Article
Biochemical Research Methods
Peter S. Thuy-Boun, Subina Mehta, Bjoern Gruening, Thomas McGowan, An Nguyen, Andrew T. Rajczewski, James E. Johnson, Timothy J. Griffin, Dennis W. Wolan, Pratik D. Jagtap
Summary: This study reanalyzed mass spectrometry data of clinical samples to determine coinfection status in individuals infected with the SARS-CoV-2 coronavirus. The use of metaproteomics for early detection and characterization of coinfections in COVID-19 patients may impact diagnosis and treatment. Detected pathogens in COVID-19 patients included Streptococcus pneumoniae, Lactobacillus rhamnosus, Pseudomonas sps. Bc-h, Acinetobacter ursingii, and Pseudomonas monteilii.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Microbiology
Laure Weisskopf, Stefan Schulz, Paolina Garbeva
Summary: Microorganisms produce and excrete a versatile array of metabolites with different physico-chemical properties and biological activities. Recent research has revealed that microbial volatiles are chemically diverse and play important roles in microbial interactions and inter-kingdom communication. The potential biotechnological applications of microbial volatiles, along with challenges and perspectives in this emerging research field, have also been discussed.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Microbiology
Samuel E. Miller, Albert S. Colman, Jacob R. Waldbauer
Summary: The study used metaproteomic methods to investigate microbial activity and metabolic functions in Alaskan soils. It found that different bacterial groups have specialized roles in acquiring and degrading organic compounds. The research also showed that Acidobacteria have a key role in hemicellulose depolymerization. This study highlights the importance of understanding soil microbial ecology in relation to carbon cycling.
Review
Microbiology
Elisa Ghitti, Eleonora Rolli, Elena Crotti, Sara Borin
Summary: Flavonoids play diverse and crucial roles in plants, helping them cope with various stresses and improve their adaptability to the environment. They not only participate in plant-to-plant interactions but also act as signaling molecules that mediate communication between plants and microorganisms or macroorganisms. Additionally, flavonoids are important phytochemicals in the human diet, with potential nutraceutical, probiotic, and medicinal properties.
Article
Microbiology
Kathryn E. Bazany, Jun-Tao Wang, Manuel Delgado-Baquerizo, Brajesh K. Singh, Pankaj Trivedi
Summary: The frequency and severity of drought caused by human-induced climate change are increasing, and they are already affecting the productivity of cropping systems worldwide. Microbial communities within plant microbiomes play a crucial role in helping their hosts adapt and maintain productivity under abiotic stress, including water deficits. However, the complexity of microbial communities requires an integrative approach to understand their responses to environmental stresses. This study investigates the impact of water deficit on the composition of bacterial, fungal, and protistan communities in the rhizospheres of corn and sugar beet. The results show that different microbial kingdoms have varying responses to water deficit and host factors, and water deficit also affects intra- and inter-kingdom microbial associations.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Microbiology
Amine Mohamed Boukerb, Melyssa Cambronel, Sophie Rodrigues, Ouiza Mesguida, Rikki Knowlton, Marc G. J. Feuilloley, Mohamed Zommiti, Nathalie Connil
Summary: The communication between microorganisms and their hosts, known as inter-kingdom signaling, involves eukaryotic signals such as hormones influencing bacterial physiology. Stress-related catecholamines like epinephrine and norepinephrine have been shown to affect the behaviors of various Gram-negative bacteria and some Gram-positive bacteria. Epinephrine and norepinephrine trigger a signaling cascade in E. coli and S. enterica by interacting with the QseC histidine sensor kinase protein.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Miaomiao Chen, Likun Wang, Xin Zheng, Michael Cohen, Xiaofang Li
Summary: This study revealed that four metabolic pathways responsible for combating Cd stress were commonly regulated in Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, indicating universal strategies used by microbes. Furthermore, the heterologous expression of an ABC transporter gene from E. coli in S. cerevisiae enhanced the yeast's tolerance to Cd, suggesting the potential for modifying microbial traits for bioremediation.
Article
Microbiology
Zongjing Kang, Xiaolin Li, Yan Li, Lei Ye, Bo Zhang, Xiaoping Zhang, Petri Penttinen, Yunfu Gu
Summary: This study found that truffle inoculation had little effect on the growth of Quercus aliena seedlings in the initial stage, but it did lead to changes in nutrient contents and richness of nirK-type bacteria. These findings provide in-depth insights into the relationships between Tuber spp. and hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Takashi Kuromori, Miki Fujita, Fuminori Takahashi, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki
Summary: Plants respond to drought stress through intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps enhance stress resistance. Abscisic acid is a key phytohormone involved in drought stress response, primarily synthesized in vascular tissues and guard cells of leaves, regulating stomatal closure and stress-related gene expression for drought stress resistance. Multiple sensors detect molecular patterns of abiotic stress signals, transmitting them through separate signaling networks to induce downstream responses such as stomatal closure and synthesis of stress-related proteins and metabolites.
Article
Microbiology
G. R. Amores, G. Zepeda-Ramos, L. Garcia-Fajardo, Emilio Hernandez, K. Guillen-Navarro
Summary: This study analyzed the composition of intestinal microorganisms in the fruit fly Anastrepha obliqua and found a higher microbial diversity in wild flies compared to laboratory species, suggesting a specialized metabolism for processing nutrients associated with an artificial diet. The study also identified previously undescribed bacterial species in the fruit fly.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Infectious Diseases
Yu Wan, Mark Ganner, Zaynab Mumin, Derren Ready, Ginny Moore, Isabelle Potterill, Karthik Paranthaman, Elita Jauneikaite, Bharat Patel, Alessandra Harley, Maria Getino, Colin S. Brown, Alicia Demirjian, Bruno Pichon
Summary: This study confirmed the widespread dissemination of the S. capitis NRCS-A clone among neonatal units in the UK through whole-genome sequencing analysis, and emphasized the need for research on improving clinical management of neonatal S. capitis infection.
JOURNAL OF INFECTION
(2023)
Article
Agronomy
Peina Lu, Cai Zhao, Wen Yin, Falong Hu, Zhilong Fan, Aizhong Yu, Hong Fan
Summary: This study aimed to assess the effects of no-till and cereal-legume intercropping on yields, soil properties, enzyme activities, and microbial community diversity and composition. The results showed that no-till intercropping significantly increased yields and organic carbon stocks, decreased nitrate content, and increased total and organic phosphorus in the soil. Additionally, no-till enhanced the diversity of bacterial and total microbial communities, but limited enzyme activities may affect organic carbon turnover and utilization.
Article
Biodiversity Conservation
Samantha Mynhardt, Esther Matthew, Jean Pierre le Roux, Ian Little, Paulette Bloomer, Cobus Theron
Summary: Environmental DNA (eDNA) sampling is an emerging approach for characterising and monitoring biodiversity, particularly for rare, elusive or endangered species. This study focused on using DNA barcoding from soil eDNA to detect and monitor four golden mole species in South Africa. The study successfully detected all four species and improved their distribution records, while also uncovering hidden species diversity.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Ecology
Jean-Baptiste Floc'h, Chantal Hamel, Mario Laterriere, Breanne Tidemann, Marc St-Arnaud, Mohamed Hijri
Summary: The fungal community in canola was influenced by crop diversification, unlike the bacterial community. No core microbiota was found in canola roots, but three core fungi were identified in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. Inter-kingdom network analysis revealed two bacterial and one fungal hub taxa in the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil, with Bradyrhizobium sp. and Mortierella sp. being particularly influential. This study is the first to use inter-kingdom network analysis to identify interaction hot spots in canola microbial communities.
Article
Biochemistry & Molecular Biology
Sapir Schlam-Babayov, Ariel Bensimon, Michal Harel, Tamar Geiger, Ruedi Aebersold, Yael Ziv, Yosef Shiloh
Summary: This study conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells to reveal the fine-tuned dynamics and relationships between PIKKs in the response to genotoxic stress. The results highlight the complex interactions among ATM, ATR, and DNA-PK in the DDR.
Review
Biochemistry & Molecular Biology
Marco Sandrini, Luca Nerva, Fabiano Sillo, Raffaella Balestrini, Walter Chitarra, Elisa Zampieri
Summary: Nowadays, global agriculture is transitioning towards more sustainable production by reducing chemical inputs and preserving microbiomes' richness and biodiversity. Plant-associated microorganisms have shown great potential in improving agriculture sustainability and helping plants cope with harsh environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Stefano Ghignone, Elisa Zampieri, Fabio Tinti, Valeria Torti, Cristina Giacoma, Antonietta Mello
Summary: Soil fungal diversity was studied in two different ecosystems in Madagascar. The dominant fungal phylum in both areas was Ascomycota, followed by unidentified fungi, Basidiomycota, and Mortierellomycota. There was significant variability in fungal richness and abundance within the Maromizaha area, indicating heterogeneity in fungal and plant composition. The representation of Madagascar fungi in existing fungal databases is limited, highlighting the need for further research to uncover the unknown fungal biodiversity in the island.
Article
Microbiology
Fabiano Sillo, Marzia Vergine, Andrea Luvisi, Alice Calvo, Gianniantonio Petruzzelli, Raffaella Balestrini, Stefano Mancuso, Luigi De Bellis, Federico Vita
Summary: This study applied metabarcoding to assess the differences among samples of T. magnatum collected from different areas in Tuscany, Italy. The results showed differences in microbial composition between different parts of the truffle (gleba and peridium) as well as between productive and unproductive soils, with distinctive associated taxa. Furthermore, the findings indicated specific characteristics associated with truffle collection areas, suggesting microbial selection related to different environments.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Stefania Daghino, Elena Martino, Samuele Voyron, Silvia Perotto
Summary: This study used a metabarcoding approach to describe the fungal assemblages in different organs of Vaccinium myrtillus plants in a subalpine meadow in Italy. They found that ericoid mycorrhizal fungi and dark septate endophytes were present in all plant organs, suggesting a closer relationship between ericoid mycorrhizal fungi and non-mycorrhizal fungal endophytes.
SCIENTIFIC REPORTS
(2022)
Article
Forestry
Arcangela Frascella, Sabrina Sarrocco, Antonietta Mello, Francesco Venice, Cristina Salvatici, Roberto Danti, Giovanni Emiliani, Sara Barberini, Gianni Della Rocca
Summary: This study evaluates the in vitro antagonistic capacity of 20 isolates of Trichoderma spp. selected from a diseased chestnut orchard for the biocontrol of Phytophthora xcambivora. The results show that Trichoderma isolates can control the pathogen by synergistically coupling antibiosis and mycoparasitism. T. hamatum SG18 and T. koningiopsis SG6 exhibit promising results in pathogen inhibition, and further research is needed to confirm their efficacy in vivo.
Review
Microbiology
Pamela Monaco, Gino Naclerio, Antonietta Mello, Antonio Bucci
Summary: This review summarizes the current knowledge on microbial communities associated with Tuber magnatum (white truffle), focusing on the role of truffle-associated bacteria and the potential use of bacteria as markers for truffle origin. The review discusses the correlation between microbial taxa and truffle productivity and highlights the importance of identifying microorganisms that can promote T. magnatum formation and serve as markers for tracing its geographic origin.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agronomy
Caterina Mare, Elisa Zampieri, Viviana Cavallaro, Julien Frouin, Cecile Grenier, Brigitte Courtois, Laurent Brottier, Gianni Tacconi, Franca Finocchiaro, Xavier Serrat, Salvador Nogues, Mireia Bundo, Blanca San Segundo, Noemi Negrini, Michele Pesenti, Gian Attilio Sacchi, Giacomo Gavina, Riccardo Bovina, Stefano Monaco, Alessandro Tondelli, Luigi Cattivelli, Giampiero Vale
Summary: The Saltol locus was successfully transferred to Vialone Nano and Onice varieties using marker-assisted backcrossing, resulting in the development of VN1, VN4, and O1 lines with improved salt tolerance. Physiological evaluations showed that these lines had lower salt stress scores and limited negative effects on growth and water content.
Article
Plant Sciences
Francesco Venice, Pasqualina Colasuonno, Emanuela Lombardo, Erica Lumini, Valeria Bianciotto, Maria Letizia Gargano, Giuseppe Venturella, Gianniantonio Domina, Antonietta Mello
Summary: This study investigated the presence of arbuscular mycorrhizal fungi (AMF) in the roots of Astragalus nebrodensis in its natural habitat, as well as the fungal diversity in the surrounding soil. The results showed that A. nebrodensis roots hosted a limited diversity of AMF species, and the fungal communities in the roots and soil were different. This finding suggests that A. nebrodensis has developed a specialized root microbiome, which enables it to survive in harsh environments.
Article
Multidisciplinary Sciences
Marco Forgia, Beatriz Navarro, Stefania Daghino, Amelia Cervera, Andreas Gisel, Silvia Perotto, Dilzara N. Aghayeva, Mary F. Akinyuwa, Emanuela Gobbi, Ivan N. Zheludev, Robert C. Edgar, Rayan Chikhi, Massimo Turina, Artem Babaian, Francesco Di Serio, Marcos de la Pena
Summary: RNA viruses are remnants of the pre-cellular RNA world, and viroid-like elements are small, circular RNA genomes that encode self-cleaving catalytic RNAs. This study identifies a higher number of candidate viroid-like elements than previously thought and reveals that fungal ambiviruses display hybrid features of viroid-like RNAs and viruses. The discovery of similar circular RNAs in fungal viruses further highlights fungi as an evolutionary hub for RNA viruses and viroid-like elements.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Elisa Zampieri, Andrea Volante, Caterina Mare, Gabriele Orasen, Francesca Desiderio, Chiara Biselli, Marco Canella, Lorena Carmagnola, Joelle Milazzo, Henri Adreit, Didier Tharreau, Nicolas Poncelet, Patrizia Vaccino, Giampiero Vale
Summary: Marker-assisted backcrossing was used to introgress four blast-resistance genes (Piz, Pib, Pita, and Pik) into a susceptible japonica Italian rice variety, and an additional blast-resistance gene (Pita2/Ptr) was found, resulting in a total of five introgressed blast-resistance genes. Molecular analysis and phenotypic evaluations confirmed the broad-spectrum resistance of the developed lines. These blast-resistant japonica lines with multiple resistance genes will be valuable donors for future rice-breeding programs.
Review
Agronomy
Elisa Zampieri, Michele Pesenti, Fabio Francesco Nocito, Gian Attilio Sacchi, Giampiero Vale
Summary: Water stress severely affects rice yield, making improving plant tolerance to water stress a priority in rice breeding programs. However, the complexity of seedling practices, water management systems, and growth stages where stress occurs makes it difficult to identify single ideotypes for overcoming drought in diverse cropping ecosystems. Genomics and biochemical knowledge can contribute to developing flexible rice ideotypes, and screening of wild rice accessions and cultivated rice germplasms has identified genes improving water stress resistance. New frontiers include the study of epigenetic control and favorable microbiota. Innovative breeding technologies are advancing the development of water stress-tolerant rice varieties.
Article
Plant Sciences
Salvatore Seddaiu, Antonietta Mello, Luca Sarais, Antonio Mulas, Clizia Sechi, Pino Angelo Ruiu, Anna Maria Vettraino, Maurizio Petruccioli, Paolo Gonthier, Fabiano Sillo, Carlo Bregant, Lucio Montecchio, Benedetto T. Linaldeddu
Summary: In recent decades, the productivity of Italian chestnut groves has been severely affected by the emergence of the fungal pathogen Gnomoniopsis castaneae, resulting in nut rots. Despite its widespread distribution in Italy, the genetic diversity and phylogeographic structure of this pathogen have not been fully explored. This study analyzed the genetic diversity and spatial distribution of G. castaneae haplotypes in different regions of Italy and Sardinia. The results showed the existence of two distinct evolutionary lineages (haplotype A and B) at a global scale, with varying frequencies in different geographic areas of Italy. Inoculation experiments confirmed the pathogenicity of both haplotypes, although their aggressiveness differed.
JOURNAL OF PLANT PATHOLOGY
(2023)
Article
Forestry
Fabiano Sillo, Cecilia Brunetti, Fabio Marroni, Federico Vita, Luana Beatriz dos Santos Nascimento, Alfredo Vizzini, Antonietta Mello, Raffaella Balestrini
Summary: The European hazelnut forms a symbiotic relationship with ectomycorrhizal fungi, and this study suggests that this symbiosis can help plants adapt to stress and regulate defense responses. This research has important implications for understanding novel aspects of ectomycorrhizal symbiosis.
Article
Virology
Marco Forgia, M. Chiapello, Stefania Daghino, D. Pacifico, D. Crucitti, D. Oliva, M. Ayllon, M. Turina
Summary: High throughput sequencing has greatly contributed to the discovery of new viruses and viral organizations. However, the current method of characterizing RNA viruses through similarity searches in annotated virus databases has limitations in detecting completely new virus-encoded proteins. In this study, a theoretical framework was used to identify conserved protein-coding RNA segments without corresponding DNA in fungi. These proteins show distant relation to viral RNA-dependent RNA polymerases (RdRP) and have unique catalytic triads.