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Soil water-holding capacity decreases due to long-term mineral fertilizer application. The objective of this study was to determine how replacing mineral fertilizer with maize straw affected the soil water retention curve, soil water content, soil water availability, and soil equivalent pore size. Replacement treatments in which 25% (S25), 50% (S50), 75% (S75), and 100% (S100) of 225 kg ha−1 nitrogen from mineral fertilizer (CK) was replaced with equivalent nitrogen from maize straw were conducted for five years in the Loess Plateau of China. The Gardner model was used to fit the soil water retention curve and calculate the soil water constant and equivalent pore size distribution. The results indicated that the Gardner model fitted well. Replacing nitrogen from mineral fertilizer with nitrogen from straw increased soil specific water capacity, soil readily available water, soil delayed available water, soil available water, soil capillary porosity, and soil available water porosity over time. S25 increased field capacity and wilting point from the fourth fertilization year. S50 enhanced soil readily available water, soil delayed available water, soil available water, and soil available water porosity from the fifth fertilization year, whereas S25 and S75 increased these from the third fertilization year or earlier. Soil specific water capacity, soil readily available water, soil delayed available water, soil available water, soil capillary porosity, and soil available water porosity could better reflect soil water-holding capacity and soil water supply capacity compared with field capacity and wilting point. [ABSTRACT FROM AUTHOR]

Metagenomic next-generation sequencing (mNGS) is useful for difficult to cultivate pathogens. Here, we use cerebrospinal fluid mNGS to diagnose invasive meningococcal disease. The complete genome sequences of Neisseria meningitidis were assembled using N. meningitidis of ST4821-serotype C isolated from four patients. To investigate the phylogeny, 165 CC4821 N. meningitidis genomes from 1972 to 2017 were also included. The core genome accumulated variation at a rate of 4.84×10−8 substitutions/nucleotide site/year. CC4821 differentiated into four sub-lineages during evolution (A, B, C, and D). While evolving from sub-lineage A (early stage) to sub-lineage D (late stage), the ST and CC4821 serotype converged into the ST4821-serotype C clone. Most strains of sub-lineage D were isolated from invasive meningococcal disease, with increasing resistance to quinolones. Phylogeographic analysis suggests that CC4821 has spread across 14 countries. Thus, the selective pressure of quinolones may cause CC4821 to converge evolutionarily, making it more invasive and facilitating its spread. Metagenomic data from cerebrospinal fluid was used to genotype Neisseria meningitidis in patients with invasive meningococcal disease and trace the origin of the pathobiont, providing a phylogeographic analysis of the strain's evolution in China and its global spread. [ABSTRACT FROM AUTHOR]

Earlier, we reported that ST239 was the 15-year predominant methicillin-resistant Staphylococcus aureus (MRSA) clone in China. In this study, MRSA strain CN79 belonging to ST239 and isolated from blood was used to determine the whole genome sequence. Comparative genomics analysis was done between MRSA CN79 and 25 sequenced S. aureus in the NCBI GenBank database. A total of 2,734 protein-encoding genes were identified in the MRSA CN79 genome, which carries 11 antibiotic resistance genes and 65 virulence genes. Two prophages phiCN79A and phiNM3-like were found on the MRSA CN79 genome. MRSA CN79 carries 30 specific genes that are absent from the 25 sequenced S. aureus genomes. Most of them were prophage-related genes. Several antibiotic resistance genes, such as β-lactamase and ABC-type multidrug transport system gene, were located on the genomic island νSaβ. The antibiotic resistance genes, such as tet ( M), ermA1, and blaZ, were also located on different transposons. The virulence genes sea, map, hlb, and sak are located on phiNM3-like prophage and the exotoxin genes are carried on the genomic island νSaα. These results suggest that ST239 MRSA strains are widespread owing to horizontal acquisition of the mobile genetic elements harbored antibiotic resistance genes and virulence genes in response to environmental selective pressures, such as antibiotics and the human immune system during evolution. [ABSTRACT FROM AUTHOR]