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  1. Free, publicly-accessible full text available December 2, 2023
  2. Free, publicly-accessible full text available April 1, 2023
  3. The process of fermenting tofu extends back thousands of years and is an indispensable part of Chinese culture. Despite a cultural resurgence in fermented foods and interest in microbiomes, there is little knowledge on the microbial diversity represented in fermented ‘hairy’ tofu, known locally in China as Mao tofu. High-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA was used to determine Mao tofu’s fungal and bacterial community diversity across four wet markets in Yunnan, China. The results show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa, and that microbial taxa differ between markets. Diversity also differed based on the specific niche of the tofu block, comparing the outside rind-like niche to that of the inside of the tofu block. Machine learning random forest models were able to accurately classify both the market and niche of sample origin. An over-abundance of yeast and Geotrichum was found, and Mucor (Mucoromycota) was abundant in the outside rind-like niche, which consists of the visible ‘hairy’ mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidetes, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant genera. Putative fungal pathogens of plants (Cercospora, Diaporthe,more »Fusarium) and animals (Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora) were also detected, as were putative bacterial pathogens identified as Legionella. Non-fungal eukaryotic taxa detected by LSU amplicon sequencing included soybean (Glycine max), Protozoa, Metazoa (e.g., Nematoda and Platyhelminthes), Rhizaria and Chromista, indicating that additional biodiversity exists in the hairy tofu microbiome.« less
  4. Abstract. Data and knowledge of surface water bodies (SWB), including large lakes andreservoirs (surface water areas > 1 km2), are critical forthe management and sustainability of water resources. However, the existingglobal or national dam datasets have large georeferenced coordinate offsetsfor many reservoirs, and some datasets have not reported reservoirs andlakes separately. In this study, we generated China's surface water bodies,Large Dams, Reservoirs, and Lakes (China-LDRL) dataset by analyzing allavailable Landsat imagery in 2019 (19 338 images) in Google Earth Engine andvery-high spatial resolution imagery in Google Earth Pro. There were∼ 3.52 × 106 yearlong SWB polygons in China for2019, only 0.01 × 106 of them (0.43 %) were of large size(> 1 km2). The areas of these large SWB polygons accountedfor 83.54 % of the total 214.92 × 103 km2 yearlongsurface water area (SWA) in China. We identified 2418 large dams, including624 off-stream dams and 1794 on-stream dams, 2194 large reservoirs (16.35 × 103 km2), and 3051 large lakes (73.38 × 103 km2). In general, most of the dams and reservoirs in Chinawere distributed in South China, East China, and Northeast China, whereasmost of lakes were located in West China, the lower Yangtze River basin, andNortheast China. The provision of the reliable, accurate China-LDRL dataseton large reservoirs/dams and lakes will enhance our understanding of waterresources management and water security in China.more »The China-LDRL dataset ispublicly available at (Wang et al., 2021b).« less
  5. Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.