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1. Highlighting the Biotechnological Potential of Deep Oceanic Crust Fungi through the Prism of Their Antimicrobial Activity

   https://doi.org/10.3390/md19080411  

   Quemener, Maxence; Dayras, Marie; Frotté, Nicolas; Debaets, Stella; Le Meur, Christophe; Barbier, Georges; Edgcomb, Virginia; Mehiri, Mohamed; Burgaud, Gaëtan (August 2021, Marine Drugs)

   null (Ed.)

   Among the different tools to address the antibiotic resistance crisis, bioprospecting in complex uncharted habitats to detect novel microorganisms putatively producing original antimicrobial compounds can definitely increase the current therapeutic arsenal of antibiotics. Fungi from numerous habitats have been widely screened for their ability to express specific biosynthetic gene clusters (BGCs) involved in the synthesis of antimicrobial compounds. Here, a collection of unique 75 deep oceanic crust fungi was screened to evaluate their biotechnological potential through the prism of their antimicrobial activity using a polyphasic approach. After a first genetic screening to detect specific BGCs, a second step consisted of an antimicrobial screening that tested the most promising isolates against 11 microbial targets. Here, 12 fungal isolates showed at least one antibacterial and/or antifungal activity (static or lytic) against human pathogens. This analysis also revealed that Staphylococcus aureus ATCC 25923 and Enterococcus faecalis CIP A 186 were the most impacted, followed by Pseudomonas aeruginosa ATCC 27853. A specific focus on three fungal isolates allowed us to detect interesting activity of crude extracts against multidrug-resistant Staphylococcus aureus. Finally, complementary mass spectrometry (MS)-based molecular networking analyses were performed to putatively assign the fungal metabolites and raise hypotheses to link them to the observed antimicrobial activities. 

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2. Niche Preference of Escherichia coli in a Peri-Urban Pond Ecosystem

   https://doi.org/10.3390/life11101020  

   NandaKafle, Gitanjali; Huegen, Taylor; Potgieter, Sarah C.; Steenkamp, Emma; Venter, Stephanus N.; Brözel, Volker S. (October 2021, Life)

   Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem. 

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3. Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

   https://doi.org/10.3390/genes11111307  

   Aljahdali, Nesreen H.; Khajanchi, Bijay K.; Weston, Kennedi; Deck, Joanna; Cox, Justin; Singh, Ruby; Gilbert, Jeffrey; Sanad, Yasser M.; Han, Jing; Nayak, Rajesh; et al (November 2020, Genes)

   null (Ed.)

   Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species. 

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4. Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection

   https://doi.org/10.1128/msystems.00212-26  

   Duque-Jaramillo, Alejandra; Symeonidi, Efthymia; Neumann, Manuela; Ashkenazy, Haim; Allen, Madelyn; Weigel, Detlef; Karasov, Talia L (June 2026, mSystems)

   Kovács, Ákos T (Ed.)

   ABSTRACT Specialized or secondary metabolites mediate biotic interactions, including virulence and defense. In plant-pathogenicPseudomonas, certain specialized metabolites can enhance colonization of plant hosts, yet their broader contribution to plant–microbe interactions and the relative importance of different metabolites remain unclear. Specialized metabolites are products of enzymes encoded in biosynthetic gene clusters (BGCs), whose prediction from genome sequences has become routine but whose functional roles are rarely tested experimentally. Here, we characterize the BGC repertoire of 225P. viridiflavaisolates fromArabidopsis thalianaand assess BGC contributions to fitness and disease severityin planta. The BGC landscape ofP. viridiflavawas dominated by non-ribosomal peptide synthetase (NRPS) and NRPS-like BGCs, which accounted for 50% of the predicted BGCs. One-third of the BGC families were restricted to a single isolate. Transposon mutagenesis coupled with random barcode transposon sequencing (RB-TnSeq) revealed that the majority of BGCs reduce rather than increase fitness duringA. thalianainfection, with the magnitude of the fitness cost varying across host genotypes. This cost could be due to exploitation of public goods by cheater mutant strains. In single-isolate plant infections, where public goods are not available, we found 11/34 BGC families correlated with disease severity. Yet, only two of these (an N-acetylglutaminylglutamine amide [NAGGN] and an NRPS) were negatively associated with disease severity, which is positively correlated with bacterial growth in this pathosystem, further indicating that BGCs are generally not beneficialin planta. Our findings reveal extensive and largely uncharacterized biosynthetic potential in populations ofP. viridiflavaand indicate that candidate metabolites are likely not adaptive for direct interactions with the plant, but perhaps for microbe-microbe interactions eitherin plantaor in other ecological niches. IMPORTANCEBacteria, including plant-associated bacteria such asPseudomonas viridiflava, produce a vast array of chemical compounds, called secondary or specialized metabolites, that can mediate their interaction with the plant host or other microorganisms. Some of these compounds are known to directly influence how bacteria interact with plants, but it has been unclear whether this is a general rule. We studied a large collection of closely related leaf-dwellingP. viridiflava—a plant pathogen—that varied in their ability to cause disease. We found that very few of the gene clusters responsible for making specialized metabolites improved the ability of the bacteria to colonize its natural hostArabidopsis thaliana. On the contrary, carrying these gene clusters often reduced bacterial growth and disease severity in plants. Specialized metabolites may instead primarily be important for interacting with other microbes, different host species, or under environmental conditions we did not test. These are questions that remain for future research. 

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5. Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix

   https://doi.org/10.1007/s00442-024-05569-0  

   Leong, Jing V; Mezzomo, Priscila; Kozel, Petr; Volfová, Tereza; de_Lima_Ferreira, Paola; Seifert, Carlo L; Butterill, Phillip T; Freiberga, Inga; Michálek, Jan; Matos-Maraví, Pável; et al (August 2024, Oecologia)

   Plants employ diverse anti-herbivore defences that can covary to form syndromes consisting of multiple traits. Such syn- dromes are hypothesized to impact herbivores more than individual defences. We studied 16 species of lowland willows occurring in central Europe and explored if their chemical and physical traits form detectable syndromes. We tested for phylogenetic trends in the syndromes and explored whether three herbivore guilds (i.e., generalist leaf-chewers, specialist leaf-chewers, and gallers) are affected more by the detected syndromes or individual traits. The recovered syndromes showed low phylogenetic signal and were mainly defined by investment in concentration, richness, or uniqueness of structurally related phenolic metabolites. Resource acquisition traits or inducible volatile organic compounds exhibited a limited cor- relation with the syndromes. Individual traits composing the syndromes showed various correlations to the assemblages of herbivores from the three studied guilds. In turn, we found some support for the hypothesis that defence syndromes are composed of traits that provide defence against various herbivores. However, individual traits rather than trait syndromes explained more variation for all studied herbivore assemblages. The detected negative correlations between various pheno- lics suggest that investment trade-offs may occur primarily among plant metabolites with shared metabolic pathways that may compete for their precursors. Moreover, several traits characterizing the recovered syndromes play additional roles in willows other than defence from herbivory. Taken together, our findings suggest that the detected syndromes did not solely evolve as an anti-herbivore defence. 

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