Transcriptome analysis provides new insights into the tolerance and reduction of Lysinibacillus fusiformis 15-4 to hexavalent chromium.

Microbial bioremediation of Cr(VI)-contaminated environments has drawn extensive concern. However, the molecular processes underlying the microbial Cr(VI) tolerance and reduction remain unclear. We isolated a Cr(VI)-reducing Lysinibacillus fusiformis strain 15-4 from soil on the Qinghai-Tibet Plateau. When grown in 1 mM and 2 mM Cr(VI)-containing medium, strain 15-4 could reduce 100% and 93.7% of Cr(VI) to Cr(III) after 36 h and 60 h of incubation, respectively. To know the molecular processes in response to Cr(VI), transcriptome sequencing was carried out using RNA-Seq technology. The results annotated a total of 3913 expressed genes in the strain. One thousand ninety-eight genes (28.1%) were significantly (fold change ≥ 2, false discovery rate ≤ 0.05) expressed in response to Cr(VI), of which 605 (55.1%) were upregulated and 493 (44.9%) were downregulated. The enrichment analysis showed that a total of 630 differentially expressed genes (DEGs) were enriched to 122 KEGG pathways, of which 8 pathways were significantly (p < 0.05) enriched in Cr(VI)-treated sample, including ATP-binding cassette (ABC) transporters (97 DEGs), ribosome (40), sulfur metabolism (16), aminoacyl-tRNA biosynthesis (19), porphyrin metabolism (20), quorum sensing (44), oxidative phosphorylation (17), and histidine metabolism (10), suggesting that these pathways play key roles to cope with Cr(VI) in the strain. The highly upregulated DEGs consisted of 29 oxidoreductase, 18 dehydrogenase, 14 cell redox homeostasis and stress response protein, and 10 DNA damage and repair protein genes. However, seven Na+:H+ antiporter complex-coding DEGs and most of transcriptional regulator-coding DEGs were significantly downregulated in the Cr-treated sample. Many of FMN/NAD(P)H-dependent reductase-encoding genes were greatly induced by Cr, suggesting the involvement of these genes in Cr(VI) reduction in strain 15-4. Sulfur and iron ions as well as the thiol-disulfide exchange reactions might play synergistic roles in Cr reduction.Key points• Lysinibacillus fusiformis 15-4 was able to tolerate and reduce Cr(VI) to Cr(III).• Transcriptome analysis revealed that 1098 DEGs and 8 key KEGG pathways significantly responded to Cr(VI).• Sulfur metabolism, protein biosynthesis, and porphyrin metabolism were the key pathways associated with the survival of strain 15-4 in response to Cr(VI).

24-epibrassinolide improves differential cadmium tolerance of mung bean roots, stems, and leaves via amending antioxidative systems similar to that of abscisic acid.

Cadmium (Cd) pollution has attracted global concern. In the present study, the biochemical mechanisms underlying the amelioration of 24-epibrassinolide (eBL) and abscisic acid (ABA) on Cd tolerance of roots, stems, and leaves in mung bean seedlings were comparatively analyzed. Foliar application of eBL markedly ameliorated the growth of mung bean seedling exposed to 100 µM Cd. eBL alone had no significant effects on the activities of antioxidative enzymes and the contents of glutathione (GSH) and polyphenols in the three organs whereas significantly increased the root, stem, and leaf proline contents on average by 54.9%, 39.9%, and 94.4%, respectively, and leaf malondialdehyde (MDA) content on average by 69.0% compared with the controls. When the plants were exposed to Cd, eBL significantly reversed the Cd-increased root ascorbate peroxidase (APX) and superoxide dismutase (SOD) activities, root polyphenol, proline, and GSH levels, leaf chlorophyll contents, and MDA levels in the three organs. eBL significantly restored the Cd-decreased leaf catalase (CAT) activity and leaf polyphenol levels. These results indicated that eBL played roles in maintaining cellular redox homeostasis and evidently alleviated Cd-caused membrane lipid peroxidation via controlling the activity of antioxidative systems. eBL mediated the differential responses of cellular biochemical processes in the three organs to Cd exposure. Furthermore, a comparative analysis revealed that, under Cd stress, the effects of eBL on the biochemical processes were very similar to those of ABA, suggesting that ABA and eBL improve plant Cd tolerance via some common downstream pathways.

Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria.

Soil microbial community structure is altered by petroleum contamination in response to compound toxicity and degradation. Understanding the relation between petroleum contamination and soil microbial community structure is crucial to determine the amenability of contaminated soils to bacterial- and fungal-aided remediation. To understand how petroleum contamination and soil physicochemical properties jointly shaped the microbial structure of soils from different oilfields, high-throughput sequencing of 16S and ITS amplicons were used to evaluate the shifts of microbial communities in the petroleum-contaminated soils in Ughelli East (UE), Utorogu (UT), and Ughelli West (UW) oilfields located in Delta State, Nigeria. The results showed 1515 bacteria and 919 fungal average OTU number, and community richness and diversity, trending as AL > UT > UW > UE and AL > UW > UT > UE for bacteria, and AL > UW > UT > UE and UW > UT > AL > UE for fungi, respectively. The bacterial taxa KCM-B-112, unclassified Saccharibacteria, unclassified Rhizobiales, Desulfurellaceae, and Acidobacteriaceae and fungal Trichocomaceae, unclassified Ascomycota, unclassified Sporidiobolales, and unclassified Fungi were found to be the dominant families in petroleum-contaminated soils. Redundancy analysis (RDA) and Spearman's correlation analysis revealed that total carbon (TC), electric conductivity (EC), pH, and moisture content (MO) were the major drivers of bacterial and fungal communities, respectively. Gas chromatography-mass spectrophotometer (GC-MS) analysis exhibited that the differences in C7-C10, C11-C16, and C12-C29 compounds in the crude oil composition and soil MO content jointly constituted the microbial community variance among the contaminated soils. This study revealed the bacterial and fungal communities responsible for the biodegradation of petroleum contamination from these oilfields, which could serve as biomarkers to monitor oil spill site restoration within these areas. Further studies on these contaminated sites could offer useful insights into other contributing factors such as heavy metals.

Molecular Bases for the Regulation of Adventitious Root Generation in Plants.

The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.

Abscisic acid modulates differential physiological and biochemical responses of roots, stems, and leaves in mung bean seedlings to cadmium stress.

Experiments were conducted to determine how exogenous abscisic acid (ABA) mediates the tolerance of plants to cadmium (Cd) exposure. Cd stress strongly reduced all the growth parameters of mung bean seedlings. Cd significantly increased ascorbate peroxidase (APX) and catalase (CAT) activities in roots and stems, and peroxidase (POD) activities in roots, stems, and leaves of mung bean seedlings. Cd caused remarkable increases in the levels of leaf chlorophyll and carotenoid, root polyphenols, and malondialdehyde (MDA) and proline in the three organs. However, Cd greatly decreased leaf CAT activity, root and leaf ascorbic acid (AsA) levels, and stem and leaf polyphenol levels. Foliar application of ABA partially alleviated Cd toxicity on the seedlings. ABA could restore most of the changed biochemical parameters caused by Cd, suggesting that ABA played roles in the protection of membrane lipid peroxidation and the modulation of antioxidative defense systems in response to Cd stress. Our results also implied the differential physiological and biochemical responsive patterns of roots, stems, and leaves to Cd and ABA in mung bean seedlings. The great changes in many biochemical parameters in roots suggested that roots were the first to be affected by Cd and play pivotal roles in response to Cd, especially in chelating Cd and reducing Cd absorption.

An insight into the current oil spills and on-site bioremediation approaches to contaminated sites in Nigeria.

Land oil spills in Nigeria have a long history of contaminating the soil, groundwater, vegetation, and streams with spill extension being the primary of numerous ordeals. These have left the host communities of oil fields and pipelines in crucial need of soil rehabilitation. Thus, this review provides insights into the current state of land oil spills and the effectiveness of on-site remediation approaches across communities. A total of 44 incidents of land oil spills of ≥ 500 bbl, amounting to 53,631 bbl between 2011 and 2019, was recorded by the Shell Petroleum Development Company, which primarily attributed to 83% of the total sabotage. Over 73% of the 53,631 bbl spills were unrecovered from the spill areas, which had deleterious impacts on farmlands, fishponds, rivers, and residential areas. Remediation by enhanced natural attenuation (RENA) is a feasible technique for restoring petroleum hydrocarbon-contaminated sites, but it might be ineffective when limited to tiling, windrows, and fertilizer applications due to the presence of non-biodegradable residues and contaminants beyond the aeration depth. However, bioremediation techniques ranging from non-supplemented in-situ and fertilizer supplemented in-situ to mixed in-situ and ex-situ bio-cells supplemented RENA are feasible approaches for spill sites. However, challenging limitations with regard to RENA application failures in the region include delayed responses to spill emergency, large amounts of un-recovered spilled oil, and un-implemented legislative guidelines for spill cleanup. Nevertheless, the temperature, moisture, nutrient, oxygen, and pH of the soil are essential parameters to be considered when implementing a landfarming remediation approach.

Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments.

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 µM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals.

The seasonal changes of core bacterial community decide sewage purification in sub-plateau municipal sewage treatment plants.

The decline of sewage purification efficiency in winter is a frequent problem in sub-plateau municipal sewage treatment plants (MSTPs). Understanding the links between activated sludge (AS) bacterial community and sewage purification is crucial for exploring the cause of this problem. In this study, Illumina high-throughput sequencing technology was applied to investigate the seasonal changes of AS bacterial community in sub-plateau MSTPs. The sequencing result indicates that the bacterial community OTU number, diversity, and relative abundance in winter are significantly lower than that in summer samples. The discriminant linear effect size analysis (LEfSe) reveals that Proteobacteria and Chloroflexi members were enriched in summer AS, while Actinobacteria and Firmicutes were enriched in winter AS. The results indicate that different core bacterial community assembly was developed in summer and winter, respectively. The changes in bacterial community may be the reasons for the lower sewage purification efficiency in winter. Furthermore, redundancy analysis (RDA) shows that temperature and dissolved oxygen (DO) are the principal factors that drive the seasonal changes in the core bacterial community diversity, richness and structure in sub-plateau MSTPs. Thus, the sub-plateau AS selects for a unique community assembly pattern and shapes the particular AS ecosystem. These results expand previous understanding and provide insight into the relationship between bacterial community and performance of sub-plateau MSTPs.

Structural and functional responses of bacterial and fungal communities to multiple heavy metal exposure in arid loess.

Concentration gradients of multiple heavy metals (HMs) in the arid loess region near a smelter were determined. In order to understand the response of soil microbes to multiple HM gradients, bacterial and fungal community structures and functions were analyzed using high-throughput RNA gene sequencing and the PICRUSt method. RDA/PCA analyses revealed that soil pH, HMs, and electrical conductivity (EC) jointly affected the bacterial communities in the soils. The soil microbial community structures responded differently to HMs, EC, and pH. High HMs increased the abundances of the bacterial phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Chloroflexi, and the genera Blastococcus, Rubrobacter, Quadrisphaera, and Tunicatimonas, whereas they decreased the abundances of the phyla Proteobacteria and Acidobacteria and the genera Streptomyces and Nocardioides. High EC and low pH decreased the abundance of most of the dominant bacterial phyla but increased the abundances of Firmicutes, Deinococcus-Thermus, and Nitrospirae. Furthermore, high HMs and EC reduced the numbers of soil-specific bacterial and fungal groups and drove the succession of certain groups that were highly resistant to increased HMs and EC. In addition, many bacterial and fungal groups exhibited different response patterns to each HM, implying that, in multiple HM-contaminated soils, HMs jointly shaped the microbial communities. PICRUSt analysis suggested that high HMs significantly decreased the total gene abundance and most KEGG modules in the soils. High EC and low pH significantly enhanced the abundances of several two-component system-, electron transfer-, and methanogenesis-related modules. We conclude that excessive multiple HMs and EC principally repressed the microbial activity and severely drove the gradient succession of bacterial and fungal communities in the arid loess region.

Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments.

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.

Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2.

The complete genome sequence of Bacillus subtilis strain DM2 isolated from petroleum-contaminated soil on the Tibetan Plateau was determined. The genome of strain DM2 consists of a circular chromosome of 4,238,631 bp for 4458 protein-coding genes and a plasmid of 84,240 bp coding for 103 genes. Thirty-four genomic islands coding for 330 proteins and 5 prophages are found in the genome. The DDH value shows that strain DM2 belongs to B. subtilis subsp. subtilis subspecies, but significant variations of the genome are also present. Comparative analysis showed that the genome of strain DM2 encodes some strain-specific proteins in comparison with B. subtilis subsp. subtilis str. 168, such as carboxymuconolactone decarboxylase family protein, gfo/Idh/MocA family oxidoreductases, GlsB/YeaQ/YmgE family stress response membrane protein, HlyC/CorC family transporters, LLM class flavin-dependent oxidoreductase, and LPXTG cell wall anchor domain-containing protein. Most of the common strain-specific proteins in DM2 and MJ01 strains, or proteins unique to DM2 strain, are involved in the pathways related to stress response, signaling, and hydrocarbon degradation. Furthermore, the strain DM2 genome contains 122 genes coding for developed two-component systems and 138 genes coding for ABC transporter systems. The prominent features of the strain DM2 genome reflect the evolutionary fitness of this strain to harsh conditions and hydrocarbon utilization.

Nocardia mangyaensis sp. nov., a novel actinomycete isolated from crude-oil-contaminated soil.

A Gram-stain-positive, aerobic, non-motile and mycolic-acid-containing strain, designated Y48T, was isolated from soil contaminated by crude oil located in the northern margin of the Qaidam Basin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y48T belongs to the genus Nocardia and is closely related to N. cummidelens DSM 44490T (99.0 % similarity), N. soli DSM 44488T (99.0 %), N. lasii 3C-HV12T (98.9 %), N. salmonicida NBRC 13393T (98.6 %), N. ignorata NBRC 108230T (98.6 %) and N. coubleae NBRC 108252T (98.6 %). The average nucleotide identity and DNA-DNA hybridization values between strain Y48T and the reference strains were 75.9-84.5 and 27.5-29.0 %, respectively, values that were below the thresholds for species delineation. Chemotaxonomic analysis indicated that the major fatty acids of strain Y48T were C16 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and C18 : 0 10-methyl (TBSA). The respiratory quinone was MK-8(H4, ω-cycl). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two glycolipids and three unidentified lipids. The cell-wall hydrolysates contained meso-diaminopimelic acid, with ribose, arabinose, glucose and galactose as whole-cell sugars. A combination of 16S rRNA gene sequence analysis, and phenotypic and chemotaxonomic characterizations demonstrated that strain Y48T represents a novel species of the genus Nocardia, for which the name Nocardia mangyaensis sp. nov. is proposed. The type strain is Y48T (=JCM 32795T=CGMCC 4.7494T).

Indole-3-butyric acid mediates antioxidative defense systems to promote adventitious rooting in mung bean seedlings under cadmium and drought stresses.

In vitro experiments were performed to determine whether auxin can mediate the formation of adventitious roots in response to heavy metal and drought stresses using a model rooting plant, mung bean [Vigna radiata (L.) Wilczek]. The treatments with CdCl2 or mannitol alone significantly inhibited the formation and growth of adventitious roots in mung bean seedlings. In contrast, when CdCl2 or mannitol was applied together with indole-3-butyric acid (IBA), IBA considerably cancelled the inhibition of adventitious rooting by stresses. Treatment with CdCl2 or mannitol alone significantly increased the soluble protein and malondialdehyde (MDA) contents. CdCl2 and mannitol stress each induced differentially significant changes in the activities of antioxidative enzyme and antioxidant levels during adventitious rooting. Notably, both CdCl2 and mannitol stress strongly reduced the peroxidase (POD) and ascorbate peroxidase (APX) activities and glutathione (GSH) and phenols levels. Catalase and superoxide dismutase (SOD) activity were enhanced by CdCl2 but reduced by mannitol. CdCl2 increased the ascorbate acid (ASA) level, which was decreased by mannitol. Furthermore, when CdCl2 or mannitol was applied together with IBA, IBA counteracted the CdCl2- or mannitol-induced increase or decrease in certain antioxidants, MDA, and antioxidative enzymes. These results suggest that Cd and mannitol stress inhibition of adventitious rooting is associated with the regulation of antioxidative enzymes and antioxidants in cells to defense the oxidative stress. Moreover, IBA alleviates the effects of Cd and mannitol stress on the rooting process partially through the regulation of antioxidative defense systems.

Transcriptomic profiling provides molecular insights into hydrogen peroxide-induced adventitious rooting in mung bean seedlings.

BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that a profound change in gene function occurred in the 6-h H2O2 treatment and that H2O2 mainly enhanced gene expression levels at the 6-h time point but reduced gene expression levels at the 24-h time point compared with the water treatment. In total, 4579 differentially expressed (2-fold change > 2) unigenes (DEGs), of which 78.3% were up-regulated and 21.7% were down-regulated; 3525 DEGs, of which 64.0% were up-regulated and 36.0% were down-regulated; and 7383 DEGs, of which 40.8% were up-regulated and 59.2% were down-regulated were selected in the 6-h, 24-h, and from 6- to 24-h treatments, respectively. The number of DEGs in the 6-h treatment was 29.9% higher than that in the 24-h treatment. The functions of the most highly regulated genes were associated with stress response, cell redox homeostasis and oxidative stress response, cell wall loosening and modification, metabolic processes, and transcription factors (TFs), as well as plant hormone signalling, including auxin, ethylene, cytokinin, gibberellin, and abscisic acid pathways. Notably, a large number of genes encoding for heat shock proteins (HSPs) and heat shock transcription factors (HSFs) were significantly up-regulated during H2O2 treatments. Furthermore, real-time quantitative PCR (qRT-PCR) results showed that, during H2O2 treatments, the expression levels of ARFs, IAAs, AUXs, NACs, RD22, AHKs, MYBs, PIN1, AUX15A, LBD29, LBD41, ADH1b, and QORL were significantly up-regulated at the 6- and/or 24-h time points. In contrast, PER1 and PER2 were significantly down-regulated by H2O2 treatment. These qRT-PCR results strongly correlated with the RNA-Seq data. CONCLUSIONS: Using RNA-Seq and qRT-PCR techniques, we analysed the global changes in gene expression and functional profiling during H2O2-induced adventitious rooting in mung bean seedlings. These results strengthen the current understanding of H2O2-induced adventitious rooting and the molecular traits of H2O2 priming in plants.

Transcriptomic analysis reveals the gene expression profile that specifically responds to IBA during adventitious rooting in mung bean seedlings.

BACKGROUND: Auxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which auxin regulate the process of adventitious rooting are less well known. RESULTS: The RNA-Seq data analysis indicated that IBA treatment greatly increased the amount of clean reads and the amount of expressed unigenes by 24.29 % and 27.42 % and by 4.3 % and 5.04 % at two time points, respectively, and significantly increased the numbers of unigenes numbered with RPKM = 10-100 and RPKM = 500-1000 by 13.04 % and 3.12 % and by 24.66 % and 108.2 % at two time points, respectively. Gene Ontology (GO) enrichment analysis indicated that the enrichment of down-regulated GOs was 2.87-fold higher than that of up-regulated GOs at stage 1, suggesting that IBA significantly down-regulated gene expression at 6 h. The GO functional category indicated that IBA significantly up- or down-regulated processes associated with auxin signaling, ribosome assembly and protein synthesis, photosynthesis, oxidoreductase activity and extracellular region, secondary cell wall biogenesis, and the cell wall during the development process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that ribosome biogenesis, plant hormone signal transduction, pentose and glucuronate interconversions, photosynthesis, phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, ribosome, cutin, flavonoid biosynthesis, and phenylalanine metabolism were the pathways most highly regulated by IBA. A total of 6369 differentially expressed (2-fold change > 2) unigenes (DEGs) with 3693 (58 %) that were up-regulated and 2676 (42 %) down-regulated, 5433 unigenes with 2208 (40.6 %) that were up-regulated and 3225 (59.4 %) down-regulated, and 7664 unigenes with 3187 (41.6 %) that were up-regulated and 4477 (58.4 %) down-regulated were detected at stage 1, stage 2, and between stage 1 and stage 2, respectively, suggesting that IBA treatment increased the number of DEGs. A total of 143 DEGs specifically involved in plant hormone signaling and 345 transcription factor (TF) genes were also regulated by IBA. qRT-PCR validation of the 36 genes with known functions indicated a strong correlation with the RNA-Seq data. CONCLUSIONS: The changes in GO functional categories, KEGG pathways, and global DEG profiling during adventitious rooting induced by IBA were analyzed. These results provide valuable information about the molecular traits of IBA regulation of adventitious rooting.

De Novo Characterization of the Mung Bean Transcriptome and Transcriptomic Analysis of Adventitious Rooting in Seedlings Using RNA-Seq.

Adventitious rooting is the most important mechanism underlying vegetative propagation and an important strategy for plant propagation under environmental stress. The present study was conducted to obtain transcriptomic data and examine gene expression using RNA-Seq and bioinformatics analysis, thereby providing a foundation for understanding the molecular mechanisms controlling adventitious rooting. Three cDNA libraries constructed from mRNA samples from mung bean hypocotyls during adventitious rooting were sequenced. These three samples generated a total of 73 million, 60 million, and 59 million 100-bp reads, respectively. These reads were assembled into 78,697 unigenes with an average length of 832 bp, totaling 65 Mb. The unigenes were aligned against six public protein databases, and 29,029 unigenes (36.77%) were annotated using BLASTx. Among them, 28,225 (35.75%) and 28,119 (35.62%) unigenes had homologs in the TrEMBL and NCBI non-redundant (Nr) databases, respectively. Of these unigenes, 21,140 were assigned to gene ontology classes, and a total of 11,990 unigenes were classified into 25 KOG functional categories. A total of 7,357 unigenes were annotated to 4,524 KOs, and 4,651 unigenes were mapped onto 342 KEGG pathways using BLAST comparison against the KEGG database. A total of 11,717 unigenes were differentially expressed (fold change>2) during the root induction stage, with 8,772 unigenes down-regulated and 2,945 unigenes up-regulated. A total of 12,737 unigenes were differentially expressed during the root initiation stage, with 9,303 unigenes down-regulated and 3,434 unigenes up-regulated. A total of 5,334 unigenes were differentially expressed between the root induction and initiation stage, with 2,167 unigenes down-regulated and 3,167 unigenes up-regulated. qRT-PCR validation of the 39 genes with known functions indicated a strong correlation (92.3%) with the RNA-Seq data. The GO enrichment, pathway mapping, and gene expression profiles reveal molecular traits for root induction and initiation. This study provides a platform for functional genomic research with this species.

Rapid determination of lovastatin in the fermentation broth of Aspergillus terreus using dual-wavelength UV spectrophotometry.

CONTEXT: Lovastatin, a hypocholesterolemic drug, is produced by submerged fermentation of Aspergillus terreus Thom (Trichocomaceae). High performance liquid chromatography is usually used to determine lovastatin in samples of the fermentation broth. However, this method is inconvenient and costly, especially in the context of high-throughput sample analysis. OBJECTIVE: A direct and simple dual-wavelength ultraviolet spectrophotometric method for quantifying lovastatin in the fermentation broth of A. terreus was developed. MATERIALS AND METHODS: A. terreus Z15-7 was used for all experiments. The liquid fermentation was conducted at 30 °C in a rotary shaker at 150 rpm for 15 d. Silica gel and neutral alumina column chromatography were used for the separation and purification of lovastatin from the fermentation broth. RESULTS: The limits of detection of lovastatin were 0.320 µg/ml in the lovastatin standard solution and 0.490 µg/ml in the fermentation broth sample and the limits of quantification of lovastatin were 1.265 µg/ml in the lovastatin standard solution and 3.955 µg/ml in the fermentation broth sample. The amounts of lovastatin in the fermentation broth ranged from 876.614 to 911.967 µg/ml, with relative standard deviations from 1.203 to 1.709%. The mean recoveries of lovastatin using silica gel and neutral alumina column chromatography were 84.2 ± 0.82 and 87.2 ± 0.21%, respectively. DISCUSSION AND CONCLUSION: Dual-wavelength UV spectrophotometry is a rapid, sensitive, accurate, and convenient method for quantifying lovastatin in fermentation broth. Neutral alumina column chromatography is more efficient than silica gel column chromatography for the purification and determination lovastatin using the developed dual-wavelength UV spectrophotometry method.

Involvement of abscisic acid in regulating antioxidative defense systems and IAA-oxidase activity and improving adventitious rooting in mung bean [Vigna radiata (L.) Wilczek] seedlings under cadmium stress.

In vitro experiments were conducted to investigate the effects of abscisic acid (ABA) and Cd on antioxidative defense systems and indole-3-acetic acid (IAA) oxidase during adventitious rooting in mung bean [Vigna radiata (L.) Wilczek] seedlings. The exogenous ABA significantly enhanced the number and fresh weight of the adventitious roots. CdCl2 strongly inhibited adventitious rooting. Pretreatment with 10 µM ABA clearly alleviated the inhibitory effect of Cd on rooting. ABA significantly reduced superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, as well as the levels of glutathione (GSH) and ascorbic acid (ASA) during adventitious rooting. ABA strongly increased IAA-oxidase activity during the induction (0-12 h) and expression (after 48 h) phases and increased the phenols levels. Cd treatment significantly reduced the activities of SOD, APX, POD, and IAA oxidase, as well as GSH level. Cd strongly increased ASA levels. ABA pretreatment counteracted Cd-induced alterations of certain antioxidants and antioxidative enzymes, e.g., remarkably rescued APX and POD activities, reduced the elevated SOD and CAT activities and ASA levels, and recovered the reduced GSH levels, caused by Cd stress. Thus, the physiological effects of the combination of ABA and Cd treatments were opposite of those obtained with Cd treatment alone, suggesting that ABA involved in the regulation of antioxidative defense systems and the alleviation of wounding- and Cd-induced oxidative stress.

Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence.

The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.

Induction of a high-yield lovastatin mutant of Aspergillus terreus by ¹²C6⁺ heavy-ion beam irradiation and the influence of culture conditions on lovastatin production under submerged fermentation.

Heavy-ion beams, possessing a wide mutation spectrum and increased mutation frequency, have been used effectively as a breeding method. In this study, the heavy-ion beams generated by the Heavy-Ion Research Facility in Lanzhou were used to mutagenize Aspergillus terreus CA99 for screening high-yield lovastatin strains. Furthermore, the main growth conditions as well as the influences of carbon and nitrogen sources on the growth and the lovastatin production of the mutant and the original strains were investigated comparatively. The spores of A. terreus CA99 were irradiated by 15, 20, 25, and 30 Gy of 80 MeV/u (12)C(6+) heavy-ion beams. Based on the lovastatin contents in the fermentation broth, a strain designated as A. terreus Z15-7 has been selected from the clone irradiated by the heavy-ion beam. When compared with the original strain, the content of lovastatin in the fermentation broth of A. terreus Z15-7 increased 4-fold. Moreover, A. terreus Z15-7 efficiently used the carbon and nitrogen sources for the growth and production of lovastatin when compared to the original strain. The maximum yield of lovastatin, 916.7 µg/ml, was obtained as A. terreus Z15-7 was submerged cultured in the chemically defined medium supplemented with 3% glycerol as a carbon source, 1% corn meal as an organic nitrogen source, and 0.2% sodium nitrate as an inorganic nitrogen source at 30 °C in the shake flask. The result shows that heavy-ion beam irradiation is an effective method for the mutation breeding of lovastatin production of A. terreus.