Article
Plant Sciences
Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai
Summary: This study reports the chloroplast genome sequences of 11 Cerasus species to investigate the evolution of their plastome. The results reveal the typical quadripartite circular structure of Cerasus chloroplast genomes and the presence of 115 unique genes. Several genes were found to have high nucleotide diversity and more polymorphic sites, including matK, rps16, and rbcL. The phylogenetic analysis sheds light on the relationships between different Cerasus species, providing insights for further research on their phylogenetics and phylogeography.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Medicine, General & Internal
Martina C. Agbo, Kenneth Ugwu, Boniface N. Ukwah, Ifeoma M. Ezeonu
Summary: This study evaluated the genetic relatedness of MDR clinical isolates of P. aeruginosa. The results showed a high prevalence of MDR P. aeruginosa in the Nskuka area and a high degree of genetic relatedness among the isolates.
AFRICAN HEALTH SCIENCES
(2023)
Article
Plant Sciences
Agron Bunjaku, Zeinab Alsaheli, Natasa Mehle, Bekri Xhemali, Gazmend Gjinovci, Arben Mehmeti, Toufic Elbeaino
Summary: This study is the first report on the presence and molecular characterization of phytoplasmas in Kosovar vineyards, with the phytoplasmas belonging to the 16SrXII group and showing similarity to 'Candidatus Phytoplasma solani'. It is recommended that testing for phytoplasma be included in the certification program for grapevine in Kosovo.
JOURNAL OF PHYTOPATHOLOGY
(2022)
Article
Infectious Diseases
Liezl Retief, Nigel C. Bennett, Armanda D. S. Bastos
Summary: The study aimed to evaluate the performance of three 16S rRNA PCR assays for detecting Mycoplasma in African mole-rat species, revealing the presence of haemoplasma in 26.5% of the rodents. A novel assay showed the highest sensitivity and specificity, confirming the presence of novel haemoplasma strains in bathyergid species from South Africa. Further studies are needed on haemoplasma prevalence, diversity, and transmission routes in other small mammal species from this region.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Microbiology
Laure Flurin, Matthew J. Wolf, Cody R. Fisher, Edison J. Cano Cevallos, James J. Vaillant, Bobbi S. Pritt, Daniel C. DeSimone, Robin Patel
Summary: This prospective pilot study evaluated the use of targeted metagenomic sequencing (tMGS) for early pathogen detection and identification in infective endocarditis (IE). The results indicate that blood-based tMGS may provide pathogen identification in subjects with IE, including culture-negative cases.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xin Shen, Wenjin Zong, Yingang Li, Xinhong Liu, Fei Zhuge, Qi Zhou, Shiliang Zhou, Dongyue Jiang
Summary: This study provides insights into the phylogeny, geographic origin, timing, and dispersal patterns of cherries (Prunus Subgenus Cerasus) through a comprehensive analysis of their chloroplast genomes. The results show that cherries can be divided into seven lineages, with the Himalayans serving as a refuge and the mainstage of cherry evolution occurring on the Qing-Tibet Plateau.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Weier Cui, Alan Zamorano, Nicolas Quiroga, Assunta Bertaccini, Nicola Fiore
Summary: Research has shown that the SSU12p and LSU36p genes are reliable additional markers for detection and differentiation of phytoplasmas.
PHYTOPATHOLOGIA MEDITERRANEA
(2021)
Article
Immunology
Hyo Lim Hong, Laure Flurin, Matthew J. Thoendel, Matthew J. Wolf, Matthew P. Abdel, Kerryl E. Greenwood-Quaintance, Robin Patel
Summary: This study compared the performance of 16S rRNA gene-based targeted metagenomic sequencing (tNGS) and shotgun metagenomic sequencing (sNGS) in detecting and identifying pathogens in sonicate fluid from failed total hip arthroplasty (THA) and total knee arthroplasty (TKA). The study found that tNGS had a higher positive percent agreement with sonicate fluid culture compared to sNGS, and detected potential pathogens in culture-negative PJIs. The study concludes that tNGS is a potential diagnostic tool for identifying PJI pathogens in sonicate fluid, with similar performance characteristics to sNGS.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Environmental Sciences
R. G. Bulgarelli, M. F. A. Leite, M. De Hollander, P. Mazzafera, S. A. L. Andrade, E. E. Kuramae
Summary: The availability of soil phosphorus can affect plant growth, root-soil interactions, and rhizosphere microbial community composition. This study investigated the rhizosphere microbial communities of 24 species of eucalypts under low or sufficient soil phosphorus availability. It was found that eucalypt species identity was the main factor determining the composition of the rhizosphere microbial community, while the effect of phosphorus availability varied among species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Immunology
Madiha Fida, Sarwat Khalil, Omar Abu Saleh, Douglas W. Challener, Muhammad Rizwan Sohail, Joshua N. Yang, Bobbi S. Pritt, Audrey N. Schuetz, Robin Patel
Summary: This study retrospectively analyzed 566 specimens from 460 patients and found a higher positivity rate of 16S rRNA PCR/sequencing in clinically infected patients with low impact on clinical care. Specimens with positive Gram stain were more likely to have a positive PCR result. Cardiovascular specimens yielded higher PCR positivity, while musculoskeletal specimens were more likely to have positive bacterial cultures.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Agriculture, Dairy & Animal Science
Livio Galosi, Nicola Ridolfi, Cristina Fellini, Igor Pelizzone, Stefano Cusaro, Gianluca Marchetti, Matteo Canonico, Elena Ghelfi, Nicola Di Girolamo, Silvia Preziuso
Summary: Some species of turtles and tortoises are threatened by pathogens such as Mycoplasmopsis agassizii, which can lead to population declines. Proper diagnosis and control of transmissible diseases are crucial for limiting the spread of pathogens in animal collections. This study highlights the importance of practitioners in collecting and sharing data for analysis and emphasizes the need to collect appropriate samples to avoid false negative results. It also suggests that other pathogens should be considered in coinfection or infection cases.
Article
Agriculture, Dairy & Animal Science
Ming -Han Li, Jin-Xin Meng, Wei Wang, Ma He, Zi-Yu Zhao, Ning Ma, Qing-Bo Lv, Yi-Feng Qin, Quan Zhao, Hong -Bo Ni, Xiao-Xuan Zhang
Summary: This study examined the diversity of bacteria and fungi in the gut microbiota of commercial broilers raised in cages. The results showed that the composition of the gut microbiota was influenced by age, with increasing richness and diversity as the broilers grew older. The gut microbiota had a unique structure in the early days after birth, and then underwent significant changes during periods of rapid growth and weight gain. Furthermore, certain bacteria and fungi played key roles in the gut microbiota of broilers, and their loss may impact the intestinal homeostasis of broilers.
Article
Biochemistry & Molecular Biology
Julia B. Gontijo, Fabiana S. Paula, Andressa M. Venturini, Caio A. Yoshiura, Clovis D. Borges, Jose Mauro S. Moura, Brendan J. M. Bohannan, Klaus Nusslein, Jorge L. Mazza Rodrigues, Siu M. Tsai
Summary: The Amazonian floodplain forests play a crucial role in regional hydrological and biogeochemical cycles, contributing significantly to the global carbon balance through CH4 emissions. Unique geochemical factors may drive the composition of microbial communities, affecting CH4 emissions. Additionally, environmental changes in floodplain areas can impact the diversity of methanotrophic communities.
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biology
Hamieh Goshtasbi, Ehsan Atazadeh, Ali Movafeghi
Summary: Instability of morphological and physiological characteristics under different environmental conditions can lead to misidentification of cyanobacteria. This study successfully identified three cyanobacteria species from an Iranian wetland using morphological, molecular, and biochemical data. The results confirmed the effectiveness of molecular markers and biochemical parameters in reliable identification of cyanobacteria.
Editorial Material
Plant Sciences
Mohammad Hajizadeh, Nasrin Ghaderi Zandan, Zahra Kashiha, Igor Koloniuk
JOURNAL OF PLANT PATHOLOGY
(2022)
Editorial Material
Plant Sciences
Nasrin Ghaderi Zandan, Mohammad Hajizadeh, Igor Koloniuk
JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Agronomy
Lucie Valentova, Martina Rejlova, Jana Franova, Radek Cmejla
Summary: High-throughput sequencing has enabled the detection of new plant pathogens like the strawberry virus 1 (StrV-1) with relative ease. The study found that a sole StrV-1 infection had varying impacts on production in two strawberry cultivars, with Karmen experiencing a significant yield loss compared to Darselect. The reduction in yield in infected plants was mainly due to a significantly reduced number of inflorescences and flowers per plant.
Review
Virology
Jiunn Luh Tan, Nina Trandem, Jana Franova, Zhibo Hamborg, Dag-Ragnar Blystad, Rostislav Zemek
Summary: The production of raspberry globally averaged 846,515 tons from 2016 to 2020. European red raspberry is the most commonly cultivated variety, but it is susceptible to multiple viruses transmitted by invertebrate vectors. Aphids and nematodes are known vectors of specific raspberry viruses, while other potential vectors need further study. The interactions between vector and non-vector herbivores may promote virus spread.
Article
Plant Sciences
Igor Koloniuk, Jaroslava Pribylova, Radek Cmejla, Lucie Valentova, Jana Franova
Summary: A novel RNA virus, named strawberry virus A (StrVA), infecting strawberry plants was discovered with unique genomic features, and a specific qPCR system for StrVA detection was designed. A survey in the Czech Republic showed that StrVA was present in 28.3% of strawberry samples, often in mixed infections with other viruses, complicating assessment of its biological relevance.
Article
Virology
Igor Koloniuk, Alena Matyasova, Sara Brazdova, Jana Vesela, Jaroslava Pribylova, Jana Franova, Santiago F. Elena
Summary: Advancements in high-throughput sequencing methods have led to the discovery of multiple viral infections in various plant systems. However, our understanding of the transmission mechanisms for these mixed infections is limited. This study investigates a mixed infection of strawberry plants with three different viruses, transmitted by individual aphids. The data suggests that multiple individual transmission events contribute to the establishment of mixed infections, which is important for the development of epidemiological models in plant virology.
Article
Virology
Eva Varallyay, Jaroslava Pribylova, Zsuzsanna Nagyne Galbacs, Almash Jahan, Tunde Varga, Josef Spak, Ondrej Lenz, Jana Franova, Jiri Sedlak, Igor Koloniuk
Summary: This study used high-throughput sequencing to identify the presence of apple hammerhead viroid, apple luteovirus 1, and citrus concave gum-associated virus in apple germplasm collections and production orchards in the Czech Republic and Hungary. Further investigations and validations confirmed the widespread presence of these pathogens, with ALV-1 and CCGaV being transmitted from rootstocks to scions. The study also found that the rosy apple aphid could potentially act as a vector for ALV-1.
Article
Virology
Karel Petrzik, Jaroslava Pribylova, Josef Spak, Tatiana Sarkisova, Jana Franova, Jan Holub, Jan Skalik, Igor Koloniuk
Summary: This study conducted a virome screen on a new breeding line of blackcurrant, and identified a novel virus BCRV2 with its complete genome sequence determined. Coinfection of blackcurrant with blackcurrant-associated rhabdovirus (BCaRV) was observed, which is likely the first evidence of a cytorhabdovirus and a nucleorhabdovirus coexisting in a single host.
Editorial Material
Plant Sciences
Jana Franova, Jaroslava Pribylova, Rostislav Zemek, Jiunn Luh Tan, Zhibo Hamborg, Dag-Ragnar Blystad, Ondrej Lenz, Igor Koloniuk
Article
Microbiology
Karel Petrzik, Josef Vacek, Martin Kmoch, Denisa Binderova, Sara Brazdova, Ondrej Lenz, Rudolf Sevcik
Summary: The study investigated the use of a mixture of lytic bacteriophages to protect potatoes from the pathogenic bacteria, Dickeya solani. Laboratory and field experiments showed that the phage treatment significantly reduced soft rot symptoms and improved leaf cover and tuber yield. The findings suggest that the phage mixture has the potential to effectively protect potatoes from D. solani infection.
Article
Biochemistry & Molecular Biology
Filis Morina, Ana Mijovilovich, Archana Mishra, Dennis Brueckner, Bojan Vujic, Syed Nadeem Hussain Bokhari, Josef Spak, Gerald Falkenberg, Hendrik Kuepper
Summary: In the Zn/Cd hyperaccumulator Noccaea caerulescens plants, high concentrations of Zn and Cd treatment enhance resistance against Turnip yellow mosaic virus (TYMV). RNAseq analysis showed TYMV-induced upregulation of Ca transporters, chloroplastic ZTP29, and defense genes in N. caerulescens. Unlike N. ochroleucum, Zn hyperaccumulation in N. caerulescens remains strongest regardless of TYMV infection.
Article
Virology
Jiri Sedlak, Jaroslava Pribylova, Igor Kolonuk, Josef Spak, Ondrej Lenz, Matej Semerak
Summary: Apple hammerhead viroid (AHVd) and Solanum nigrum ilarvirus 1 (SnIV-1) were detected in different apple cultivars, and both pathogens were successfully eliminated using a combination of meristem tip cultures and antiviral drugs. SnIV-1 was effectively eliminated in all cultivars with different concentrations of ribavirin, rimantadine, and zidovudine, while AHVd elimination was less effective and could only be achieved with ribavirin at specific concentrations.
Article
Plant Sciences
Igor Koloniuk, Alena Matyasova, Sara Brazdova, Jana Vesela, Jaroslava Pribylova, Eva Varallyay, Jana Franova
Summary: It has been found that plants can be infected with multiple viruses. This study used high-throughput sequencing to investigate the small interfering RNAs (siRNAs) in a single strawberry plant co-infected with different strains of strawberry mottle virus (SMoV), strawberry crinkle virus (SCV), and strawberry virus 1 (StrV-1). The results revealed complex interactions between the antiviral response and multiple viruses within a single infected plant.
