Comparative Genomic and Functional Analysis of c-di-GMP Metabolism and Regulatory Proteins in Bacillus velezensis LQ-3.

Bacillus velezensis is a promising candidate for biocontrol applications. A common second messenger molecule, bis-(3,5)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has the ability to regulate a range of physiological functions that impact the effectiveness of biocontrol. However, the status of the c-di-GMP signaling pathway in biocontrol strain LQ-3 remains unknown. Strain LQ-3, which was isolated from wheat rhizosphere soil, has shown effective control of wheat sharp eyespot and has been identified as B. velezensis through whole-genome sequencing analyses. In this study, we investigated the intracellular c-di-GMP signaling pathway of LQ-3 and further performed a comparative genomic analysis of LQ-3 and 29 other B. velezensis strains. The results revealed the presence of four proteins containing the GGDEF domain, which is the conserved domain for c-di-GMP synthesis enzymes. Additionally, two proteins were identified with the EAL domain, which represents the conserved domain for c-di-GMP degradation enzymes. Furthermore, one protein was found to possess a PilZ domain, indicative of the conserved domain for c-di-GMP receptors in LQ-3. These proteins are called DgcK, DgcP, YybT, YdaK, PdeH, YkuI, and DgrA, respectively; they are distributed in a similar manner across the strains and belong to the signal transduction family. We selected five genes from the aforementioned seven genes for further study, excluding YybT and DgrA. They all play a role in regulating the motility, biofilm formation, and colonization of LQ-3. This study reveals the c-di-GMP signaling pathway associated with biocontrol features in B. velezensis LQ-3, providing guidance for the prevention and control of wheat sharp eyespot by LQ-3.

Spatial Distribution and Estimation Model of Soil pH in Coastal Eastern China.

Soil pH is an essential indicator for assessing soil quality and soil health. In this study, based on the Chinese farmland soil survey dataset and meteorological dataset, the spatial distribution characteristics of soil pH in coastal eastern China were analyzed using kriging interpolation. The relationships between hydrothermal conditions and soil pH were explored using regression analysis with mean annual precipitation (MAP), mean annual temperature (MAT), the ratio of precipitation to temperature (P/T), and the product of precipitation and temperature (P*T) as the main explanatory variables. Based on this, a model that can rapidly estimate soil pH was established. The results showed that: (a) The spatial heterogeneity of soil pH in coastal eastern China was obvious, with the values gradually decreasing from north to south, ranging from 4.5 to 8.5; (b) soil pH was significantly correlated with all explanatory variables at the 0.01 level. In general, MAP was the main factor affecting soil pH (r = -0.7244), followed by P/T (r = -0.6007). In the regions with MAP < 800 mm, soil pH was negatively correlated with MAP (r = -0.4631) and P/T (r = -0.7041), respectively, and positively correlated with MAT (r = 0.6093) and P*T (r = 0.3951), respectively. In the regions with MAP > 800 mm, soil pH was negatively correlated with MAP (r = -0.6651), MAT (r = -0.5047), P/T (r = -0.3268), and P*T (r = -0.5808), respectively. (c) The estimation model of soil pH was: y = 23.4572 - 6.3930 × lgMAP + 0.1312 × MAT. It has been verified to have a high accuracy (r = 0.7743, p < 0.01). The mean error, the mean absolute error, and the root mean square error were 0.0450, 0.5300, and 0.7193, respectively. It provides a new path for rapid estimation of the regional soil pH, which is important for improving the management of agricultural production and slowing down soil degradation.

Molecular Variability and Distribution of Sugarcane Mosaic Virus in Shanxi, China.

BACKGROUND: Sugarcane mosaic virus (SCMV) is responsible for large-scale economic losses in the global production of sugarcane, maize, sorghum, and some other graminaceous species. To understand the evolutionary mechanism of SCMV populations, this virus was studied in Shanxi, China. A total of 86 maize leaf samples (41 samples in 2012 and 45 samples in 2013) were collected from 4 regions of Shanxi. RESULTS: Double-antibody sandwich (DAS)-ELISA and RT-PCR showed 59 samples (30 samples in 2012 and 29 samples in 2013) to be positive for SCMV, from which 10 new isolates of SCMV were isolated and sequenced. The complete genomes of these isolates are 9610 nt long, including the 5' and 3' non-coding regions, and encode a 3063-amino acid polyprotein. Phylogenetic analyses revealed that 24 SCMV isolates could be divided on the basis of the whole genome into 2 divergent evolutionary groups, which were associated with the host species. Among the populations, 15 potential recombination events were identified. The selection pressure on the genes of these SCMV isolates was also calculated. The results confirmed that all the genes were under negative selection. CONCLUSIONS: Negative selection and recombination appear to be important evolutionary factors shaping the genetic structure of these SCMV isolates. SCMV is distributed widely in China and exists as numerous strains with distinct genetic diversity. Our findings will provide a foundation for evaluating the epidemiological characteristics of SCMV in China and will be useful in designing long-term, sustainable management strategies for SCMV.