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1. Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

   https://doi.org/10.7717/peerj.7744  

   Benucci, Gian Maria; Longley, Reid; Zhang, Peng; Zhao, Qi; Bonito, Gregory; Yu, Fuqiang (January 2019, PeerJ)

   Morels ( Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter , Pseudomonas , Stenotrophomonas , and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella , Phialophora , and Mortierella . This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production. 

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2. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae

   https://doi.org/10.1093/nar/gkad047  

   McNutt, Zakkary_A; Roy, Bappaditya; Gemler, Bryan_T; Shatoff, Elan_A; Moon, Kyung-Mee; Foster, Leonard J.; Bundschuh, Ralf; Fredrick, Kurt (February 2023, Nucleic Acids Research)

   Abstract Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. Inhibition of SD-ASD pairing is due to sequestration of the 3’ tail of 16S rRNA in a pocket formed by bS21, bS18, and bS6 on the 30S platform. Interestingly, in many Flavobacteriales, the gene encoding bS21, rpsU, contains an extended SD sequence. In this work, we present genetic and biochemical evidence that bS21 synthesis in Flavobacterium johnsoniae is autoregulated via a subpopulation of ribosomes that specifically lack bS21. Mutation or depletion of bS21 in the cell increases translation of reporters with strong SD sequences, such as rpsU’-gfp, but has no effect on other reporters. Purified ribosomes lacking bS21 (or its C-terminal region) exhibit higher rates of initiation on rpsU mRNA and lower rates of initiation on other (SD-less) mRNAs than control ribosomes. The mechanism of autoregulation depends on extensive pairing between mRNA and 16S rRNA, and exceptionally strong SD sequences, with predicted pairing free energies of < –13 kcal/mol, are characteristic of rpsU across the Bacteroidota. This work uncovers a clear example of specialized ribosomes in bacteria. 

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3. Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae

   https://doi.org/10.1261/rna.079721.123  

   Naeem, Fawwaz M; Gemler, Bryan T; McNutt, Zakkary A; Bundschuh, Ralf; Fredrick, Kurt (January 2024, RNA)

   Ribosomes of Bacteroidia fail to recognize Shine–Dalgarno (SD) sequences due to sequestration of the 3′ tail of the 16S rRNA on the 30S platform. Yet in these organisms, theprfBgene typically contains the programmed +1 frameshift site with its characteristic SD sequence. Here, we investigateprfBautoregulation inFlavobacterium johnsoniae, a member of the Bacteroidia. We find that the efficiency ofprfBframeshifting inF. johnsoniaeis low (∼7%) relative to that inEscherichia coli(∼50%). Mutation or truncation of bS21 inF. johnsoniaeincreases frameshifting substantially, suggesting that anti-SD (ASD) sequestration is responsible for the reduced efficiency. The frameshift site of certain Flavobacteriales, such asWinogradskyella psychrotolerans, has no SD. InF. johnsoniae, thisW. psychrotoleranssequence supports frameshifting as well as the native sequence, and mutation of bS21 causes no enhancement. These data suggest thatprfBframeshifting normally occurs without SD–ASD pairing, at least under optimal laboratory growth conditions. Chromosomal mutations that remove the frameshift or ablate the SD confer subtle growth defects in the presence of paraquat or streptomycin, respectively, indicating that both the autoregulatory mechanism and the SD element contribute toF. johnsoniaecell fitness. Analysis ofprfBframeshift sites across 2686 representative bacteria shows loss of the SD sequence in many clades, with no obvious relationship to genome-wide SD usage. These data reveal unexpected variation in the mechanism of frameshifting and identify another group of organisms, the Verrucomicrobiales, that globally lack SD sequences. 

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4. Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley, MA

   https://doi.org/10.1128/mra.00861-24  

   Behar, Sasha; Zadvornaya, Arina; Wren, Elizabeth; Andreadis, Marina; Tariq, Ayesha; Tian, Mary E; Krishna, Sachi; Keita, Kadidia; Eich, Helena; Enriquez, Jennifer; et al (February 2025, Microbiology Resource Announcements)

   Putonti, Catherine (Ed.)

   ABSTRACT We present the genomes of nine cultured microbes isolated from two freshwater sites in Wellesley, MA. The dataset is useful for exploring genomic diversity among freshwater taxa, includingPedobacter,Pseudomonas,Rhodoferax,Rouxiella,andFlavobacterium. 

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5. Coinfection of channel catfish ( Ictalurus punctatus ) with virulent Aeromonas hydrophila and Flavobacterium covae exacerbates mortality

   https://doi.org/10.1111/jfd.13912  

   Wise, Allison L; LaFrentz, Benjamin R; Kelly, Anita M; Liles, Mark R; Griffin, Matt J; Beck, Benjamin H; Bruce, Timothy J (January 2024, Journal of Fish Diseases)

   Abstract Flavobacterium covaeand virulentAeromonas hydrophilaare prevalent bacterial pathogens within the US catfish industry that can cause high mortality in production ponds. An assessment of in vivo bacterial coinfection with virulentA. hydrophila(ML09‐119) andF. covae(ALG‐00‐530) was conducted in juvenile channel catfish (Ictalurus punctatus). Catfish were divided into seven treatments: (1) mock control; (2) and (3) high and low doses of virulentA. hydrophila; (4) and (5) high and low doses ofF. covae; (6) and (7) simultaneous challenge with high and low doses of virulentA. hydrophilaandF. covae. In addition to the mortality assessment, anterior kidney and spleen were collected to evaluate immune gene expression, as well as quantify bacterial load by qPCR. At 96 h post‐challenge (hpc), the high dose of virulentA. hydrophilainfection (immersed in 2.3 × 10⁷ CFU mL⁻¹) resulted in cumulative percent mortality (CPM) of 28.3 ± 9.5%, while the high dose ofF. covae(immersed in 5.2 × 10⁶ CFU mL⁻¹) yielded CPM of 23.3 ± 12.9%. When these pathogens were delivered in combination, CPM significantly increased for both the high‐ (98.3 ± 1.36%) and low‐dose combinations (76.7 ± 17.05%) (p < .001). Lysozyme activity was found to be different at 24 and 48 hpc, with the high‐dose vAh group demonstrating greater levels than unexposed control fish at each time point. Three proinflammatory cytokines (tnfα,il8,il1b) demonstrated increased expression levels at 48 hpc. These results demonstrate the additive effects on mortality when these two pathogens are combined. The synthesis of these mortality and health metrics advances our understanding of coinfections of these two important catfish pathogens and will aid fish health diagnosticians and channel catfish producers in developing therapeutants and prevention methods to control bacterial coinfections. 

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