Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils. More abundant beneficial microbes including Bacillus, Agromyces, Micromonospora, Pseudonocardia, Acremonium, Lysobacter, Mesorhizobium, Microvirga, Bradyrhizobium, Acremonium and Chaetomium were found in the healthy soils rather than the bacterial wilt infected soils. Compared to bacterial wilt infected soils, the activities of catalase, invertase and urease, as well as soil pH, available phosphorous and potassium content, were all significantly increased in the healthy soils. In a conclusion, the higher abundance of beneficial microbes are positively related the higher soil quality, including better plant growth, lower disease incidence, and higher nutrient contents, soil enzyme activities and soil pH.

The Chinese cabbage is a crop belonging to the family Cruciferae; very few studies have focused on the analysis of gene expression in this economically important crop. In this study, we used real-time quantitative polymerase chain reaction to identify the control genes that are the most stably expressed in a given set of tissues and under conditions of drought stress and downy mildew infection. We characterized the transcript stability of nine candidate reference genes, namely, those encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ubiquitin (Ubc), elongation-factor-1-α (EF-1-α), adenine phosphoribosyltransferase (Apr), clathrin, cyclophilin (Cyp), tubulin (Tub), Actin, and 18s rRNA, using the geNorm and Normfinder software programs. The results of a geNorm analysis indicated that EF-1-α and Apr were the most suitable reference genes among the given set of tissues and that GAPDH and Ubc were the most stable genes under conditions of drought stress and downy mildew infection. Furthermore, the results of an analysis performed using the Normfinder software program indicated EF-1-α to be the best normalization factor in the given set of tissues and under conditions of downy mildew infection and GAPDH to be the best factor under drought stress conditions. The results of the geNorm analysis also helped determine the minimum number of genes required to calculate a reliable normalization factor. A study on the variability of expression of PSY expression showed that the relative quantification of this gene varied depending on the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments.

Plant-parasitic nematodes cause serious crop losses worldwidely. This study intended to discover the antagonistic mechanism of Bacillus cereus strain S2 against Meloidogyne incognita. Treatment with B. cereus strain S2 resulted in a mortality of 77.89% to Caenorhabditis elegans (a model organism) and 90.96% to M. incognita. In pot experiment, control efficiency of B. cereus S2 culture or supernatants were 81.36% and 67.42% towards M. incognita, respectively. In field experiment, control efficiency was 58.97% towards M. incognita. Nematicidal substances were isolated from culture supernatant of B. cereus S2 by polarity gradient extraction, silica gel column chromatography and HPLC. Two nematicidal compounds were identified as C16 sphingosine and phytosphingosine by LC-MS. The median lethal concentration of sphingosine was determined as 0.64 μg/ml. Sphingosine could obviously inhibit reproduction of C. elegans, with an inhibition rate of 42.72% for 24 h. After treatment with sphingosine, ROS was induced in intestinal tract, and genital area disappeared in nematode. Furthermore, B. cereus S2 could induce systemic resistance in tomato, and enhance activity of defense-related enzymes for biocontrol of M. incognita. This study demonstrates the nematicidal activity of B. cereus and its product sphingosine, as well provides a possibility for biocontrol of M. incognita.

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Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.

Soil degradation is a serious global problem, but little is known about how soil microbial communities respond to soil degradation as well as their feedback to ecosystem functioning. In this study, we found the microbial community composition, structure and functional potential significantly altered in the degraded soils with bacterial wilt (termed as degraded soils). Compared with healthy soils, OTU richness of beneficial microorganisms were significantly decreased, but OTU richness of pathogenic microorganisms were significantly increased in the degraded soils. Functional gene array (GeoChip 5.0) analysis showed the functional metabolic potential of genes involved in stress, virulence, sulfur cycle, metal resistance, degradation of plant cell wall was significantly increased in the degraded soils. Increased functional metabolic potential of these genes may be related to the acidification and severe plant disease of degraded soils. Biological activity of degraded soils was obviously decreased with weakened soil enzyme activities when compared to the healthy soils. Soil pH and enzyme activities were negatively correlated with the abundance of genes involved in sulfur cycle, virulence, and stress responses. This study provides new insights into our understanding of soil microbial community responses to soil degradation.

Chinese cabbage varieties with orange inner leaves are of interest due to their attractive appearance and high carotenoid content. Previously, a recessive locus, Br-or, that confers this trait was mapped to linkage group A09 in Brassica rapa, and Bra031539 was identified as the candidate gene. We used a backcross population consisting of 1,392 individuals for fine mapping; three linked markers delimited the Br-or locus to a region of 9.47 kb, which contained only one predicted functional gene, Bra031539 (the carotenoid isomerase gene BrCRTISO). We identified two bacterial artificial chromosome (BAC) clones carrying Br-or and confirmed that this allele of BrCRTISO confers the mutant phenotype by sequencing. Many DNA sequence variations are present in Br-or, including a 90-bp DNA deletion in the promoter and a 501-bp insertion at the 3′ end of the gene. GUS staining showed that the spatial expression of BrCRTISO was perfectly coincident with the site of carotenoid synthesis and that the 90-bp deletion in the promoter slightly downregulated expression of the gene. Using an in vitro enzyme assay, we showed that the mutant Br-or protein cannot convert prolycopene to all-trans-lycopene. Light has a positive effect on the expression of carotenoid biosynthesis genes, except for beta-ring carotene hydroxylase (CHXB), and this coincided with the increase in total lycopene and β-carotene in the Br-or mutant. We also demonstrated that loss of BrCRTISO function, upregulation of the upstream genes, and downregulation of downstream genes lead to the accumulation of prolycopene and confer an orange color to the inner head leaves in Chinese cabbage. Keywords Brassica rapa L. ssp. pekinensis . Orange leaf . Br-or . BrCRTISO . Carotenoid biosynthesis Abbreviations CHXB Beta-ring carotene hydroxylase DH Doubled haploid GAPDH Glyceraldehyde-3-phosphate dehydrogenase IPI Isopentenyl pyrophosphate isomerase LCYB Lycopene beta-cyclase LCYE Lycopene epsilon-cyclase PDS Phytoene desaturase PSY Phytoene synthase VDE Violaxanthin de-epoxidase ZDS Zeta-carotene desaturase ZEP Zeaxanthin epoxidase

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