Article
Agronomy
Jaime Aguayo, Claude Husson, Emilie Chancerel, Olivier Fabreguettes, Anne Chandelier, Celine Fourrier-Jeandel, Nadine Dupuy, Cyril Dutech, Renaud Ioos, Cecile Robin, Michel Thibaudon, Benoit Marcais, Marie-Laure Desprez-Loustau
Summary: Forest disease management relies on a preventive approach with epidemiological surveillance, but efficient methods for large spatial scales are lacking. Utilizing aerobiological networks and molecular methods, this study shows that permanent surveillance networks can be a useful tool for monitoring forest pathogens, with results validating the approach through comparison with field data.
Article
Microbiology
Danielle Machado Pagani, Stefania P. R. Ventura, Duong Vu, Thairine Mendes-Pereira, Luiz Marcelo Ribeiro Tome, Daniel Santana de Carvalho, Diogo Henrique Costa-Rezende, Rodrigo Bentes Kato, Glen Jasper Yupanqui Garcia, Jozsef Geml, Vincent Robert, Ng Haig They, Bertram Brenig, Vasco Azevedo, Maria Lucia Scroferneker, Patricia Valente, Aristoteles Goes-Neto
Summary: Studies on the fungal communities in aquatic environments are relatively recent, especially in freshwater ecosystems. Human activities, such as effluent discharge, pose threats to these water bodies. This study found that the fungal diversity and specific operational taxonomic units (OTUs) were higher in ecotones, highlighting our limited understanding of subtropical freshwater mycobiota.
Article
Forestry
Laszlo Benedek Dalya, Milon Dvorak, Petr Sedlak
Summary: This study aimed to test if an automatic volumetric spore trap (AVST) could be used as a sensitive alternative to passive traps in quantifying Heterobasidion airspora in forest stands. The AVST detected more target species than the routinely used wood disc exposure method (WDE), and the concentration of specific spores varied with seasons.
Article
Food Science & Technology
Davide Porcellato, Hanne Kristiansen, Misti D. Finton, Sabina Leanti La Rosa, Vinicius da Silva Duarte, Siv Borghild Skeie
Summary: This study investigated the impact of milk treatment and milk powder production on the composition and survival of anaerobic spore-forming bacteria. The results showed that the milk separation process significantly influenced the presence and composition of these bacteria. This has important implications for the quality and safety of dairy products.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Veterinary Sciences
Yanfang Lan, Yaonan Li, Gang Yu, Zhengyi Zhang, Irfan Irshad
Summary: The gut fungal community in diarrheic horses showed significant changes in alpha and beta diversity, as well as taxonomic compositions. Several differential fungal phyla and genera were identified, with decreased abundances during diarrhea. The study highlights the important role of gut fungal community in equine health and provides insights into the characterization of gut microbial dysbiosis in diarrhea.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Food Science & Technology
Eugenio Parente, Teresa Zotta, Annamaria Ricciardi
Summary: With the development of high-throughput sequencing technology, our understanding of the structure and dynamics of food microbial communities has significantly improved. This article introduces the fourth version of the FoodMicrobionet database, which is the largest and best annotated database on bacterial microbial communities in foods and food environments. A representative case study demonstrates the confident taxonomic assignment at the genus level using commonly used 16S rRNA gene target regions and cautions about confirming the assignment at species level. The database and related data and software adhere to FAIR principles and are freely accessible on public repositories.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Article
Plant Sciences
Paola Pilo, Anna M. M. Tiley, Colleen Lawless, Sujit J. Karki, James Burke, Angela Feechan
Summary: Current DNA extraction methods from filamentous fungi can be time-consuming and expensive, but a new sonication technique described in this study allows for quick and inexpensive extraction of genomic DNA from various sources of fungi in under an hour.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2022)
Article
Plant Sciences
Collin L. Juurakko, George C. diCenzo, Virginia K. Walker
Summary: Research found that the bacterial and fungal communities on leaves of plants that underwent cold acclimation significantly changed, with an increase in beneficial bacteria and decrease in ice-nucleating pathogens. This change may help plants combat cold and pathogens, enhancing their survival in freezing events.
Article
Agronomy
Miriam Calderon, Chuanyu Yang, Veronica Ancona
Summary: Irrigation is crucial for crop production, but it can also spread plant pathogens that cause crop damage and yield losses. This study used the ITS2 amplicon metagenomic method to evaluate the fungal diversity and presence of plant pathogens in irrigation water. The results showed the presence of potential plant pathogens in both the water reservoir and the irrigation valve at a farm, indicating the need for measures to mitigate the risks.
Article
Plant Sciences
Nick C. C. Snelders, Jordi C. C. Boshoven, Yin Song, Natalie Schmitz, Gabriel L. L. Fiorin, Hanna Rovenich, Grardy C. M. van den Berg, David E. E. Torres, Gabriella C. C. Petti, Zoe Prockl, Luigi Faino, Michael F. F. Seidl, Bart P. H. J. Thomma
Summary: Plant pathogens secrete effector proteins to support host colonization, while plant immune systems recognize effectors to activate immune responses. Plants actively shape their microbiota as a determinant of health. Researchers have found that the soil-borne fungal pathogen Verticillium dahliae exploits an effector protein called VdAve1 to manipulate the host microbiota and promote disease. This discovery opens up new strategies for targeted biocontrol of plant pathogens.
Article
Biochemistry & Molecular Biology
Polina Kazakova, Nerea Abasolo, Sara Martinez de Cripan, Emili Marques, Adria Cereto-Massague, Lorena Garcia, Nuria Canela, Ramon Tormo, Helena Torrell
Summary: In this article, the interactions between the gut bacteriome, virome, and smallRNome were characterized in meconium and stool samples from infants. The results showed differences in bacteriome composition among the different groups, as well as significant differences in virome and smallRNome profiles between meconium and stool samples from milk-fed infants. These findings suggest that the gut environment rapidly adapts after birth and is influenced by environmental factors, and that transkingdom interactions between viruses and bacteria can affect host and smallRNome profiles. However, there are limitations in the characterization of the virome that should be considered.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Benedicte Riber Albrectsen, Benedicte Riber Albrectsen, Hulya Ilbi, Abu Bakar Siddique
Summary: This study optimized the protocol for metagenomic studies of aspen leaves and successfully prepared an amplicon library for high-throughput sequencing. The optimized DNA extraction protocol and PCR conditions improved the efficiency and accuracy of the sequencing.
APPLIED SCIENCES-BASEL
(2022)
Article
Plant Sciences
Paola Pilo, Colleen Lawless, Anna M. M. Tiley, Sujit J. J. Karki, James I. I. Burke, Angela Feechan
Summary: This study investigated the incidence of spores from major fungal pathogens of cereals using microscopic and metagenomic approaches. The results showed that metagenomic BLAST analysis had a higher accuracy in species-specific identification. The study also found that the release of Zymoseptoria spp. and Fusarium spp. ascospores was positively correlated with relative humidity, while negatively affected by air temperature.
FRONTIERS IN PLANT SCIENCE
(2022)
Editorial Material
Ecology
Phillip C. Watts, Tapio Mappes, Eugene Tukalenko, Timothy A. Mousseau, Zbyszek Boratynski, Anders P. Moller, Anton Lavrinienko
Summary: This study used amplicon sequencing to analyze the gut microbiota and mycobiota composition of rodents inhabiting the Chernobyl Exclusion Zone, investigating the potential effects of exposure to radionuclides. However, due to the limitations in sample type and data analysis, the conclusions regarding the gut mycobiota composition are not accurate.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Food Science & Technology
Mediha Nur Zafer Yurt, Esra Ersoy Omeroglu, Behiye Busra Tasbasi, Elif Esma Acar, Osman Altunbas, Veli Cengiz Ozalp, Mert Sudagidan
Summary: The bacterial and fungal diversities of 24 mould-ripened cheeses from Konya-Turkiye were analyzed using metagenomic analysis. The dominant bacteria were from the Firmicutes phylum, including the genera Enterococcus, Clostridium sensu stricto, and Lactobacillus (Levilactobacillus). The dominant fungi belonged to the Ascomycota phylum and included the genera Penicillium and Pichia, with species such as Penicillium roqueforti and Pichia membranifaciens. A total of 30 Enterococcus faecium and 6 Enterococcus faecalis strains were identified, and they showed susceptibility to several antibiotics.
INTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY
(2023)
Editorial Material
Microbiology
Tomislav Cernava, Gabriele Berg
Summary: Recent discoveries have shown that certain bacteria have disease-preventing abilities within the microbiota of crop plants, a phenomenon that is new in the field of plant microbiome research. Technological constraints have limited these findings, but similar discoveries are likely in other plant species.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Ahmed Abdelfattah, Ayco J. M. Tack, Birgit Wasserman, Jia Liu, Gabriele Berg, John Norelli, Samir Droby, Michael Wisniewski
Summary: The study found that the endophytic microbiome of domesticated apples and their wild progenitors exhibit higher diversity and abundance, and the microbiome of domesticated apples is a mixture of its wild progenitors. Additionally, there is a significant correlation between the evolutionary distance of Malus species and their microbiome composition.
Article
Plant Sciences
Jia Liu, Ahmed Abdelfattah, Birgit Wasserman, Michael Wisniewski, Samir Droby, Gennaro Fazio, Mark Mazzola, Xuehong Wu
Summary: The composition of the endophytic microbiome in apple root systems is influenced by genotype and root size, with the fungal community more affected by genotype and the bacterial community more influenced by root size. Microbial abundance is higher in rhizosphere samples compared to root endosphere samples.
HORTICULTURE RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Antonino Malacrino, Ahmed Abdelfattah, Gabriele Berg, Maria-Soledad Benitez, Alison E. Bennett, Laura Boettner, Shuqing Xu, Leonardo Schena
Summary: The science of plant microbiomes is revolutionizing concepts in plant biology, highlighting the importance of their structures and functions in protecting plants from pathogens and guiding towards sustainable production.
BIOLOGICAL CONTROL
(2022)
Article
Microbiology
Gabriele Berg, Tomislav Cernava
Summary: This commentary discusses the specific signatures in microbiota affected by human activities and highlights the importance of microbiome research in addressing the challenges associated with anthropogenic-driven changes. The findings suggest that these changes in microbiota diversity and composition have implications for both plant health and planetary health, leading to dysbiosis, loss of resilience, and increased pathogen outbreaks.
Article
Food Science & Technology
Serena A. Minutillo, David Ruano-Rosa, Ahmed Abdelfattah, Leonardo Schena, Antonino Malacrino
Summary: Consumers are increasingly demanding higher quality and safety standards for products such as wheat flour, which may be contaminated by various fungi producing mycotoxins. This study highlights the need for more attention to the fungal diversity in commercial wheat flour to address potential concerns for consumers' health.
Article
Plant Sciences
Antonino Malacrino, Saveria Mosca, Maria Giulia Li Destri Nicosia, Giovanni E. Agosteo, Leonardo Schena
Summary: The plant microbiome plays a crucial role in plant biology, ecology, and evolution. The study reveals that plant genotype has varying impacts on the diversity, structure, and composition of bacterial microbiomes in fruits, leaves, and soil, with a stronger effect observed in fruits. This suggests that plant genotype is an important factor in shaping the structure of plant microbiomes, providing potential insights for enhancing plant productivity, nutrition, and defenses.
Article
Agriculture, Multidisciplinary
Angela Zappia, Antonino Malacrino, Imen Belgacem, Ahmed Abdelfattah, Amalia Piscopo
Summary: Ready-to-eat minimally processed fruits and vegetables can support the growth of microorganisms, potentially affecting their quality and safety. This study investigates the impact of storage light condition on the microbiological and physico-chemical parameters of minimally processed rocket leaves at different shelf life timepoints. The results suggest an increase in total microbial load during the shelf life, and light condition storage leads to a higher bacterial load.
ANNALS OF APPLIED BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Ahmed Abdelfattah, Ayco J. M. Tack, Carolina Lobato, Birgit Wassermann, Gabriele Berg
Summary: This study proposes dividing the microbial inheritance process into three stages: plant to seed, seed dormancy, and seed to seedling. It discusses the factors affecting microbiome assembly during these stages, highlights future research directions, and emphasizes the implications of microbial inheritance for fundamental science and society.
TRENDS IN MICROBIOLOGY
(2023)
Article
Microbiology
Antonino Malacrino, Ahmed Abdelfattah, Imen Belgacem, Leonardo Schena
Summary: Plant genotype is crucial for the structure and diversity of plant-associated microbial communities. This study investigated the variation of fungal microbiomes in wheat species and genotypes. The results showed that both host species and cultivar influenced the fungal communities in the seeds. Stochastic processes played a more important role in T. aestivum, while selection had a major impact in T. turgidum. These findings contribute to our understanding of wheat seed microbiome assembly and have implications for improving agricultural sustainability.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Simona Prencipe, Giada Schiavon, Marco Rosati, Luca Nari, Leonardo Schena, Davide Spadaro
Summary: Since 2012, the kiwifruit vine decline syndrome (KVDS) has been affecting Italian kiwifruit orchards. The presence of Phytopythium spp. has been identified in KVDS-affected orchards in north-western Italy. Inoculation experiments demonstrated the pathogenicity of P. vexans, P. litorale, P. chamaehyphon, and P. helicoides in potted plants. The study suggests that different species of Phytopythium play a significant role in the establishment and development of KVDS.
Article
Gastroenterology & Hepatology
Wisnu Adi Wicaksono, Tomislav Cernava, Birgit Wassermann, Ahmed Abdelfattah, Maria J. Soto-Giron, Gerardo V. Toledo, Suvi M. Virtanen, Mikael Knip, Heikki Hyoty, Gabriele Berg
Summary: This study reveals evidence that bacteria derived from fruits and vegetables could be found in the human gut and contribute to gut microbiome diversity. The consumption of fruits and vegetables potentially benefits the gut microbiota by providing health-promoting genes for the production of vitamins and short-chain fatty acids.
Article
Genetics & Heredity
Adrian Wolfgang, Ayco J. M. Tack, Gabriele Berg, Ahmed Abdelfattah
Summary: This study investigates the effects of soil microbiomes on plant and aphid microbiomes, as well as the reciprocal impact of aphid herbivory on the plant and soil microbiomes. The results indicate that soil microbiomes significantly influence the microbial communities of phyllospheres and aphids, and aphid herbivory also affects the composition of soil microbiomes.
ENVIRONMENTAL MICROBIOME
(2023)