Article
Microbiology
Yiheng Hu, Laszlo Irinyi, Minh Thuy Vi Hoang, Tavish Eenjes, Abigail Graetz, Eric A. Stone, Wieland Meyer, Benjamin Schwessinger, John P. Rathjen
Summary: Our study compared classification and community composition analysis pipelines using different sequencing technologies for fungal communities. We found that sequence alignment against a fungal-specific database achieved the highest accuracy of species identification. Applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. Our study also generated draft genome assemblies for three fungal species that were not present in genome databases. This study provides a practical guide for metagenomics analyses focusing on fungi.
Article
Agronomy
Yasuaki Akaji, Tomomi Inoue, Takeshi Taniguchi, Shigeyuki Baba
Summary: The study found that salinity influences the composition of AM fungal communities in mangrove soils, and that Acaulosporaceae species form nutritional associations with Bruguiera gymnorhiza, helping mangrove trees in saline and low-nutrient environments.
Article
Forestry
Celia Herrero de Aza, Sergio Armenteros, James McDermott, Stefano Mauceri, Jaime Olaizola, Maria Hernandez-Rodriguez, Olaya Mediavilla
Summary: This study conducted a comprehensive analysis of the fungal and bacterial communities associated with T. melanosporum oak plantations. The competitive effect of T. melanosporum on other fungal species was demonstrated, and its association with specific bacteria and fungi was identified.
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
Food Science & Technology
B. Misery, P. Legendre, O. Rue, V. Bouchart, H. Guichard, JM. Laplace, M. Cretenet
Summary: The study reveals significant differences in bacterial and fungal communities at different stages of apple cider distillation and between producers. The maturation period leads to an increase in microorganisms responsible for off-flavors. The alcoholic fermentation stage is mainly dominated by alcoholic yeasts.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Soil Science
Limin Fan, Fajun Li, Xi Chen, Lihong Shen, Yuyao Chu, Liping Qiu, Gengdong Hu, Chao Song, Dandan Li, Shunlong Meng, Jiazhang Chen
Summary: In this study, researchers investigated the effects of the red swamp crayfish on the glycoside hydrolase families and fungal communities in soils. They found that the introduction of crayfish was the main factor responsible for the variations in GH families and fungi. Furthermore, they discovered that the abundance of fungi in soils influenced the bacterial chitinase gene abundance, rather than the crayfish exoskeleton.
APPLIED SOIL ECOLOGY
(2023)
Article
Microbiology
Hao Qu, Yaqin Long, Xuesong Wang, Kaibo Wang, Long Chen, Yunqiu Yang, Linbo Chen
Summary: This study investigated the bacterial and fungal communities in tea plant rhizospheric soil and leaf compared to the gut of the tea moth at different developmental stages. The results showed that the soil samples had higher diversity than leaf and tea moth samples. The bacterial and fungal diversity did not differ significantly between different stages of tea moth development. The microbiome of soil and leaf samples differed significantly from tea moth gut samples.
Article
Forestry
Philip Bell-Doyon, Virginie Bellavance, Louis Belanger, Marc J. Mazerolle, Juan Carlos A. Villarreal
Summary: The composition and diversity of soil microbiomes differ between old-growth and regenerating stands after either an insect outbreak or a clearcut, suggesting that the nature of stand-replacing disturbances influences the soil microbiome composition. The mechanisms underlying these differences remain unclear.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Ecology
Patrick Baudy, Jochen P. Zubrod, Marco Konschak, Sara Kolbenschlag, Annika Pollitt, Christiane Baschien, Ralf Schulz, Mirco Bundschuh
Summary: Fungi play a critical role in decomposing dead organic matter in ecosystems. Using biomolecular tools, researchers investigated fungal interactions in aquatic environments, finding that fungal diversity significantly impacts leaf colonization.
Article
Microbiology
Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Huebner, Zandra Fagernaes, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche, Kirsten Kuesel
Summary: By adapting methods from microbial archaeology and paleogenomics, we recovered sufficient DNA from seven rock specimens for metagenomic analysis. Limestones serve as archives for genetic records of past microbial communities, including those sensitive to environmental stress, due to specific conditions facilitating long-term DNA preservation.
Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Article
Environmental Sciences
Lihua Niu, Shiqin Zhao, Yamei Chen, Yi Li, Guanhua Zou, Ye Tao, Wenlong Zhang, Longfei Wang, Huanjun Zhang
Summary: This study explored the diversity, composition, and potential function characteristics of phage communities living in the biofilms of PP, PE, and PET micro-plastics and stones using the metagenome method. The results showed the presence of 240 non-redundant virus OTUs distributed in at least four orders and seven families in the biofilm metagenomes of microplastics. Some phages were selectively enriched by micro-plastic biofilms, with 13 OTUs uniquely colonized on three microplastics. The abundance and composition of phages and bacterial hosts showed significant correlations for microplastics.
ENVIRONMENTAL RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Katie Hsia, Naisi Zhao, Mei Chung, Khalid Algarrahi, Laleh Montaser Kouhsari, May Fu, Hannah Chen, Siddharth Singh, Dominique S. Michaud, Sushrut Jangi
Summary: This retrospective study found that Saccharomyces and Candida were increased during endoscopic inflammation in ulcerative colitis, while Penicillium was increased during endoscopic remission. These findings suggest that Saccharomyces and Candida may serve as potential biomarkers and therapeutic targets for personalized approaches in the treatment of ulcerative colitis.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Microbiology
Alyssa A. A. Carrell, Brittany B. B. Hicks, Emilie Sidelinger, Eric R. R. Johnston, Sara S. S. Jawdy, Miranda M. M. Clark, Dawn M. M. Klingeman, Melissa A. A. Cregger
Summary: Plants and microorganisms have important symbiotic interactions that influence plant growth. This study found that nitrogen addition altered plant growth factors and affected the fungal communities in the soil. These findings emphasize the importance of soil origin and plant species in establishing plant-fungal interactions.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Moein Khalighi, Guilhem Sommeria-Klein, Didier Gonze, Karoline Faust, Leo Lahti
Summary: Ecological memory refers to the influence of past events on the response of an ecosystem to changes. Memory introduces inertia into the dynamics and favors coexistence, resistance to state shifts, and mitigates hysteresis.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Food Science & Technology
Irini Bosmali, Georgios Lagiotis, Evangelia Stavridou, Nadia Haider, Maslin Osathanunkul, Kostas Pasentsis, Panagiotis Madesis
Summary: Coffee, a popular and heavily traded commodity, is often targeted by fraudulent practices. However, through the use of an ITS2-based marker and HRM analysis, coffee authenticity can be effectively determined, even from brewed beverages.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Plant Sciences
Aliki Xanthopoulou, Theodoros Moysiadis, Christos Bazakos, Evangelos Karagiannis, Ioanna Karamichali, George Stamatakis, Martina Samiotaki, Maria Manioudaki, Michail Michailidis, Panagiotis Madesis, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou
Summary: The study provides new insights into plant biology through the integration of genomics and proteomics, identifying a large number of genes and proteins in sweet cherries. Analysis reveals differences between gene and protein quantities, key regulators of fruit development, and novel cherry proteins. Additionally, a new protein-level annotation and database were developed for further research in Prunus species.
Article
Biodiversity Conservation
Susanne Masters, Bastien Anthoons, Panagiotis Madesis, Seethapathy G. Saroja, Maarten Schermer, Wilfred Gerritsen, Arzu Karahan, Rick Verdoes, Rachel Schwallier, Tinde van Andel, Hugo de Boer, Barbara Gravendeel
Summary: This study reveals the illegal trade of legally protected orchids through online platforms, with salep being a prominent product. Despite being restricted by national and international legislation, the sale and collection of salep still pose a significant threat to the survival of certain orchid species.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Multidisciplinary Sciences
Maslin Osathanunkul, Panagiotis Madesis
Summary: Capture-based aquaculture in Southeast Asia is receiving attention, but the abundance and distribution of wild stock are crucial for management. Detection of target organisms using eDNA can be an effective monitoring method, but conventional approaches have limitations.
Article
Agronomy
Aristeides P. Papapanagiotou, Christos A. Damalas, Irene Bosmali, Panagiotis Madesis, Georgios Menexes, Ilias Eleftherohorinos
Summary: Field and pot experiments in Greece revealed resistance in silky windgrass to certain herbicides. The resistance to chlorsulfuron was confirmed in most populations, while other ALS inhibitors provided adequate control. The gene sequencing showed mutations causing resistance. It is crucial to adopt integrated management practices to delay the evolution of resistant populations due to limited chemistries/modes of action for grass weed control in cereals.
Article
Plant Sciences
Irene Bosmali, Georgios Lagiotis, Nadia Haider, Maslin Osathanunkul, Costas Biliaderis, Panagiotis Madesis
Summary: By analyzing DNA barcoding regions, this study identified 71 Vicia specimens of Eurasian descent. The trnL and ITS2 regions were effective in discriminating the analyzed species, while the rpoC1 region could not identify all selected species due to sequence conservation or missing sequences in GenBank. The combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus.
Article
Food Science & Technology
Bastien Anthoons, Georgios Lagiotis, Andreas D. Drouzas, Hugo de Boer, Panagiotis Madesis
Summary: This study developed a high-resolution melting DNA-based protocol for discriminating between phenotypically similar toxic and edible plant species in mixtures, even in simulated gastric acid, which has important implications for application in medicine, forensics, and the agricultural industry.
JOURNAL OF FOOD SCIENCE
(2022)
Article
Chemistry, Analytical
Xanthoula Eirini Pantazi, Anastasia L. Lagopodi, Afroditi Alexandra Tamouridou, Nathalie Nephelie Kamou, Ioannis Giannakis, Georgios Lagiotis, Evangelia Stavridou, Panagiotis Madesis, Georgios Tziotzios, Konstantinos Dolaptsis, Dimitrios Moshou
Summary: The aim of this study was to develop supervised self-organizing map (SOM) models for automatic recognition of systemic resistance state in plants after resistance inducer application. The models were validated using fluorescence kinetics data obtained from a handheld fluorometer. The best performing model achieved 97.22% to 100% accuracy and was confirmed using gene expression data.
Article
Forestry
Maslin Osathanunkul, Nipitpong Sawongta, Panagiotis Madesis, Wittaya Pheera
Summary: This study investigated the application of a hybrid method of DNA barcoding and high-resolution melting analysis (Bar-HRM) for native plant species confirmation. The nuclear ribosomal internal transcribed spacer (ITS) region was identified as a primer set that can clearly discriminate native plant species. The study demonstrated the usefulness of Bar-HRM in native plant species confirmation, even without molecular data.
Article
Biology
Evangelia Stavridou, Ioanna Karamichali, Georgios Lagiotis, Elena Patsea, Maslin Osathanunkul, Panagiotis Madesis
Summary: This study investigated the effects of seasonal changes on the soil microbiome associated with runner bean cultivation. The presence of the runner bean differentially shaped the soil microbial community structure, which is important for understanding the role of soil microbiomes in agriculture.
Article
Plant Sciences
Lefkothea Karapetsi, Emmanouil Pratsinakis, Fotis Xirakias, Maslin Osathanunkul, Ioannis Vagelas, Panagiotis Madesis
Summary: The destructive effects of Fusarium wilts on crop production have been mitigated through soil fumigation and the use of fungicides. However, due to restrictions on residue tolerances and environmental impacts, alternative methods using natural compounds like essential oils are being investigated. Oregano essential oil has been found to inhibit the growth of several fungal species, including Fusarium oxysporum. This study aims to utilize metabarcoding to evaluate the impact of oregano essential oil on F. oxysporum and other fungal species present in soil samples.
Article
Plant Sciences
Eleni Avramidou, Efi Sarri, Ioannis Ganopoulos, Panagiotis Madesis, Leonidas Kougiteas, Evgenia-Anna Papadopoulou, Konstantinos A. Aliferis, Eleni M. Abraham, Eleni Tani
Summary: This study compared the genetic diversity and seed metabolite profiles of five genetic materials of faba bean. Genetic diversity was assessed by SCoT markers and genetic distances were estimated by UPGMA dendrogram. The advanced line KK18 displayed the best nutritional profile and showed the highest potential for further exploration in breeding programs.
Article
Agronomy
Pavlina Drogoudi, Georgios Pantelidis, Lefkothea Karapetsi, Konstantina Ziakou, Konstantinos Kazantzis, Panagiotis Madesis, Thomas Thomidis
Summary: This study conducted a prospection of local traditional and underutilized peach genetic resources in Greece and investigated their genetic and morphological variations and susceptibility to shoot blight. A total of 32 peach cultivars/accessions were collected, and leaf and fruit morphological characterization was performed. The results showed that the local peach genotypes were different from foreign cultivars in several leaf and fruit phenotypic traits. Local cultivars exhibited greater resistance to Cylindrocarpon destructans, with certain cultivars showing the highest resistance. Genetic characterization revealed moderate to low genetic diversity among the peach cultivars, and several markers were found to be significantly correlated with fruit traits. These findings are valuable for breeding programs and future research on peach.
Article
Biochemistry & Molecular Biology
Nikolaos D. Georgakis, Elisavet Ioannou, Marianna Chatzikonstantinou, Marian Merino, Evangelia G. Chronopoulou, Jose Luis Mullor, Panagiotis Madesis, Nikolaos E. Labrou
Summary: In this study, the cosmeceutical properties of aqueous extracts from the microalgae strain Trachydiscus minutus were evaluated and compared with three widely used Chlorella strains. The T. minutus extracts showed the highest total antioxidant capacity and inhibitory potency towards elastase, indicating potential in controlling skin aging. The extracts also exhibited anti-inflammatory activity and protection against UVA-induced cell damage. The results suggest that T. minutus extract has promising cosmeceutical properties and potential for skincare use.
Review
Biochemistry & Molecular Biology
Alexandros Mavrommatis, Eleni Tsiplakou, Anastasia Zerva, Panagiota D. Pantiora, Nikolaos D. Georgakis, Georgia P. Tsintzou, Panagiotis Madesis, Nikolaos E. Labrou
Summary: Microalgae are a renewable source with beneficial effects on nutrition and health. They have been explored as feed additives in livestock animals, improving their health, product quality, and environmental impact. However, the cost-effective production and use of microalgae remains a challenge.