Comprehensive analysis of flavor formation mechanisms in the mechanized preparation Cantonese soy sauce koji using absolute quantitative metabolomics and microbiomics approaches.

Based on the widespread application and under-research of mechanized preparation Cantonese soy sauce koji (MP), absolute quantitative approaches were utilized to systematically analyze the flavor formation mechanism in MP. The results indicated that the enzyme activities increased greatly during MP fermentation, and 4 organic acids, 15 amino acids, and 2 volatiles were identified as significantly different flavor actives. The flavor parameters of MP4 were basically identical to those of MP5. Furthermore, microorganisms were dominated by Staphylococcus, Weissella, and Aspergillus in MP, and their biomass demonstrated an increasing trend. A precise enumeration of microorganisms exposed the inaccuracy of relative quantitative data. Concurrently, Staphylococcus and Aspergillus were positively correlated with numerous enzymes and flavor compounds, and targeted strains for enhancing MP quality. The flavor formation network comprises pathways including carbohydrate metabolism, lipid metabolism and oxidation, and protein degradation and amino acid metabolism. In summary, the fermentation period of MP can be substantially shortened without compromising the product quality. These findings lay the groundwork for refining parameters in modern production processes.

Impacts of Aspergillus oryzae 3.042 on the flavor formation pathway in Cantonese soy sauce koji.

To investigate the mechanism of flavor formation during the traditional preparation Cantonese soy sauce koji (TP), the changes of microorganisms, physicochemical properties, and flavor compounds in TP were comprehensively and dynamically monitored by absolute quantitative methods. Results demonstrated that inoculating Aspergillus oryzae 3.042 in TP was crucial role in enhancing enzyme activity properties. Absolute quantification of flavor combined with multivariate statistical analysis yielded 5 organic acids, 15 amino acids, and 2 volatiles as significantly different flavors of TP. Amplicon sequencing and RT-qPCR revealed that the dominant genera were Staphylococcus, Weissella, Enterobacter, Lactic streptococci, Lactobacillus, and Aspergillus, which exhibited a increasing trend in TP. Correlation analysis exhibited that Staphylococcus and Aspergillus were the pivotal genera contributing to the enzyme activities and flavor of TP. The flavor formation network involved lipid and protein degradation, carbohydrate metabolism and other pathways. Simultaneously, TP can appropriately increase the fermentation time to improve product quality.

GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.

Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.

Small Auxin Up RNA 56 (SAUR56) regulates heading date in rice.

Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01409-w.

Smart G-quadruplex hydrogels: From preparations to comprehensive applications.

In recent years, the accelerated development of G-quadruplexes and hydrogels has driven the development of intelligent biomaterials. Based on the excellent biocompatibility and special biological functions of G-quadruplexes, and the hydrophilicity, high-water retention, high water content, flexibility and excellent biodegradability of hydrogels, G-quadruplex hydrogels are widely used in various fields by combining the dual advantages of G-quadruplexes and hydrogels. Here, we provide a systematic and comprehensive classification of G-quadruplex hydrogels in terms of preparation strategies and applications. This paper reveals how G-quadruplex hydrogels skillfully utilize the special biological functions of G-quadruplexes and the skeleton structure of hydrogels, and expounds its applications in the fields of biomedicine, biocatalysis, biosensing and biomaterials. In addition, we deeply analyze the challenges in preparation, applications, stability and safety of G-quadruplex hydrogels, as well as potential future development directions.

Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice.

Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01345-1.

Deciphering the brewing process of Cantonese-style rice vinegar: Main flavors, key physicochemical factors, and important microorganisms.

Cantonese-style rice vinegar is one of the most important Chinese rice vinegars and is quite popular all over the southeast coast of China, especially in Guangdong. This study identified 31 volatile compounds, including 11 esters, 6 alcohols, 3 aldehydes, 3 acids, 2 ketones, 1 phenol, and 5 alkanes, using headspace solid-phase microextraction-gas chromatography-mass spectrometry. Six organic acids were detected by high performance liquid chromatography. The ethanol content was detected by gas chromatography. During acetic acid fermentation, physicochemical analysis showed that the initial concentrations of reducing sugar and ethanol were 0.0079 g/L and 23.81 g/L, respectively, and the final value of total acid was 46.5 g/L, and the pH value was stable at 3.89. High-throughput sequencing was used to identify the microorganisms, and Acetobacter, Komagataeibacter, and Ralstonia were the top three bacterial genera. Quantitative real-time polymerase chain reaction revealed patterns that were different from those of high-throughput sequencing. The co-occurrence network of microorganisms and the correlation analysis between microorganisms and flavor substances indicate that Acetobacter and Ameyamaea played crucial roles as the main functional AAB, and the failure of Cantonese-style rice vinegar fermentation can be attributed to the abnormal increase in Komagataeibacter. Microbial co-occurrence network analysis indicated that Oscillibacter, Parasutterella, and Alistipes were the top three microorganisms. Redundancy analysis disclosed that total acid and ethanol were the key environmental factors influencing the microbial community. Fifteen microorganisms closely related to the metabolites were identified using the bidirectional orthogonal partial least squares model. Correlation analysis showed that these microorganisms were strongly associated with flavor metabolites and environmental factors. The findings of this study deepen our understanding of the fermentation of traditional Cantonese-style rice vinegar.

Characterization of GshAB of Tetragenococcus halophilus: a two-domain glutathione synthetase.

The γ-glutamyl tripeptide glutathione (γ-Glu-Cys-Gly) is a low molecular thiol that acts as antioxidant in response to oxidative stress in eukaryotes and prokaryotes. γ-Glutamyl dipeptides including γ-Glu-Cys, γ-Glu-Glu, and γ-Glu-Gly also have kokumi activity. Glutathione is synthesized by first ligating Glu with Cys by γ-glutamylcysteine ligase (Gcl/GshA), and then the resulting dipeptide γ-glutamylcysteine is ligated with Gly by glutathione synthetase (Gs/GshB). GshAB/GshF enzymes that contain both Gcl and Gs domains are capable of catalyzing both reactions. The current study aimed to characterize GshAB from Tetragenococcus halophilus after heterologous expression in Escherichia coli. The optimal conditions for GshAB from T. halophilus were pH 8.0 and 25 °C. The substrate specificity of the Gcl reaction of GshAB was also determined. GshAB has a high affinity to Cys. γ-Glu-Cys was the only dipeptide generated when Glu, Cys, Gly, and other amino acids were present in the reaction system. This specificity differentiates GshAB from T. halophilus from Gcl of heterofermentative lactobacilli and GshAB of Streptococcus agalactiae, which also use amino acids other than Cys as glutamyl-acceptor. Quantification of gshAB in cDNA libraries from T. halophilus revealed that gshAB was overexpressed in response to oxidative stress but not in response to acid, osmotic, or cold stress. In conclusion, GshAB in T. halophilus served as part of the oxidative stress response but this study did not provide any evidence for a contribution to the resistance to other stressors.Key points Glutathione synthesis in Tetragenococcus halophilus is carried out by the two-domain enzyme GshAB. GshAB is inhibited by glutathione and is highly specific for Cys as acceptor. T. halophilus synthesizes glutathione in response to oxidative stress.

The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa).

Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.

Effects of Jiuqu inoculating Rhizopus oryzae Q303 and Saccharomyces cerevisiae on chemical components and microbiota during black glutinous rice wine fermentation.

In this study, the physicochemical properties, metabolites, sensory characteristics, and microbiota of black glutinous rice wine (BGRW) during traditional fermentation (TF) and inoculated fermentation (IF) were investigated, and their correlation relationships were revealed. Results indicated that IF promoted total sugar utilization and ethanol and esters synthesis in BGRW. Altogether 67 reliable metabolites were identified, 36 of which were labeled components, primarily esters (OAV > 1). Meanwhile, the concentrations of ethanol, esters, and total flavor on the 11th day of IF were close to those on the 22nd day of TF. Combined with the sensory description indicated that the IF could improve the quality of BGRW. Besides, TF contains vast unfavorable microorganisms, such as Chaetomium, Penicillium, Stachybotrys, and Trichocladium. Therefore, IF can accelerate the fermentation and enhance the flavor of BGRW, and inhibit the growth of pathogenic and spoilage organisms. Finally, Pearson's correlation analysis demonstrated that Saccharomyces, Rhizopus, Lactobacillus, Aspergillus, and Bacillus were the pivotal functional microorganisms in BGRW. The study provided scientific and effective basis for improving the quality, shortening the fermentation cycle, and controlling pathogenic and spoilage organisms of BGRW.

Effects of microbial community structure and its co-occurrence on the dynamic changes of physicochemical properties and free amino acids in the Cantonese soy sauce fermentation process.

The soy sauce produced by Cantonese fermentation has a unique flavor, among which brine fermentation plays an important role. In this fermentation process, 61 volatile compounds, including 19 esters, 10 aldehydes, 9 alcohols, 5 phenols, and 18 others, were identified by headspace solid-phase microextraction-gas chromatography-mass spectrometry. Seventeen kinds of free amino acids were detected by high-performance liquid chromatography. Results showed that Touyou, which comprised 1.5 g/100 g total nitrogen, 1.0 g/100 mL amino acid nitrogen, 3.66 g/100 g reducing sugar, 1.44 g/100 mL total acid, 17.04 g/100 mL salt content, and 27.3% umami free amino acids, had excellent quality. High-throughput sequencing was used to identify microorganisms. The top 3 of bacteria were Weissella, Staphylococcus, and Lactobacillus, and the top 3 fungi were Aspergillus, Zygosaccharomyces, and Candida. The co-occurrence network analysis of microorganisms showed that the top-ranked microorganisms were Plectosphaerella, Aureobasidium, unidentified_Mortierellales_sp, Glutinomyces, Faecalibacterium, and Cladophialophora. Then, eight microorganisms (VIP[pred] > 1) were obtained by two-way orthogonal partial least squares model, namely, Staphylococcus, Candida, Weissella, Aspergillus, Zygosaccharomyces, Lactobacillus, Monilinia, and Clavispora. Correlation analysis showed that these microorganisms were strongly related to flavor metabolites. This study explored the dynamics of traditional Cantonese fermentation, which has positive implications for optimizing this traditional fermentation process.

Quantitative proteomic analysis reveals the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 in the process of simultaneous nitrogen and phenol removal.

Phenol and ammonia in wastewater pose a serious threat to ecosystems and human health. However, the currently limited studies on single bacterium simultaneously removing phenol and nitrogen pollution have not fully elucidated the relevant metabolic mechanisms. The differences in proteomic profile after supplementing with phenol and ammonia for 6 and 24 h, respectively, were evaluated to explore the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 during the simultaneous removal process of phenol and nitrogen. Results revealed that a new potential phenol para-degradation pathway appeared in T2. Phenol induced changes in nitrogen metabolism, resulting in increased denitrification and decreased synthesis of glutamate from ammonia at 6 h. In addition, phenol exposure enhanced the expression of cytochrome oxidases with high oxygen affinity and increased ATP synthesis. The increase in chemotaxis and flagellar assembly was conducive to the uptake and utilization of phenol. The synthesis of lipoic acid and biotin was also promoted to resist phenol toxicity. Moreover, phenol triggered cellular stress response, thereby leading to the upregulation of anti-stress proteins, such as universal stress protein, iron­sulfur cluster protein, and chaperones. This study contributes to revealing the metabolic characteristics and adaptive mechanism of T2 during simultaneous nitrogen and phenol removal. SIGNIFICANCE: Phenol and ammonia often co-exist in wastewater, causing serious environmental problems. The information on the metabolic mechanism of simultaneously removing these two pollutants by bacteria is insufficient at present. Moreover, phenol is toxic to microbial and causes cells damage. Therefore, exploring the response mechanism of bacteria to phenol stress is conducive to understand their tolerance mechanism to aromatic compounds. In this study, the metabolic characteristics and adaptive mechanism of C. oxalaticus T2 during the simultaneous removal of phenol and nitrogen process were evaluated by comparing the proteome profiles at different stages. The results revealed the degradation pathways of phenol and nitrogen by strain T2. A variety of phenol response mechanisms were determined, including enhanced energy production, improved cell motility, increased the synthesis of lipoic acid and biotin, and combined action of multiple anti-stress proteins. This study is potentially useful to future phenol and nitrogen co-pollution bioremediation strategies and provides insight into the phenolic compound resistance mechanism in bacteria.

Characterization of DinJ-YafQ toxin-antitoxin module in Tetragenococcus halophilus: activity, interplay, and evolution.

Tetragenococcus halophilus is a moderately halophilic lactic acid bacterium widely used in high-salt food fermentation because of its coping ability under various stress conditions. Bacterial toxin-antitoxin (TA) modules are widely distributed and play important roles in stress response, but those specific for genus Tetragenococcus have never been explored. Here, a bona fide TA module named DinJ1-YafQ1tha was characterized in T. halophilus. The toxin protein YafQ1tha acts as a ribonuclease, and its overexpression severely inhibits Escherichia coli growth. These toxic effects can be eliminated by introducing DinJ1tha, indicating that YafQ1tha activity is blocked by the formed DinJ1-YafQ1tha complex. In vivo and in vitro assays showed that DinJ1tha alone or DinJ1-YafQ1tha complex can repress the transcription of dinJ1-yafQ1tha operon by binding directly to the promoter sequence. In addition, dinJ1-yafQ1tha is involved in plasmid maintenance and stress response, and its transcriptional level is regulated by various stresses. These findings reveal the possible roles of DinJ1-YafQ1tha system in the stress adaptation processes of T. halophilus during fermentation. A single antitoxin DinJ2tha without a cognate toxin protein was also found. Its sequence shows low similarity to that of DinJ1tha, indicating that this antitoxin may have evolved from a different ancestor. Moreover, DinJ2tha can cross-interact with noncognate toxin YafQ1tha and cross-regulate with dinJ1-yafQ1tha operon. In summary, DinJ-YafQtha characterization may be helpful in investigating the key roles of TA systems in T. halophilus and serves as a foundation for further research. KEY POINTS: • dinJ1-yafQ1tha is the first functional TA module characterized in T. halophilus and upregulated significantly upon osmotic and acidic stress. • DinJ2tha can exhibit physical and transcriptional interplay with DinJ1-YafQ1tha. • dinJ2tha may be acquired from bacteria in distant affiliation and inserted into the T. halophilus genome through horizontal gene transfer.

Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice.

BACKGROUND: In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. RESULTS: In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (-log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG. CONCLUSION: The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.

Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism.

The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.

Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages.

BACKGROUND: Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice. RESULTS: Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0-2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate-glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials. CONCLUSIONS: In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.

Mechanisms of Cr(VI) reduction by Bacillus sp. CRB-1, a novel Cr(VI)-reducing bacterium isolated from tannery activated sludge.

Cr(VI) reduction by microorganisms has been extensively reported, however, the mechanism of Cr(VI) reduction varies among different microorganisms. In this study, a Cr(VI)-reducing bacterium identified as Bacillus sp. was isolated from tannery activated sludge, strain CRB-1 was able to completely reduce 50 mg/L of Cr(VI) within 24 h under aerobic conditions and exhibited considerable Cr(VI) removal efficiency in the pH range from 7.0 to 9.0, temperature 24-42 °C. Cr(VI) reduction assays with resting cells, permeabilized cells, and subcellular fractions suggested that Cr(VI) reduction mainly occurred in the cytoplasm. According to qRT-PCR analysis, a chrA gene and a nitR2 gene were up-regulated under Cr(VI) stress. Heterologous expression of the chrA gene and the nitR2 gene indicated that ChrA was associated with Cr(VI) resistance, while NitR2 was responsible for Cr(VI) reduction. Furthermore, soluble end products were detected. On the basis of FTIR, it was speculated that the formation of soluble end products may be due to the complexation of EPS with Cr(III). Consequently, the Cr(VI)-reducing ability of strain CRB-1 and its chromate reductases enables CRB-1 a potential candidate for Cr(VI) bioremediation.

Corrigendum: Characterizing the Intra-Vineyard Variation of Soil Bacterial and Fungal Communities.

[This corrects the article DOI: 10.3389/fmicb.2019.01239.].

Characterizing the Intra-Vineyard Variation of Soil Bacterial and Fungal Communities.

Vineyard soil microbial communities potentially mediate grapevine growth, grape production as well as wine terroir. Simultaneously assessing shifts of microbial community composition at the intra-vineyard scale allows us to decouple correlations among environmental variables, thus providing insights into vineyard management. Here we investigated bacterial and fungal community compositions and their relationships with edaphic properties in soils collected from a commercial vineyard at four different soil depths (0-5, 5-10, 10-20, and 20-40 cm). Soil organic carbon (SOC) content, invertase activity and phosphatase activity decreased along depth gradient in the 0-20 cm soil fraction (P < 0.001). The soil bacterial biomass and α-diversity were significantly higher than those of fungi (P ≤ 0.001). Statistical analyses revealed that SOC content, pH, C/N ratio and total phosphorus (TP) were significant determinants of soil bacterial (R = 0.494, P = 0.001) and fungal (R = 0.443, P = 0.001) community structure. The abundance of dominated bacterial phyla (Proteobacteria, Acidobacteria and Actinobacteria) and fungal phyla (Ascomycota, Zygomycota and Basidiomycota) slightly varied among all soil samples. Genus Lactococcus, which comprised 2.72% of the soil bacterial community, showed increasing pattern with depth. Importantly, Candidatus Nitrososphaera, Monographella and Fusarium were also detected with high abundances in soil samples, indicating their ecological function in soil nitrogen cycle and the potential risk in grapevine disease. Overall, this work detected the intra-vineyard variation of bacterial and fungal communities and their relationships with soil characteristics, which was beneficial to vineyard soil management and grapevine disease prevention.

Identification of a GntR family regulator BusRTha and its regulatory mechanism in the glycine betaine ABC transport system of Tetragenococcus halophilus.

Glycine betaine is one of the most effective compatible solutes of the halophilic lactic acid bacterium Tetragenococcus halophilus, the transportation of which is essential for its survival under salinity stress condition. In the current study, we attempted to define a glycine betaine ABC transporter system of T. halophilus, busATha, which plays an important role in adapting to salinity condition. The expression of busATha enhanced the growth of the recombinant strain under high salinity. BusRTha, a transcription regulator that represses the expression of busATha, was characterized, and the repression was abrogated under high salinity. The binding of the regulator was demonstrated through electrophoretic mobility shift assays, and the binding sites were characterized as 5'-AAA(T/G)TGAC(C/A)(G/A)T(C/A)C-3'. This is the first studied transcription regulator of T. halophilus, and our findings provide insights into the molecular mechanism of halophilic life and tools for further application of halophiles as chassis in industrial biotechnology.