{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T02:14:36Z","timestamp":1784081676084,"version":"3.55.0"},"reference-count":81,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,29]],"date-time":"2024-02-29T00:00:00Z","timestamp":1709164800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The fungus <jats:italic>Rhizopus arrhizus<\/jats:italic> (=<jats:italic>R. oryzae<\/jats:italic>) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of <jats:italic>R. arrhizus<\/jats:italic>, were identified using live\/dead staining, fluorescence <jats:italic>in situ<\/jats:italic> hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, <jats:italic>Pandoraea sputorum<\/jats:italic> EFB03792 and <jats:italic>Mycetohabitans endofungorum<\/jats:italic> EFB03829, were purified from the host fungal strains <jats:italic>R. arrhizus<\/jats:italic> XY03792 and XY03829, respectively. Notably, this study marks the first report of <jats:italic>Pandoraea<\/jats:italic> as an EFB genus. Compared to its free-living counterparts, <jats:italic>P. sputorum<\/jats:italic> EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces <jats:italic>R. arrhizus<\/jats:italic> as a new host for EFB <jats:italic>M. endofungorum<\/jats:italic>, with EFB contributing to host sporulation. Despite a visibly reduced genome, <jats:italic>M. endofungorum<\/jats:italic> EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in <jats:italic>R. arrhizus<\/jats:italic>, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within <jats:italic>R. arrhizus<\/jats:italic>, laying the groundwork for identifying suitable <jats:italic>R. arrhizus<\/jats:italic> strains for fermentation processes.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1346252","type":"journal-article","created":{"date-parts":[[2024,2,29]],"date-time":"2024-02-29T15:03:27Z","timestamp":1709219007000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus"],"prefix":"10.3389","volume":"15","author":[{"given":"Xiao-Ling","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heng","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Xin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin-Ye","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng-Fei","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Yong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,2,29]]},"reference":[{"key":"ref1","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2943","DOI":"10.1128\/AEM.00452-16","article-title":"Isolation of endohyphal bacteria from foliar ascomycota and in vitro establishment of their symbiotic associations","volume":"82","author":"Arendt","year":"2016","journal-title":"Appl. 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