More Like this

1. The biocontrol potential of endophyte Bacillus velezensis to reduce post-harvest tomato infection caused by Rhizopus microsporus

   https://doi.org/10.1128/spectrum.01064-25  

   Kock, Alicia; Napo, Mmanoko; Viviers, Dionné; Akinmoladun, Oluwakemi V; Alayande, Kazeem A; Yusuf, Abdullahi; Uehling, Jessie; Pawlowska, Teresa E; Adeleke, Rasheed A (October 2025, Microbiology Spectrum)

   Hockett, Kevin Loren (Ed.)

   ABSTRACT Rhizopus microsporusis a necrotrophic post-harvest pathogen that causes significant economic losses in the agricultural sector. To explore alternatives to conventional management strategies for the mitigation of post-harvest infections, we investigated the potential of two previously identified endophyticBacillus velezensisstrains as biological control agents. Throughin vitroandin vivoexperiments, we examined the mechanisms of biocontrol displayed by twoB. velezensisstrains (KV10 and KV15) against threeR. microsporusstrains (W2-50, W2-51, and W2-58).In vitroassays assessed co-cultivability and the inhibitory effects ofB. velezensisagainstR. microsporus. The results demonstrated strain-specific antifungal activity with a reduction in fungal growth across treatments. Further analysis revealed that volatile organic compounds produced byB. velezensiscontributed to its antifungal properties. To evaluate the biocontrol efficacyin vivo, tomato fruits were inoculated withR. microsporusand subsequently treated withB. velezensis. The results support the strain-specific reduction in tomato spoilage, yielding various spoilage rates observed across treatments. Our findings highlight the potential ofB. velezensisas a promising biocontrol agent for the management ofR. microsporuspost-harvest infections in tomatoes. Further research is warranted to optimize the applicationof B. velezensisas a sustainable and environmentally friendly approach for controlling post-harvest diseases in tomatoes.IMPORTANCEOur study shows the significance of improving sustainable agriculture by offering an alternative to the use of chemical fungicides in post-harvest applications. Opportunistic fungal pathogens likeRhizopus microsporuscan have detrimental effects on post-harvest commodities like tomatoes. Post-harvest fungal infections are mainly controlled by chemical fungicides that pose health risks to humans and the environment. Utilizing biocontrol agents provides an environmentally safe alternative. Understanding the mechanisms of biocontrol employed by beneficial bacteria likeBacillus velezensison fungal pathogens gives insight into safer, more environmentally friendly alternatives to protect food crops. Our results suggest that targeted microbial solutions can mitigate post-harvest losses. 

   more » « less
2. Photo-addressable microwell devices for rapid functional screening and isolation of pathogen inhibitors from bacterial strain libraries

   https://doi.org/10.1063/5.0188270  

   Barua, Niloy; Herken, Ashlee_M; Melendez-Velador, Natalie; Platt, Thomas_G; Hansen, Ryan_R (February 2024, Biomicrofluidics)

   Discovery of new strains of bacteria that inhibit pathogen growth can facilitate improvements in biocontrol and probiotic strategies. Traditional, plate-based co-culture approaches that probe microbial interactions can impede this discovery as these methods are inherently low-throughput, labor-intensive, and qualitative. We report a second-generation, photo-addressable microwell device, developed to iteratively screen interactions between candidate biocontrol agents existing in bacterial strain libraries and pathogens under increasing pathogen pressure. Microwells (0.6 pl volume) provide unique co-culture sites between library strains and pathogens at controlled cellular ratios. During sequential screening iterations, library strains are challenged against increasing numbers of pathogens to quantitatively identify microwells containing strains inhibiting the highest numbers of pathogens. Ring-patterned 365 nm light is then used to ablate a photodegradable hydrogel membrane and sequentially release inhibitory strains from the device for recovery. Pathogen inhibition with each recovered strain is validated, followed by whole genome sequencing. To demonstrate the rapid nature of this approach, the device was used to screen a 293-membered biovar 1 agrobacterial strain library for strains inhibitory to the plant pathogen Agrobacterium tumefaciens sp. 15955. One iterative screen revealed nine new inhibitory strains. For comparison, plate-based methods did not uncover any inhibitory strains from the library (n = 30 plates). The novel pathogen-challenge screening mode developed here enables rapid selection and recovery of strains that effectively suppress pathogen growth from bacterial strain libraries, expanding this microwell technology platform toward rapid, cost-effective, and scalable screening for probiotics, biocontrol agents, and inhibitory molecules that can protect against known or emerging pathogens. 

   more » « less
3. Polystyrene Upcycling into Fungal Natural Products and a Biocontrol Agent

   https://doi.org/10.1021/jacs.2c12285  

   Rabot, Chris; Chen, Yuhao; Lin, Shu-Yi; Miller, Ben; Chiang, Yi-Ming; Oakley, C. Elizabeth; Oakley, Berl R.; Wang, Clay C.; Williams, Travis J. (February 2023, Journal of the American Chemical Society)

   Polystyrene (PS) is one of the most used, yet infrequently recycled plastics. Although manufactured on the scale of 300 million tons per year globally, current approaches toward PS degradation are energy- and carbon-inefficient, slow, and/or lim- ited in the value that they reclaim. We recently reported a scalable process to degrade post-consumer polyethylene-containing waste streams into carboxylic diacids. Engineered fungal strains then upgrade these diacids biosynthetically to synthesize pharmacologi- cally active secondary metabolites. Herein, we apply a similar reaction to rapidly convert PS to benzoic acid in high yield. Engi- neered strains of the filamentous fungus Aspergillus nidulans then biosynthetically upgrade PS-derived crude benzoic acid to the structurally diverse secondary metabolites ergothioneine, pleuromutilin, and mutilin. Further, we expand the catalog of plastic- derived products to include spores of the industrially relevant biocontrol agent Aspergillus flavus Af36 from crude PS-derived ben- zoic acid. 

   more » « less
4. An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

   https://doi.org/10.1093/molbev/msab118  

   Kumar, Sudhir; Tao, Qiqing; Weaver, Steven; Sanderford, Maxwell; Caraballo-Ortiz, Marcos A; Sharma, Sudip; Pond, Sergei L; Miura, Sayaka (May 2021, Molecular Biology and Evolution)

   Yeager, Meredith (Ed.)

   Abstract Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/). 

   more » « less
5. A Bacterial Symbiont Protects Honey Bees from Fungal Disease

   https://doi.org/10.1128/mBio.00503-21  

   Miller, Delaney L.; Smith, Eric A.; Newton, Irene L. (June 2021, mBio)

   Graf, Joerg (Ed.)

   ABSTRACT Fungal pathogens, among other stressors, negatively impact the productivity and population size of honey bees, one of our most important pollinators (1, 2), in particular their brood (larvae and pupae) (3, 4). Understanding the factors that influence disease incidence and prevalence in brood may help us improve colony health and productivity. Here, we examined the capacity of a honey bee-associated bacterium, Bombella apis , to suppress the growth of fungal pathogens and ultimately protect bee brood from infection. Our results showed that strains of B. apis inhibit the growth of two insect fungal pathogens, Beauveria bassiana and Aspergillus flavus , in vitro . This phenotype was recapitulated in vivo ; bee broods supplemented with B. apis were significantly less likely to be infected by A. flavus . Additionally, the presence of B. apis reduced sporulation of A. flavus in the few bees that were infected. Analyses of biosynthetic gene clusters across B. apis strains suggest antifungal candidates, including a type 1 polyketide, terpene, and aryl polyene. Secreted metabolites from B. apis alone were sufficient to suppress fungal growth, supporting the hypothesis that fungal inhibition is mediated by an antifungal metabolite. Together, these data suggest that B. apis can suppress fungal infections in bee brood via secretion of an antifungal metabolite. IMPORTANCE Fungi can play critical roles in host microbiomes (5–7), yet bacterial-fungal interactions are understudied. For insects, fungi are the leading cause of disease (5, 8). In particular, populations of the European honey bee ( Apis mellifera ), an agriculturally and economically critical species, have declined in part due to fungal pathogens. The presence and prevalence of fungal pathogens in honey bees have far-reaching consequences, endangering other species and threatening food security (1, 2, 9). Our research highlights how a bacterial symbiont protects bee brood from fungal infection. Further mechanistic work could lead to the development of new antifungal treatments. 

   more » « less