bioRxiv - Microbiology最新文献

{"title":"Evaluating Best Practices for Isolating Pyrophilous Bacteria and Fungi from Burned Soil","authors":"Dylan J Enright, Ryan J Quaal, Aishwarya Veerabahu, Anna Nguyen, Jenna Maddox, Sydney I Glassman","doi":"10.1101/2024.09.16.612975","DOIUrl":"https://doi.org/10.1101/2024.09.16.612975","url":null,"abstract":"A live microbial culture is invaluable to assess traits and functions via 'omics and biophysical assays. However, it is not always logistically feasible to culture immediately from freshly obtained soil, and selecting the proper media for culturing is not trivial. While building a culture collection of pyrophilous microbes obtained from burnt soil, we tested the best 1) method of storing soil to retain culturable viability and 2) media to garner the most microbial diversity. We tested four methods of soil storage (dried, stored at 4°C, stored at -80°C alone or in glycerol) and compared to fresh soil obtained 6 months after a severe California chapparal shrubland wildfire. For bacteria, soil frozen at -80°C with glycerol preserved the greatest diversity (25 species, 13 genera) compared to fresh soil (26 species, 13 genera). For fungi, soil stored at -80°C alone preserved the greatest diversity (10 species, 3 genera) compared to fresh soil (13 species, 7 genera). We also tested 3 media types: rich media (Lysogeny Broth (LB) for bacteria; Malt Yeast Agar (MYA) for fungi), oligotrophic media (Reasoner's 2 Agar (R2A) and media made from pyrogenic organic matter (PyOM). For bacteria, culturing on LB and R2A garnered the greatest diversity (LB = 26 species, 13 genera, R2A = 27 species, 15 genera). For fungi a combination of R2A and PyOM captured the greatest diversity (R2A = 15 species, 8 genera, PyOM = 12 species, 6 genera). For both bacteria and fungi, some species of interest were only captured using the PyOM media. Using a combination of these methods from 2018-2022, we cultured >500 isolates (286 bacteria; 258 fungi) from burned soils of 7 Southern California wildfires.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure-guided assembly of an influenza spike nanobicelle vaccine provides pan H1 intranasal protection","authors":"Mallory L Myers, John R Gallagher, DeMarcus D Woolfork, Noah D Khorrami, William B Park, Samantha Maldonado-Puga, Eric Bohrnsen, Benjamin H Schwarz, Derron A Alves, Kevin W Bock, Altaira D Dearborn, Audray K Harris","doi":"10.1101/2024.09.16.613335","DOIUrl":"https://doi.org/10.1101/2024.09.16.613335","url":null,"abstract":"Development of intranasal vaccines for respiratory viruses has gained popularity. However, currently only a live-attenuated influenza vaccine is FDA-approved for intranasal administration. Here, we focused on influenza virus as it circulates seasonally, has pandemic potential, and has vaccine formulations that present hemagglutinin (HA) in different structural arrangements. These display differences have not been correlated with induction of pan-H1 antibodies or shown to provide intranasal protection. Using electron microscopy, biochemistry and animal studies, we identified HA complexes arranged as lipid discs with multiple trimeric HAs displayed along the perimeter, termed spike nanobicelles (SNB). We utilized a structure-guided approach to synthesize in vitro assembled spiked nanobicelles (IA-SNB) from a classical 1934 H1N1 influenza virus. IA-SNBs elicited pan-H1 antibodies and provided protection against antigenically divergent H1N1 viruses via intranasal immunizations. Viral glycoprotein spikes displayed as SNBs could aid in combating antigenic variation and provide innovative intranasal vaccines to aid universal influenza vaccine development.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Orchestrated long-distance gene activation by a ParB-like BisD-CTP DNA clamp in low-frequency transfer competence development in Pseudomonas putida","authors":"Hammam Antar, Nicolas Carraro, Stephan Gruber, Jan Roelof van der Meer","doi":"10.1101/2024.09.16.613209","DOIUrl":"https://doi.org/10.1101/2024.09.16.613209","url":null,"abstract":"Integrative conjugative elements (ICEs) are mobile DNA that remain integrated within the host bacterial genome until they activate their excision and transfer to recipient cells via conjugation. ICE transfer is initiated in a small subpopulation of cells that undergo a hierarchical gene expression cascade leading to transfer competence formation. In this study, we demonstrate that transfer competence formation of the ICEclc element in stationary phase Pseudomonas putida cells is regulated by the coordinated activity of a two-component transcriptional activator, BisC and BisD. Chromatin immunoprecipitation of tagged BisC or BisD followed by high throughput sequencing showed that both proteins accumulate at similar sites around ICEclc transfer competence promoters in P. putida cells. Genetic dissection and single cell microscopy showed that BisD is a dual domain protein, with a C-terminal gene activator domain and an N-terminal ParB-like domain, forming dimeric DNA clamps that self-load at distant sites and reach target promoters after extensive one-dimensional DNA sliding. Expressed mCherry-BisD in P. putida ICEclc cells form discrete fluorescent foci, dependent on parS-like sequences on the ICE. This focus formation is similar as what is seen with canonical ParB proteins accumulating on chromosomal DNA, but in case of BisD corresponds to both chromosomal and excised ICE-molecules. Sliding of BisD over ~50 kb of ICE-DNA is asymmetric and follows the direction of ICE gene transcription. This may help to establish a temporal order of activation of transfer competence formation, optimizing ICE transfer. Given that ICEclc is activated in stationary phase cells, we hypothesize that BisD is not involved in segregating excised ICE-DNA among daughter cells, but rather in actively directing ICE-DNA molecules towards the (multiple) conjugative systems that are produced in transfer competent cells. BisD thus serves as a twin function protein, integrating gene activation and DNA segregation functions.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extensive intrachromosomal duplications in a virulence-associated fungal accessory chromosome","authors":"Jelmer Dijkstra, Anouk C. van Westerhoven, Lucia Gomez-Gil, Carolina Aguilera-Galvez, Giuliana Nakasato-Tagami, Sebastien D. Garnier, Masaya Yamazaki, Tsutomu Arie, Takashi Kamakura, Takayuki Arazoe, Antonio Di Pietro, Michael F. Seidl, Gert H.J. Kema","doi":"10.1101/2024.09.16.611982","DOIUrl":"https://doi.org/10.1101/2024.09.16.611982","url":null,"abstract":"Filamentous fungi have evolved compartmentalized genomes consisting of conserved core regions and dynamic accessory regions, which aid the adaptation to changing environments including the interaction with host organisms. In the Fusarium oxysporum species complex, accessory regions play an important role during infection and it has been reported that these regions undergo extensive duplications, however, it is currently unknown how such duplications shape accessory regions. Moreover, the function of accessory regions apart from encoding virulence effectors is not completely understood. Here we determined the karyotype of F. oxysporum Tropical Race 4 (TR4), which causes the ongoing pandemic of Fusarium wilt of banana (FWB). We show that the single accessory chromosome of TR4 isolate II5 has undergone extensive intrachromosomal duplications, resulting in triplication of the chromosome size compared to other closely related TR4 strains. By obtaining mutant strains that have lost the accessory chromosome, we demonstrate that this chromosome is dispensable for vegetative growth but is required for full virulence on banana. Lastly, we found that the loss of chromosome 12 co-occurs with structural rearrangements of core chromosomes, which are generally co-linear between members of the F. oxysporum species complex. Together, our results provide new insights into the chromosome dynamics of the banana infecting TR4 lineage of the F. oxysporum species complex.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making yogurt with the ant holobiont uncovers bacteria, acids, and enzymes for food fermentation","authors":"Veronica M Sinotte, Veronica Ramos Viana, Diego Prado Vasquez, Sevgi Mutlu Sirakova, Nabila Rodriguez Valeron, Ana Cuesta Mate, Shannara K Taylor Parkins, Esther Merino Velasco, David Zilber, Rasmus Munk, Sandra B Andersen, Robert R Dunn, Leonie J Jahn","doi":"10.1101/2024.09.16.613207","DOIUrl":"https://doi.org/10.1101/2024.09.16.613207","url":null,"abstract":"Milk fermentation has a rich history in which food culture, the environment, and microbes intersect. However, the biocultural origins of fermentation practices and microbes have largely been replaced by industrial processes. Here, we consider a historical fermentation originating from Turkey and Bulgaria, ant yogurt. We revisit the traditional practices and modern gastronomic applications that use red wood ants (Formica rufa group) to initiate milk fermentation. Subsequently, we characterize the ants and experimental ant-derived yogurts. We uncover that the ant holobiont, which consists of the ants and their microbes, contributes key acids and enzymes to fermentation. Metabarcoding and culturing revealed that lactic and acetic acid bacteria, including species related to those in conventional yogurt and sourdough, originate from the live ants and proliferate in the milk. The ants and bacteria consequently introduce formic, lactic, and acetic acid, advantageous for yogurt acidification and coagulation. Last, proteases with the potential to act on casein and alter yogurt texture are produced by the ants and bacteria. The ant holobiont thus facilitates fermentation akin to the microbial consortia in other ferments. Our findings highlight the value of integrating traditional, gastronomic, and biological frameworks to uncover the origins and applications of microbes for fermented foods.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"214 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of three novel neutralizing antibody epitopes on the human astrovirus capsid spike and mechanistic insights into virus neutralization","authors":"Sarah Lanning, Nayeli Aguilar-Hernández, Vitor Hugo Balasco Serrão, Tomás López, Sara M O'Rourke, Adam Lentz, Lena Ricemeyer, Rafaela Espinosa, Susana López, Carlos Federico Arias, Rebecca M. DuBois","doi":"10.1101/2024.09.14.613010","DOIUrl":"https://doi.org/10.1101/2024.09.14.613010","url":null,"abstract":"Human astroviruses (HAstVs) are a leading cause of viral childhood diarrhea that infect nearly every individual during their lifetime. Although human astroviruses are highly prevalent, no approved vaccine currently exists. Antibody responses appear to play an important role in protection from HAstV infection, however knowledge about the neutralizing epitope landscape is lacking, as only 3 neutralizing antibody epitopes have previously been determined. Here, we structurally define the epitopes of 3 uncharacterized HAstV-neutralizing monoclonal antibodies: antibody 4B6 with X-ray crystallography to 2.67 Å, and antibodies 3H4 and 3B4 simultaneously with single-particle cryogenic-electron microscopy to 3.33 Å. We assess the epitope locations relative to conserved regions on the capsid spike and find that while antibodies 4B6 and 3B4 target the upper variable loop regions of the HAstV spike protein, antibody 3H4 targets a novel region near the base of the spike that is more conserved. Additionally, we found that all 3 antibodies bind with high affinity, and they compete with receptor FcRn binding to the capsid spike. These studies inform which regions of the HAstV capsid can be targeted by monoclonal antibody therapies and could aid in rational vaccine design.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The endosymbiont Rickettsiella viridis increases the virulence of Diuraphis noxia but reduces alate frequency","authors":"Xinyue Gu, Alex Gill, Qiong Yang, Perran A Ross, Ella Yeatman, Mel Berran, Monica Stelmach, Sonia Sharma, Paul A. Umina, Ary A. Hoffmann","doi":"10.1101/2024.09.15.613162","DOIUrl":"https://doi.org/10.1101/2024.09.15.613162","url":null,"abstract":"Aphids are among the world's most economically damaging pests and carry a diverse range of bacterial endosymbionts. There is increasing interest in exploring potential applications of natural and novel strains of endosymbionts in aphid control. One endosymbiont, Rickettsiella viridis, has a large fitness cost following transfer from its natural aphid host Acyrthosiphon pisum into a novel host aphid Myzus persicae. Here, we investigated host impacts after transferring the same Rickettsiella strain to an important cereal aphid, the Russian wheat aphid Diuraphis noxia. Rickettsiella in this host resulted in modest fitness effects, with a minor increase in heat tolerance and a decrease in development time at 25C. The infection persisted in mixed caged populations under different temperatures. Surprisingly, Rickettsiella increased aphid virulence to wheat plants and to two non-crop hosts of D. noxia, barley grass and brome grass. This was evident from sharper decreases in leaf number and leaf area, as well as an increase in chlorotic streaking when plants were exposed to Rickettsiella-infected D. noxia. Rickettsiella also reduced the proportion of alates in aphids held in small cages and in larger mesocosms containing multiple wheat plants where short-distance dispersal of aphids was impacted. These results provide compelling evidence that Rickettsiella can affect virulence - the first case of an endosymbiont transfer directly influencing aphid virulence to host plants - and highlight the species-specific impacts of endosymbiont transfers on aphids which can involve multiple traits.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a fungal antibacterial endopeptidase that modulates immune responses","authors":"Silke Machata, Ute Bertsche, Franziska Hoffmann, Zaher M. Fattal, Franziska Kage, Michal Flak, Alexander N. J. Iliou, Falk Hillmann, Ferdinand von Eggeling, Hortense Slevogt, Axel A. Brakhage, Ilse D. Jacobsen","doi":"10.1101/2024.09.13.612890","DOIUrl":"https://doi.org/10.1101/2024.09.13.612890","url":null,"abstract":"Aspergillus fumigatus is a saprophytic fungus dwelling in soil and on decaying plant material, but also an opportunistic pathogen in immunocompromised patients. In its environmental niche, A. fumigatus faces competition from other microorganisms including bacteria. Here, we describe the discovery of the first secreted antibacterial protein in A. fumigatus. We identified a secreted fungal endopeptidase, designated CwhA, that cleaves peptidoglycan of Gram-positive bacteria at specific residues within the peptidoglycan stem peptide. Cleavage leads to bacterial lysis and the release of peptidoglycan cleavage products. Expression of cwhA is induced by the presence of bacteria. Furthermore, CwhA is highly abundant in murine lungs during invasive pulmonary aspergillosis and peptidoglycan cleavage products generated by CwhA stimulate cytokine production of human immune cells. Although CwhA does not affect human cells directly, this novel player in fungal-bacterial interactions could affect A. fumigatus infections by inhibiting Gram-positive bacteria in its vicinity, and modulating the immune system.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"214 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome and climate: Skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate","authors":"Madhava Meegaskumbura, Dan Sun, Yewei Liu, Shipeng Zhou","doi":"10.1101/2024.09.16.613297","DOIUrl":"https://doi.org/10.1101/2024.09.16.613297","url":null,"abstract":"The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Given that amphibians are poikilotherms, and thus more susceptible to temperature fluctuations, understanding these effects is particularly important. Here, we investigated the skin microbiome of the rhacophorid tree frog <em>Polypedates megacephalus</em> across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of <em>P. megacephalus</em> adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus <em>Pseudomonas</em>. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to greater climate variability, particularly in temperature fluctuations. Additionally, the functional attributes of microbial communities changed in parallel with shifts in community diversity and composition, suggesting that environmental filtering driven by climate changes negatively impacts microbial community functional redundancy. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Plastisphere: Marine fungi communities in the plastics age","authors":"Inga Kirstein, Marlis Reich, Yanyan Yang, Maike Timmermann, Antje Wichels, Gunnar Gerdts","doi":"10.1101/2024.09.16.613245","DOIUrl":"https://doi.org/10.1101/2024.09.16.613245","url":null,"abstract":"Fungi play important roles in biofilms, are very versatile in their ecological role, and are considered as plastic degraders. Here we aim to increase the resolution of the fungal members of the Plastisphere, to understand fungal substrate specificities and related potential ecological impacts. Fifteen-month-old fungal Plastisphere communities were investigated on 9 different plastic types and glass in seawater from the North Sea. By integrating scanning electron microscopy (SEM) imaging, ITS-based fingerprinting, and re-evaluated 18S rRNA gene sequence data through a fungal-specific phylogeny-based pipeline, we observed fungal Plastispheres and identified specific characteristics based on morphotypes, phylogeny, and biodiversity across different substrate types. Plastic types selected for specific fungal communities with polyolefine communities indicating significantly higher diversity compared to all other plastic types. Furthermore, specific plastic types may select for specific fungal taxa and their potential hosts, highlighting the complexity of marine biofilm food webs, and related ecological implications.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}