Veterinary manure is an important pollution reservoir of antibiotics and antibiotic-resistant bacteria (ARB). However, little is known of the distribution of ARB in plant endophytic bacteria and the number/types of ARB in chicken manure. In this study, 454-pyrosequencing was used to investigate the distribution and composition of ARBs in chicken manure and fertilized vegetables. The prevalence of ARB in the samples of the chicken manure compost recovered from farms on which amoxicillin, kanamycin, gentamicin, and cephalexin were used was 20.91-65.9% for ARBs and 8.24-20.63% simultaneously resistant to two or more antibiotics (multiple antibiotic resistant bacteria (MARB)). Antibiotic-resistant endophytic bacteria were widely detected in celery, pakchoi, and cucumber with the highest rate of resistance to cephalexin. The pyrosequencing indicated that the chicken manure dominantly harbored Firmicutes, Bacteroidetes, Synergistetes, and Proteobacteria and that Bacteroidetes was significantly enhanced in farms utilizing antibiotics. In the total cultivable colonies, 62.58-89.43% ARBs and 95.29% MARB were clustered in Bacteroidetes with the dominant species (Myroides ordoratimimus and Spningobacterium spp., respectively) related to human clinical opportunistic pathogens.
Compared to free (free-living) cells, biofilm cells show increased resistance and stability to high-pressure fermentation conditions, although the reasons underlying these phenomena remain unclear. Here, we investigated biofilm formation with immobilized Saccharomyces cerevisiae cells grown on fiber surfaces during the process of ethanol fermentation. The development of biofilm colonies was visualized by fluorescent labeling and confocal microscopy. RNA from yeast cells at three different biofilm development periods was extracted and sequenced by high-throughput sequencing. We quantitated gene expression differences between biofilm cells and free cells and found that 2098, 1556, and 927 genes were significantly differentially expressed, respectively. We also validated the expression of previously reported genes and identified novel genes and pathways under the control of this system. Statistical analysis revealed that biofilm genes show significant gene expression changes principally in the initial period of biofilm formation compared to later periods. Carbohydrate metabolism, amino acid metabolism, signal transduction, and oxidoreductase activity were needed for biofilm formation. In contrast to previous findings, we observed some differential expression performances of FLO family genes, indicating that cell aggregation in our immobilized fermentation system was possibly independent of flocculation. Cyclic AMP-protein kinase A and mitogen-activated protein kinase pathways regulated signal transduction pathways during yeast biofilm formation. We found that carbohydrate metabolism, especially glycolysis/gluconeogenesis, played a key role in the development of S. cerevisiae biofilms. This work provides an important dataset for future studies aimed at gaining insight into the regulatory mechanisms of immobilized cells in biofilms, as well as for optimizing bioprocessing applications with S. cerevisiae.
True morels (Morchella, Pezizales) are world-renowned edible mushrooms (ascocarps) that are widely demanded in international markets. Morchella has been successfully artificially cultivated since 2012 in China and is rapidly becoming a new edible mushroom industry occupying up to 16,466 hectares in the 2021–2022 season. However, nearly 25% of the total cultivation area has annually suffered from fungal diseases. While a variety of morel pathogenic fungi have been reported their epidemic characteristics are unknown, particularly in regional or national scales. In this paper, ITS amplicon sequencing and microscopic examination were concurrently performed on the morel ascocarp lesions from 32 sites in 18 provinces across China. Results showed that Diploöspora longispora (75.48%), Clonostachys solani (5.04%), Mortierella gamsii (0.83%), Mortierella amoeboidea (0.37%) and Penicillium kongii (0.15%) were the putative pathogenic fungi. The long, oval, septate conidia of D. longispora was observed on all ascocarps. Oval asexual spores and sporogenic structures, such as those of Clonostachys, were also detected in C. solani infected samples with high ITS read abundance. Seven isolates of D. longispora were isolated from seven selected ascocarps lesions. The microscopic characteristics of pure cultures of these isolates were consistent with the morphological characteristics of ascocarps lesions. Diploöspora longispora had the highest amplification abundance in 93.75% of the samples, while C. solani had the highest amplification abundance in six biological samples (6.25%) of the remaining two sampling sites. The results demonstrate that D. longispora is a major culprit of morel fungal diseases. Other low-abundance non-host fungi appear to be saprophytic fungi infecting after D. longispora. This study provides data supporting the morphological and molecular identification and prevention of fungal diseases of morel ascocarps.
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