Review
Food Science & Technology
Anton E. Shikov, Iuliia A. Savina, Anton A. Nizhnikov, Kirill S. Antonets
Summary: Bacterial organisms have undergone homologous recombination and horizontal gene transfer multiple times, resulting in enhanced adaptation to new environments, specialization, the emergence of new species, and changes in virulence. Analysis of genomic studies of bacterial species in the past 30 years reveals that these genetic exchanges are associated with ecological diversification, pathogenesis, and symbiosis.
Review
Plant Sciences
Rebecca T. Batstone
Summary: Many important plant traits are influenced not only by the plant's genome, but also by genes within microbes and mobile genetic elements (MGEs) due to nested symbiosis. Understanding the evolution of plant traits is facilitated by combining quantitative genetic and functional genomics approaches to consider sources of nested genetic variation. Additionally, studying coevolution within nested symbiosis can help in designing or selecting for MGEs that promote plant health.
Article
Microbiology
Timothy L. Haskett, Hayley E. Knights, Beatriz Jorrin, Marta D. Mendes, Philip S. Poole
Summary: Utilizing a modified in situ acetylene reduction assay (ARA) with barley as the host, nitrogenase activity in diazotrophic bacteria can be rapidly and reliably assessed, aiding in the identification of high-quality plant-associative diazotrophs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Emma K. Bueren, Alaina R. Weinheimer, Frank O. Aylward, Bryan B. Hsu, David C. Haak, Lisa K. Belden
Summary: This study examines the prophage community in the gut of European honeybees and honey bee pathogens. Results show that prophages can have beneficial effects on bacterial hosts and play a role in maintaining the stability of the gut microbiome. The number and composition of prophages vary among different bacterial species, with some species having higher prophage counts and composition than others.
Article
Microbiology
Suegene Noh, Benjamin J. Capodanno, Songtao Xu, Marisa C. Hamilton, Joan E. Strassmann, David C. Queller
Summary: The three symbiotic species of D. discoideum present a unique opportunity to study a naturally occurring symbiosis in a laboratory model protist. The reduced genomes of P. bonniea and P. hayleyella display characteristics indicative of genome streamlining rather than deterioration during adaptation to their protist hosts. Sets of genes present in all three amoeba-symbiont genomes are potentially used for host-symbiont interactions.
Article
Microbiology
Luis Guillermo Teheran-Sierra, Michelli Inacio Goncalves Funnicelli, Lucas Amoroso Lopes de Carvalho, Maria Ines Tiraboschi Ferro, Marcos Antonio Soares, Daniel Guariz Pinheiro
Summary: The study identified beneficial bacterial communities from sugarcane microbiome, showing plant growth-promoting effects and compatibility with plants of the same family (Poaceae). These communities have the potential to be utilized as bioinoculants for crops, providing evidence of synergistic action to benefit plants.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Plant Sciences
Laurent Sauviac, Antoine Remy, Emeline Huault, Melanie Dalmasso, Theophile Kazmierczak, Marie-Francoise Jardinaud, Ludovic Legrand, Corentin Moreau, Bryan Ruiz, Anne-Claire Cazale, Sophie Valiere, Benjamin Gourion, Laurence Dupont, Veronique Gruber, Eric Boncompagni, Eliane Meilhoc, Pierre Frendo, Florian Frugier, Claude Bruand
Summary: This study identified hundreds of plant and bacterial genes associated with nodule senescence through dual plant-bacteria RNA sequencing, providing a valuable resource for exploring the mechanisms of nodule senescence. The study revealed that genes related to both plant and bacterial cell cycle and stress responses play important roles in nodule senescence, suggesting complex regulatory networks involved in this process.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Microbiology
Michael Sweet, Helena Villela, Tina Keller-Costa, Rodrigo Costa, Stefano Romano, David G. Bourne, Anny Cardenas, Megan J. Huggett, Allison H. Kerwin, Felicity Kuek, Monica Medina, Julie L. Meyer, Moritz Muller, F. Joseph Pollock, Michael S. Rappe, Mathieu Sere, Koty H. Sharp, Christian R. Voolstra, Nathan Zaccardi, Maren Ziegler, Raquel Peixoto
Summary: Our study provides a comprehensive overview of the diversity and function of culturable bacteria isolated from corals across various habitats. Comparative genomic analysis uncovered potential signatures of beneficial bacterium-coral symbioses, with over 400 biosynthetic gene clusters identified. Novel genomic features potentially involved in host interactions were also discovered, suggesting new targets for coral probiotics.
Article
Plant Sciences
Jose Eduardo Marques-Galvez, Shingo Miyauchi, Francesco Paolocci, Alfonso Navarro-Rodenas, Francisco Arenas, Manuela Perez-Gilabert, Emmanuelle Morin, Lucas Auer, Kerrie W. Barry, Alan Kuo, Igor Grigoriev, Francis M. Martin, Annegret Kohler, Asuncion Morte
Summary: Desert truffles, edible hypogeous fungi forming ectendomycorrhizal symbiosis with Cistaceae plants, have unique genetic and transcriptomic features compared to other fungi. The study identified fungal genes related to sexual reproduction and desert-truffle-specific genomic and secretomic traits, along with a core set of plant genes differentially expressed in mycorrhiza. The research sheds light on plant and fungal determinants involved in the symbiotic switch from ecto to endo under dry conditions in desert truffles.
Review
Biology
Goodluck Benjamin, Gaurav Pandharikar, Pierre Frendo
Summary: Plants form beneficial symbioses with endophytes, arbuscular mycorrhizal fungi, and nitrogen-fixing rhizobia, promoting plant nutrition and growth while enhancing host plant tolerance to environmental stress. Salicylic acid plays a crucial role in plant defense against pathogens and has been shown to impact plant-microbe symbiotic interactions.
Article
Multidisciplinary Sciences
Hannah Buettner, Sarah P. Niehs, Koen Vandelannoote, Zoltan Cseresnyes, Benjamin Dose, Ingrid Richter, Ruman Gerst, Marc Thilo Figge, Timothy P. Stinear, Sacha J. Pidot, Christian Hertweck
Summary: Fungi of the genus Mortierella are protected from nematode attacks by an endosymbiotic bacterium called Mycoavidus, which produces anthelmintic metabolites, highlighting the important role of endofungal bacteria in defending fungi against mycophagous nematodes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Delaney L. Miller, Eric A. Smith, Irene L. G. Newton
Summary: The study found that the honey bee-associated bacterium Bombella apis can inhibit the growth of insect fungal pathogens, effectively protecting bee broods from infection in vivo, possibly through the secretion of antifungal metabolites. This research provides clues for the development of new antifungal treatments.
Article
Biotechnology & Applied Microbiology
Robin Jugas, Karel Sedlar, Martin Vitek, Marketa Nykrynova, Vojtech Barton, Matej Bezdicek, Martina Lengerova, Helena Skutkova
Summary: CNV detection in bacteria is less focused on compared to eukaryotes, but with increasing interest due to challenges in bacterial drug resistance. CNproScan is a bacterial genome CNV detection method that can detect shorter events and provide classification, showing improvements over existing methods.
Article
Biology
Raul A. Gonzalez-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, Sarah Shah, Katherine E. Dougan, Michael D. A. Fortuin, Remi Lagorce, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Summary: Genome sequences of Symbiodiniaceae are still scarce due to their large genome sizes and unique genome features. This study presented de novo genome assemblies of seven members of the genus Symbiodinium, revealing high sequence and structural divergence among different lineages, with some Symbiodinium isolates showing comparable divergence to distinct genera of Symbiodiniaceae.
Article
Microbiology
Li Sun, Dandan Wang, Zhiqiu Yin, Chengsheng Zhang, Amber Bible, Zhihong Xie
Summary: This study characterized the transcriptional regulator ActR in Azorhizobium caulinodans and investigated its biological function by constructing an actR gene deletion mutant. The results showed that ActR is involved in flagellar biosynthesis and essential for competitive nodulation in symbiosis with Sesbania rostrata.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Valentina Riva, Francesca Mapelli, Agnese Bagnasco, Alessio Mengoni, Sara Borin
Summary: This review established a comprehensive data set of cultured plant endophytic bacteria at the genus level, revealing a recurrent set of culturable bacterial genera and identifying rarely isolated bacterial genera. It demonstrates the potential of culturomics in capturing previously uncultured bacteria from the plant microbiome.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
Gina Elena Giacomazzo, Luca Conti, Annalisa Guerri, Marco Pagliai, Camilla Fagorzi, Patrick Severin Sfragano, Ilaria Palchetti, Giangaetano Pietraperzia, Alessio Mengoni, Barbara Valtancoli, Claudia Giorgi
Summary: This study successfully tuned the mode of action of nitroimidazole derivatives by synthesizing different architectures of ruthenium complexes, and improved their antibacterial activity upon light exposure. This is of significant importance for the design of novel antimicrobials and their application in biologically relevant environments.
INORGANIC CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Cristina Vieitez, Bede P. Busby, David Ochoa, Andre Mateus, Danish Memon, Marco Galardini, Umut Yildiz, Matteo Trovato, Areeb Jawed, Alexander G. Geiger, Michaela Oborska-Oplova, Clement M. Potel, Sibylle C. Vonesch, Chelsea Szu Tu, Mohammed Shahraz, Frank Stein, Lars M. Steinmetz, Vikram G. Panse, Kyung-Min Noh, Mikhail M. Savitski, Athanasios Typas, Pedro Beltrao
Summary: Phosphorylation plays a critical role in regulating various cellular processes, but functional annotations for the majority of discovered phosphosites are lacking. A chemical genetic approach was used to study the functional relevance of phosphosites in yeast, revealing potential functional significance for 42% of the sites. This high-throughput method allows for the functional characterization of individual phosphosites at scale.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Erick Denamur, Benedicte Condamine, Marina Esposito-Farese, Guilhem Royer, Olivier Clermont, Cedric Laouenan, Agnes Lefort, Victoire de Lastours, Marco Galardini
Summary: In this genome-wide association study, the researchers used data from 912 patients with Escherichia coli bloodstream infections to search for genetic variants associated with patient outcomes and the entry of the bacteria through different portals. While no associations were found between genetic variants and patient outcomes, a strong association was identified between the papGII operon and urinary tract entry of E. coli. The study suggests that increasing the sample size may lead to the discovery of causal variants in the future.
Article
Multidisciplinary Sciences
Jacob Bobonis, Karin Mitosch, Andre Mateus, Nicolai Karcher, George Kritikos, Joel Selkrig, Matylda Zietek, Vivian Monzon, Birgit Pfalz, Sarela Garcia-Santamarina, Marco Galardini, Anna Sueki, Callie Kobayashi, Frank Stein, Alex Bateman, Georg Zeller, Mikhail M. Savitski, Johanna R. Elfenbein, Helene L. Andrews-Polymenis, Athanasios Typas
Summary: This study shows that Retron-Sen2 of Salmonella enterica serovar Typhimurium encodes an accessory toxin protein, RcaT, which is neutralized by the reverse transcriptase-msDNA antitoxin complex and becomes active upon perturbation of msDNA biosynthesis. The highly prevalent RcaT-containing retron family constitutes a new type of tripartite DNA-containing toxin-antitoxin system. The research also demonstrates that retron toxin-antitoxin systems act as abortive infection anti-phage defence systems.
Review
Biochemistry & Molecular Biology
Francesca Mapelli, Alessio Mengoni, Valentina Riva, Sara Borin
Summary: Despite the abundance of microbiome information obtained through high-throughput sequencing methods, its translation into practical solutions for societal needs remains limited. This article highlights the significance of bacterial culturing in microbiology and its crucial role in the effective application of plant probiotics in sustainable agriculture.
TRENDS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Christopher Riccardi, Iacopo Passeri, Lisa Cangioli, Camilla Fagorzi, Marco Fondi, Alessio Mengoni
Summary: DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Chiara Vergata, Felice Contaldi, Ivan Baccelli, Alberto Santini, Francesco Pecori, Matteo Buti, Alessio Mengoni, Francesca Vaccaro, Barbara Basso Moura, Francesco Ferrini, Federico Martinelli
Summary: This study aimed to investigate the gene regulatory networks and leaf microbiome changes in response to air particulate matter (PM) pollution in plants, with the goal of exploring the potential of Phylloremediation in improving air quality. The results showed that plants under high PM levels had 28 differentially expressed genes, primarily involved in restructuring of the cell wall and membrane and repression of lipid desaturases. In addition, high PM levels suppressed genes related to primary metabolism and carbon assimilation pathways. Microbiome analysis revealed different effects on fungi belonging to the genera Epicoccum and Dioszegia. A transcriptional regulation model for plants in response to air PMs was proposed.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Chemistry, Inorganic & Nuclear
Gina Elena Giacomazzo, Luca Conti, Camilla Fagorzi, Marco Pagliai, Claudia Andreini, Annalisa Guerri, Brunella Perito, Alessio Mengoni, Barbara Valtancoli, Claudia Giorgi
Summary: New light-activated antimicrobial therapy using ruthenium complexes has been developed to treat anaerobic bacterial infections, overcoming the reliance on molecular oxygen in traditional photodynamic therapy.
INORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Guilhem Royer, Olivier Clermont, Julie Marin, Benedicte Condamine, Sara Dion, Francois Blanquart, Marco Galardini, Erick Denamur
Summary: The virulence of extra-intestinal pathogenic Escherichia coli is associated with various genes encoding adhesins, toxins, and iron capture systems, but the contribution of these genes to virulence depends on the genetic background and is not well understood. In this study, genome analysis of 232 strains reveals that the high-pathogenicity island (HPI), which encodes siderophores, is responsible for the emergence of virulence in a subgroup of strains. Furthermore, the presence of the aer or sit operons, in addition to the HPI, is associated with full virulence in E. coli, and their prevalence and genomic location depend on strain phylogeny. Overall, specific associations of virulence-associated genes indicate strong epistatic interactions shaping the emergence of virulence in E. coli.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Annalisa Pisciotta, Alessia Maria Sampino, Alessandro Presentato, Marco Galardini, Angel Manteca, Rosa Alduina
Summary: DNA methylation is an epigenetic modification that has been detected in both prokaryotic and eukaryotic genomes. This study focused on the role of cytosine methylation in Streptomyces coelicolor and found that it affects gene expression, growth, and antibiotic biosynthesis. The researchers identified methylated cytosines and methylation motifs in the genome, and demonstrated that cytosine methylation influences gene transcription. This study provides new insights into the role of cytosine methylation in controlling bacterial gene expression.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Christopher Riccardi, Piotr Koper, Gabriel Innocenti, George C. diCenzo, Marco Fondi, Alessio Mengoni, Elena Perrin
Summary: Multipartite genomes are found in approximately 10% of bacteria, mainly belonging to the phylum Proteobacteria. This study focused on the class Gammaproteobacteria and found that multipartite genomes are mainly present in the order Alteromonadales and the family Vibrionaceae. Secondary replicons in Gammaproteobacteria are rare and likely derived from plasmids. These secondary replicons play a role in gene acquisition and adaptation to different ecological niches.
MICROBIAL GENOMICS
(2023)
Editorial Material
Food Science & Technology
Ahmed Idris Hassen, Abe Shegro Gerrano, Olubukola Oluranti Babalola, Alessio Mengoni, Mojgan Rabiey
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2023)
Article
Biochemical Research Methods
Hannah M. Doherty, George Kritikos, Marco Galardini, Manuel Banzhaf, Danesh Moradigaravand
Summary: ChemGAPP is a comprehensive analytical package for chemical genomic screens that provides valuable insights into unknown gene function. It includes three sub-packages for different scales of screens and has been successfully tested and benchmarked against known interaction types.
Article
Microbiology
George C. DiCenzo, Lisa Cangioli, Quentin Nicoud, Janis H. T. Cheng, Matthew J. Blow, Nicole Shapiro, Tanja Woyke, Emanuele G. Biondi, Benoit Alunni, Alessio Mengoni, Peter Mergaert
Summary: DNA methylation plays important roles in immunity and cellular processes regulation in Ensifer bacteria, especially in nitrogen-fixing symbiosis with legumes. Six genome-wide methylated motifs were identified using single-molecule real-time sequencing, with five of them being strain-specific. The GANTC motif recognized by the cell cycle-regulated CcrM methyltransferase was methylated in all strains. The methylation of GANTC motifs increased progressively from ori to ter regions in actively dividing cell cultures, while near full genome-wide GANTC methylation was observed in the early stage of symbiotic differentiation, followed by a moderate decrease in overall methylation and a progressive decrease in chromosomal GANTC methylation in later stages of differentiation. These findings suggest dysregulated and constitutive CcrM activity during terminal differentiation may be a driving factor for endoreduplication of terminally differentiated bacteroids.