mZVI in the ICH. Within the PRB, autotrophic and iron-reducing bacteria are more prevalent, and their abundance increases as the ratio of PHB to mZVI in the ICH decreases. These findings emphasize the downgradient aquifer's substantial role in nitrate removal, particularly driven by dissolved organic carbon provided by PHB. This research holds significant implications for nutrient waste management, including the prevention of secondary pollution, and the development of cost-effective PRBs.

Genome-Wide Analysis of the BAHD Family in Welsh Onion and CER2-LIKEs Involved in Wax Metabolism.

BAHD acyltransferases (BAHDs), especially those present in plant epidermal wax metabolism, are crucial for environmental adaptation. Epidermal waxes primarily comprise very-long-chain fatty acids (VLCFAs) and their derivatives, serving as significant components of aboveground plant organs. These waxes play an essential role in resisting biotic and abiotic stresses. In this study, we identified the BAHD family in Welsh onion (Allium fistulosum). Our analysis revealed the presence of AfBAHDs in all chromosomes, with a distinct concentration in Chr3. Furthermore, the cis-acting elements of AfBAHDs were associated with abiotic/biotic stress, hormones, and light. The motif of Welsh onion BAHDs indicated the presence of a specific BAHDs motif. We also established the phylogenetic relationships of AfBAHDs, identifying three homologous genes of CER2. Subsequently, we characterized the expression of AfCER2-LIKEs in a Welsh onion mutant deficient in wax and found that AfCER2-LIKE1 plays a critical role in leaf wax metabolism, while all AfCER2-LIKEs respond to abiotic stress. Our findings provide new insights into the BAHD family and lay a foundation for future studies on the regulation of wax metabolism in Welsh onion.

Distinct chromium removal mechanisms by iron-modified biochar under varying pH: Role of iron and chromium speciation.

Iron-modified biochar (Fe-biochar) has been widely developed to attenuate Cr(VI) pollution in both acid and alkaline environments. However, there are few comprehensive studies on how the iron speciation in Fe-biochar and chromium speciation in solution influencing the removal of Cr(VI) and Cr(III) under varying pH. Here, multiple Fe-biochar containing Fe3O4 or Fe(0) were prepared and applied to remove aqueous Cr(VI). Kinetics and isotherms suggested that all Fe-biochar could efficiently remove Cr(VI) and Cr(III) via adsorption-reduction-adsorption. The Fe3O4-biochar immobilized Cr(III) by forming FeCr2O4, while amorphous Fe-Cr coprecipitate and Cr(OH)3 was formed when using Fe(0)-biochar. Density functional theory (DFT) analysis further indicated that pH increase caused more negative adsorption energies between Fe(0)-biochar and the pH-dependent Cr(VI)/Cr(III) species. Consequently, the adsorption and immobilization of Cr(VI) and Cr(III) species by Fe(0)-biochar was more favored at higher pH. In comparison, Fe3O4-biochar exhibited weaker adsorption abilities for Cr(VI) and Cr(III), which were in consistent with their less negative adsorption energies. Nonetheless, Fe(0)-biochar merely reduced ∼70% of adsorbed Cr(VI), while ∼90% of adsorbed Cr(VI) was reduced by Fe3O4-biochar. These results unveiled the importance of iron and chromium speciation for chromium removal under varying pH, and might guide the application-oriented design of multifunctional Fe-biochar for broad environmental remediation.

Detoxification mechanisms of biochar on plants in chromium contaminated soil: Chromium chemical forms and subcellular distribution.

The complete pathway of chromium (Cr) transfer from soil to plant tissues and subcellular components under biochar amendment remains to be quantified, as well as the involved diverse detoxification processes in roots and stems respectively. Pot experiments and quantitative analysis were conducted to investigate Cr fixation in soil amended with Enteromorpha prolifera-derived biochar and subsequent phytoprocesses (Cr uptake, transfer, and phytotoxicity) in cultivated Secale cereale L. (rye). The results indicated that adding 5-30 g kg-1 of biochar increased the residual form of Cr (B4) in soil by 8-21% and decreased the bioavailable form of Cr (B1) by 9-29%. For Cr transferred to rye, Cr in the rye was mainly present in the low-toxicity bound state, with the acetic acid-extracted Cr (F4) (45-54%) in roots and the NaCl-extracted Cr (F3) (37-47%) in stems. The subcellular distribution of Cr in both roots and stems was predominantly in the cell wall and residues (T1), followed by the cytoplasm (T4). Partial least squares path model (PLS-PM) was used for quantifying the effect of biochar on the form changes and subcellular detoxification of Cr from soil to roots and stems to sub-cells. In soils, biochar reduced the bioavailability of Cr and decreased the transfer of Cr to rye. In plant roots, Cr was distributed mainly as low-toxicity phosphate complexes in cell walls and vacuoles in sub-cells (with the largest path coefficients of 0.90 and -0.91, respectively). In the stems, Cr was distributed mainly as proteins integrated into the cell walls and vacuoles. This was due to the difference in subcellular compartmentalization of detoxification in the roots and stems. These PLS-PM results provide new insights into the entire process of pollutant detoxification in complex environments.

AfCHIL, a Type IV Chalcone Isomerase, Enhances the Biosynthesis of Naringenin in Metabolic Engineering.

Naringenin is an essential precursor for all flavonoids, and effectively promoting naringenin production is crucial in metabolic engineering. The interaction between plant metabolic enzymes ensures metabolic flux. The effect can effectively improve the natural product synthesis of engineering microbial systems. In this study, chalcone isomerase genes in Allium fistulosum have been identified. The expression of AfCHIL is closely related to the accumulation of anthocyanins, and the expression of AfCHIL and AfCHS was highly synchronized. Yeast two-hybrid and firefly luciferase complementation imaging assay further confirmed AfCHIL physically interacted with AfCHS/AfCHI. The bioconversion experiment confirmed that AfCHIL reduced the derailment produced by AfCHS and increased the yield of naringenin. In addition, a system of biosynthesis naringenin involved in AfCHS was constructed, and these results suggested that the potential function between CHS with CHIL advanced naringenin production effectively. In conclusion, this study illustrated the function of AfCHIs in Allium fistulosum and provided new insight into improving the synthesis efficiency of naringenin.

Effect of biochar on the uptake, translocation and phytotoxicity of chromium in a soil-barley pot system.

Remediation of Cr-contaminated soils with biochar is an effective method, but its effect on plant detoxification has not been clarified, and the translocation pathways of different chemical forms of Cr in the soil-plant system have not been quantitatively evaluated. This study investigated the effects of magnetically modified Enteromorpha prolifera biochar (FBC) on Cr uptake, translocation and phytotoxicity in the soil and barley (Hordeum vulgare L.). When the FBC dosage increased to 30 g·kg-1, the content of bioavailable Cr in the soil decreased by 56.82%. Additionally, the contents of Cr in H. vulgare decreased by 53.22%, and growth recovered to the normal level. Partial least squares path modelling (PLS-PM) was applied to establish two influence paths to explain how FBC impacted the whole system of soil and plants upon Cr exposure. The phytotoxic effect path of Cr suggested that FBC decreased the contents of Cr in soil and H. vulgare and then recovered growth by alleviating oxidative stress (ß = -0.45) and promoting chlorophyll synthesis (ß = 0.53) in shoots. The translocation and conversion path of Cr further indicated that Cr in the shoots was converted into low-migration forms and mainly trapped in cell walls and vacuoles rather than in organelles, consequently decreasing the phytotoxicity of Cr (ß = -0.73). These two soil-plant paths offer new insights into the application of biochar and plants in Cr-contaminated soils.

Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media.

The fate and transport of bacteria in porous media are essential for bioremediation and water quality control. However, the influence of biological activities like extracellular electron transfer (EET) and swimming motility toward granular media on cell transport remains unknown. Here, electroactive bacteria with higher Fe(III) reduction abilities were found to demonstrate greater retention in ferrihydrite-coated sand. Increasing the concentrations of the electron donor (1-10 mM lactate), shuttle (0-50 µM anthraquinone-2,6-disulfonate), and acceptor (ferrihydrite, MnO2, or biochar) under flow conditions significantly reduced Shewanella oneidensis MR-1's mobility through redox-active porous media. The deficiency of EET ability or flagellar motion and inhibition of intracellular proton motive force, all of which are essential for energy taxis, enhanced MR-1's transport. It was proposed that EET could facilitate MR-1 to sense, tactically move toward, and attach on redox-active media surface, eventually improving its retention. Positive linear correlations were established among parameters describing MR-1's energy taxis ability (relative taxis index), cell transport behavior (dispersion coefficient and relative change of effluent percentage), and redox activity of media surface (reduction potential or electron-accepting rate), providing novel insights into the critical impacts of bacterial microscale motility on macroscale cell transport through porous media.

Interaction between hexavalent chromium and biologically formed iron mineral-biochar composites: Kinetics, products and mechanisms.

Biogenic Fe(II) is a dominant natural reductant to convert carcinogenic Cr(VI) to less toxic Cr(III). Field-applied biochar could promote microbial production of Fe(II) and form iron-biochar composites. Although there have been mounting research on the interactions of biochar or Fe(II) with Cr(VI), their coupling effects on Cr(VI) immobilization have been largely neglected. Here, iron mineral-biochar composite (IMBC) was prepared via biochar-mediated dissimilatory reduction of ferrihydrite or goethite by Shewanella oneidensis MR-1, and its reaction with Cr(VI) was investigated. IMBC was able to effectively remove aqueous Cr(VI) via reductive transformation by adsorbed Fe(II). The removal process nicely followed pseudo-second-order kinetics and Langmuir isotherm model. The removal ability of IMBC decreased with increasing pH (5.5-8.0) but was independent of ionic strength changes (0-100 mM). After reaction, the Fe-Cr coprecipitates formed on IMBC exhibited slightly higher Fe/Cr ratios (0.93-0.96) than those on corresponding iron mineral controls (0.88-0.94). For IMBC, while the presence of biochar decreased the reactivity of adsorbed Fe(II), their removal capacities were ~30% higher than those of iron minerals alone, due to the enhanced yields of adsorbed Fe(II). These findings improved our knowledge of interactions among biochar, iron mineral and iron-reducing bacteria and their contribution to chromium immobilization.

Evolutionary Conservation and Expression Patterns of Neutral/Alkaline Invertases in Solanum.

The invertase gene family in plants is composed of two subfamilies of enzymes, namely, acid- and neutral/alkaline invertases (cytosolic invertase, CIN). Both can irreversibly cleave sucrose into fructose and glucose, which are thought to play key roles in carbon metabolism and plant growth. CINs are widely found in plants, but little is reported about this family. In this paper, a comparative genomic approach was used to analyze the CIN gene family in Solanum, including Solanumtuberosum, Solanumlycopersicum, Solanumpennellii, Solanumpimpinellifolium, and Solanummelongena. A total of 40 CINs were identified in five Solanum plants, and sequence features, phylogenetic relationships, motif compositions, gene structure, collinear relationship, and expression profile were further analyzed. Sequence analysis revealed a remarkable conservation of CINs in sequence length, gene number, and molecular weight. The previously verified four amino acid residues (D188, E414, Arg430, and Ser547) were also observed in 39 out of 40 CINs in our study, showing to be deeply conserved. The CIN gene family could be distinguished into groups α and ß, and α is further subdivided into subgroups α1 and α2 in our phylogenetic tree. More remarkably, each species has an average of four CINs in the α and ß groups. Marked interspecies conservation and collinearity of CINs were also further revealed by chromosome mapping. Exon-intron configuration and conserved motifs were consistent in each of these α and ß groups on the basis of in silico analysis. Expression analysis indicated that CINs were constitutively expressed and share similar expression profiles in all tested samples from S. tuberosum and S.lycopersicum. In addition, in CIN genes of the tomato and potato in response to abiotic and biotic stresses, phytohormones also performed. Overall, CINs in Solanum were encoded by a small and highly conserved gene family, possibly reflecting structural and functional conservation in Solanum. These results lay the foundation for further expounding the functional characterization of CIN genes and are also significant for understanding the evolutionary profiling of the CIN gene family in Solanum.

Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles.

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

Identification of cucumber circular RNAs responsive to salt stress.

BACKGROUND: Circular RNAs (circRNAs) are 3'-5' head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition. RESULTS: In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Characteristics analysis of these circRNAs revealed following features: most of them are exon circRNAs (79.51%) and they prefer to arise from middle exon(s) of parent genes (2035/2516); moreover, most of circularization events (88.3%) use non-canonical-GT/AG splicing signals; last but not least, pairing-driven circularization is not the major way to generate cucumber circRNAs since very few circRNAs (18) contain sufficient flanking complementary sequences. Annotation and enrichment analysis of both parental genes and target mRNAs were launched to uncover the functions of differentially expressed circRNAs induced by salt stress. The results showed that circRNAs may be paly roles in salt stress response by mediating transcription, signal transcription, cell cycle, metabolism adaptation, and ion homeostasis related pathways. Moreover, circRNAs may function to regulate proline metabolisms through regulating associated biosynthesis and degradation genes. CONCLUSIONS: The present study identified large number of cucumber circRNAs and function annotation revealed their possible biological roles in response to salt stress. Our findings will lay a solid foundation for further structure and function studies of cucumber circRNAs.

Cotransport of biochar and Shewanella oneidensis MR-1 in saturated porous media: Impacts of electrostatic interaction, extracellular electron transfer and microbial taxis.

Biochar widely applied to soil can influence microbial community composition and participate in extracellular electron transfer (EET). However, little is known about the cotransport behaviors of bacteria and biochar in aquifer and soil-water environments, which can affect the fate and application performance of biochar. In this study, we found that in comparison to their individual transport behaviors, the mobilities of cotransporting Shewanella oneidensis MR-1 and biochar colloid (BC) were significantly inhibited. The decreasing colloidal mobilities at higher ionic strengths signified the importance of electrostatic interaction between cell and BC in cotransport. Moreover, the less suppressed cotransport of BC and mutants defective of EET and the elevated inhibition effects on cotransport by adding exogenous electron donor suggested the importance of EET. Difference in cotransport behavior was also observed with BC having different redox states. Compared with oxidized BC, reduced BC with higher hydrophobicity led to easier aggregation with cell and higher retention in column. More importantly, MR-1 exhibited EET-dependent taxis towards biochar, which also contributed to the enhanced heteroaggregation and decreased mobilities of cell and biochar. Our results highlight that metabolic activities of microbes towards abiotic colloids cannot be neglected when assessing their transport behaviors, especially in subsurface environments abounded with redox-active inorganic particles and microbes performing extracellular respiration.

[BcMF4 gene, encoding a leucine-rich repeat protein, plays a role in male fertility in Chinese cabbage-pak-choi].

The BcMF4 (Brassica campestris Male Fertility 4) gene was previously isolated from the fertile B line of Chinese cabbage-pak-choi (Brassica campestris ssp. chinensis var. communis, syn. B. rapa ssp. chinensis var. communis). In the present paper, based on the cDNA sequence of BcMF4, primers were designed and used to amplify two fragments from the cDNA of flower buds of Chinese cabbage-pak-choi. Two produced fragments were introduced separately into binary vector pBI121 in antisense and sense orientations. The generated RNA interference (RNAi) vector was then mobilized into Agrobacterium tumefaciens strain LBA4404. The A. tumefaciens harboring the BcMF4 fragments was transformed to flowering Chinese cabbage (B. campestris ssp. chinensis var. parachinensis) via tissue culture. Approximately 45.8% of the pollen grains from 72.2% of RNAi plants exhibited abnormal in their shapes, and only 23.7% of the pollen grains from these plants germinated normally. Northern blotting demonstrated that the phenotypic change of pollen grains resulted from the inhibition of expression of the BcMF4 due to the insertion of the transgene. This indicates that functional interrupting of BcMF4 by RNAi resulted in partial pollen abortion in flowering Chinese cabbage, suggesting that the product of BcMF4 gene plays an important role during pollen development of Chinese cabbage such as Chinese cabbage-pak-choi and flowering Chinese cabbage.