Article
Food Science & Technology
Alice Giusti, Enrica Ricci, Laura Gasperetti, Marta Galgani, Luca Polidori, Francesco Verdigi, Roberto Narducci, Andrea Armani
Summary: This study aimed to build an ITS gene dataset to aid the Italian Health Service in mushroom identification. By retrieving and filtering ITS sequences from GenBank and BOLD databases, as well as collecting wild specimens, a dataset of 5977 sequences was successfully established to support regional poisoning cases.
Article
Microbiology
Shuqian Hu, Xiang Li, Xin Yin, Runmeng Li, Ruiyang Zhang, Junhao Zang, Yin Liu
Summary: This study developed a species-specific method for identification and classification of Pseudomonas based on ITS sequences combined with next-generation sequencing (NGS).
Article
Microbiology
Fernando Martinez-Hernandez, Fabiola Sanchez-Aguillon, Joel Martinez-Ocana, Nelly Raquel Gonzalez-Arenas, Mirza Romero-Valdovinos, Eduardo Lopez-Escamilla, Pablo Maravilla, Guiehdani Villalobos
Summary: This study evaluated the genetic variability of the ITS region and pfor A gene of Trichomonas vaginalis from female patients and explored its implications in the host-parasite relationship. Results showed two main clusters in the ITS haplotypes and suggested that pfor A could be used as a marker for confirming trichomonads genus and species.
Article
Microbiology
Nadia Stoppani, Silvia Colussi, Paolo Pastorino, Marino Prearo, Simona Sciuto, Ilhan Altinok, Rafet Cagri Ozturk, Mustafa Ture, Ana Isabel Vela, Maria del Mar Blanco, Charalampos Kotzamanidis, Konstantina Bitchava, Andigoni Malousi, Lucio Fariano, Donatella Volpatti, Pier Luigi Acutis, Jose Francisco Fernandez-Garayzabal
Summary: The aim of this study was to use the transcribed spacer (ITS) region between 16S rRNA and 23S rRNA as a potential useful molecular target to differentiate L. garvieae from L. petauri for accurate discrimination between these two species. Seven SNPs were identified that separate L. garvieae from L. petauri based on the ITS region sequence. The 16S-23S rRNA ITS region can be used as a diagnostic marker to quickly identify the pathogens in a lactococcosis outbreak.
Article
Microbiology
Ricardo Franco-Duarte, Isabel Fernandes, Vladislav Gulis, Fernanda Cassio, Claudia Pascoal
Summary: Aquatic hyphomycetes play an important role in decomposing organic matter in freshwater ecosystems. This study used the ITS rDNA barcodes database to explore their molecular diversity and distribution patterns. The findings showed an increase in the number of aquatic hyphomycete species, providing insights into their taxonomic placement and biogeographical origins. Future research should focus on expanding the ITS sequence database for species with unclear phylogenetic relationships and limited sequences.
Article
Plant Sciences
Claudia Gonzalez-Toral, Herminio S. Nava, Jose Antonio Fernandez Prieto, Eduardo Cires
Summary: Bromus picoeuropeanus is a recently described species of grasses found in stony soils at heights ranging from 1600 to 2200 m in Picos de Europa, Spain. Phylogenetic analyses based on nuclear and chloroplastic markers suggest that B. picoeuropeanus is a separate species with a larger distribution than previously thought. However, more research is needed to understand its susceptibility to temperature rises.
Article
Mycology
Junichiro Hiruma, Honoka Nojo, Hitoshi Tsuchihashi, Hiromitsu Noguchi, Masataro Hiruma, Kazutoshi Harada, Rui Kano
Summary: In this study, T. interdigitale isolates were obtained from Japanese patients and their ITS types were investigated. The results showed that all 29 isolates belong to ITS type II, while one clinical isolate of T. mentagrophytes was similar to ITS type II*. Additionally, a terbinafine-resistant strain of T. interdigitale also belonged to ITS type II.
Review
Ecology
Havard Kauserud
Summary: This text discusses the inherent limitations of using the rDNA Internal Transcribed Spacer (ITS) region as a DNA barcode marker in fungal ecology studies. It highlights the challenges in species delimitation, the lack of significant interspecific divergence, and the uncertainty in species-level taxonomy. It also emphasizes the complexity and variation introduced by PCR and sequencing errors in DNA metabarcoding data. The importance of the ITS region as a general DNA (meta)barcoding marker for fungi is acknowledged but caution against naïve or simplistic use is stressed.
Article
Immunology
Gobena Ameni, Alebachew Messele Kebede, Aboma Zewude, Musse Girma Abdulla, Rahel Asfaw, Mesfin Mamo Gobena, Martina Kyalo, Francesca Stomeo, Balako Gumi, Teshale Sori
Summary: This study conducted a phylogenetic analysis of Histoplasma capsulatum isolated from cases of epizootic lymphangitis (EL) in horses in central Ethiopia and evaluated their relationship with isolates from other countries and clades. By analyzing the internal transcribed spacer (ITS) region of rRNA genes, the study identified different clades of H. capsulatum and revealed that the Ethiopian isolates were closely related to isolates from Latin America and Eurasia, but distantly related to isolates from North America.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Plant Sciences
Jiao Zhang, Xiulian Chi, Juying Zhong, Alisdair Fernie, Saleh Alseekh, Luqi Huang, Dan Qian
Summary: This study found non-concerted evolution of internal transcribed spacer (ITS) sequences in the genus Lycium, showing high levels of polymorphism. The ITS paralogues were identified as pseudogenes or functional copies, with distinct differences from their corresponding functional copies. The results suggest a link between the non-concerted evolution of ITS and recent divergence of tandem repeats within the Lycium genome and hybridization between species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Pingping Lin, Xuguang Hu, Li Xue, Xinyi Li, Ping Wang, Xinwang Zhao, Muqing Zhang, Zuhu Deng, Fan Yu
Summary: The study analyzed the relationship and ploidy of wild sugarcane using DNA sequencing and fluorescence in situ hybridization. The results showed that rDNA sequences can be used as a useful marker for identifying the relationship and ploidy of wild sugarcane in sugarcane breeding.
Article
Ecology
Yasmin A. Alomia, J. Tupac Otero, Jana Jersakova, Pablo R. Stevenson
Summary: The relationship between orchids and fungi has been studied due to the reliance of orchid seeds on fungi for germination support. Through isolating cultivable endophytic and mycorrhizal fungi from the orchid Dichaea andina, a diverse range of fungi from Ascomycota orders and Basidiomycota genus Ceratobasidium were identified, some of which have been recognized as orchid endophytes. Further investigation is needed to understand the significance of endophytic fungi to orchid hosts.
Article
Multidisciplinary Sciences
Michael Olbrich, Anna Lara Ernst, Foteini Beltsiou, Katja Bieber, Sascha Staender, Melanie Harder, Waltraud Anemueller, Birgit Koehler, Detlef Zillikens, Hauke Busch, Axel Kuenstner, Ralf J. Ludwig
Summary: This study used next generation sequencing to investigate fungal diversity in healthy individuals and patients with onychomycosis. The results showed variations in the abundance of Trichophyton in onychomycosis patients. Compared to low abundance cases, high abundance cases had lower fungal diversity. The study also found differences in the community structure between cases and controls, driven mainly by high abundance cases. These findings provide valuable insights into the development mechanisms of onychomycosis.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Wael A. Fathy, Natascha Techen, Khaled N. M. Elsayed, Ehab A. Essawy, Eman Tawfik, Khairiah Mubarak Alwutayd, Mohamed S. Abdelhameed, Ola Hammouda, Samir A. Ross
Summary: The absence of proper identification and documentation of microalgae is a common concern in the field of applied phycology, algal physiology, and biochemistry publications. A promising solution lies in employing DNA barcoding techniques and establishing comprehensive databases of reference sequences. This study focuses on the molecular characterization and strain identification of Tetraselmis and Chlorella species using the internal transcribed spacer (ITS) barcode approach.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Ram Prasnna Meena, Vasudha A. Kadam
Summary: Safed mush is affected by a severe leaf blight disease possibly caused by Macrophomina phaseolina fungus, characterized by dark pycnidia, black round to oblong microsclerotia, conidia, and dark to greyish membranous pycnidia, identified through molecular sequencing of internal transcribed spacer (ITS) and actin gene. Metalaxyl 4.0% + mancozeb 64% and Pseudomonas fluorescence (PF7) show high mycelial growth inhibition against the pathogen.
JOURNAL OF APPLIED RESEARCH ON MEDICINAL AND AROMATIC PLANTS
(2021)
Article
Plant Sciences
Yosuke Matsuda, Yusuke Yamaguchi, Naoko Matsuo, Takashi Uesugi, Junko Ito, Takahiro Yagame, Tomas Figura, Marc-Andre Selosse, Yasushi Hashimoto
JOURNAL OF PLANT RESEARCH
(2020)
Article
Soil Science
Yudai Kitagami, Toko Tanikawa, Yosuke Matsuda
SOIL BIOLOGY & BIOCHEMISTRY
(2020)
Article
Forestry
Chisato Takenaka, Akihisa Fukushi, Yosuke Matsuda
Summary: The research found that arbuscular mycorrhizal fungi (AMF) contribute significantly to Cs-137 uptake by Eleutherococcus sciadophylloides, particularly in the presence of potassium (K) in the rhizosphere. Field and greenhouse experiments confirmed this contribution, providing valuable insights for enhanced phytoremediation utilizing AMF and K.
JOURNAL OF FOREST RESEARCH
(2021)
Article
Biodiversity Conservation
Hirofumi Nakashima, Yosuke Matsuda, Naoki Hijii
Summary: Cenococcum geophilum shows a high tolerance to fenitrothion, which may explain its dominance over other ectomycorrhizal species in coastal forests in Japan where the insecticide is routinely sprayed. The growth of all three ectomycorrhizal fungi, including C. geophilum, Rhizopogon roseolus, and Pisolithus arhizus, decreased significantly with increasing fenitrothion dosage.
LANDSCAPE AND ECOLOGICAL ENGINEERING
(2021)
Article
Forestry
Etsuko Harada, Naoto Tada, Ichiro Kamei, Toshihiro Morizono, Yosuke Matsuda
Summary: This study investigated the cultivation of L. giganteus in sugi forests in Japan, finding that the mushroom showed high yields and could be a profitable forest product in the region. The research established a method for cultivating L. giganteus in sugi forests, highlighting the potential for marketable forest products.
JOURNAL OF FOREST RESEARCH
(2021)
Article
Agronomy
Yosuke Matsuda, Kohei Kita, Yudai Kitagami, Toko Tanikawa
Summary: The study revealed that AM fungal communities in the root systems of Cryptomeria japonica are influenced by soil conditions and vary among different root orders. It also found that the abundance and species richness of AM fungi change as roots age.
Article
Forestry
Keita Henry Okada, Hiroshi Abe, Yosuke Matsuda, Kazuhide Nara
Summary: The study found that R. togasawarius has the ability to disperse and extend the range of spore banks outside the forest of host trees, with a significant increase in occurrence near forest boundaries. This is important for understanding the dispersal ecology of ectomycorrhizal fungi.
JOURNAL OF FOREST RESEARCH
(2022)
Article
Plant Sciences
Yudai Kitagami, Yosuke Matsuda
Summary: This study investigates the propagation and food preference of fungivorous nematodes on different ectomycorrhizal fungi. The results show that different fungal species have different effects on nematode numbers and body size, with S. granulatus being the most attractive to nematodes.
Article
Plant Sciences
Keita Henry Okada, Yosuke Matsuda
Summary: This study investigated the EcM fungal spore bank communities in soil in remnant patches of Japanese Douglas-fir forest. The results showed that these spore banks were not restricted to Douglas-fir forests and extended to surrounding forest dominated by arbuscular mycorrhizal trees. The community structure of EcM fungal spore banks differed significantly between study sites but not between forest types.
Article
Ecology
Yudai Kitagami, Keisuke Obase, Yosuke Matsuda
Summary: This study compared the community structures of soil nematodes at different altitudes using morphological and high-throughput sequencing analyses, revealing differences in nematode community structures between the two methods but similar responses to environmental gradients.
Article
Forestry
Taichiro Mine, Yudai Kitagami, Toko Tanikawa, Yosuke Matsuda
Summary: This study found that the phylum Thaumarchaeota is the dominant archaeal group in the fine roots of Japanese cedars and that the community structure is influenced by soil acidity.
JOURNAL OF FOREST RESEARCH
(2023)
Article
Ecology
Yudai Kitagami, Yosuke Matsuda
Summary: This study compared the community structures of soil nematodes determined by high-throughput sequencing (HTS) and morphological analyses in natural Japanese cedar forests. The results showed that HTS analysis is more useful for uncovering hidden diversity of nematode communities in natural ecosystems.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2022)
Article
Agronomy
Ryota Hayashi, Nagamitsu Maie, Rota Wagai, Yasuhiro Hirano, Yosuke Matsuda, Naoki Makita, Takeo Mizoguchi, Ryusei Wada, Toko Tanikawa
Summary: The purpose of this study was to investigate why the cation exchange capacity (CEC) was not enhanced in low acid buffering capacity (ABC) soils despite higher fine-root biomass and total carbon (TC) content. The results showed that increased SOM degradation in the low ABC soils prevented the increase in carboxyl group content in the stabilized SOM fraction, leading to no increase in CEC.
Review
Environmental Sciences
Toko Tanikawa, Nagamitsu Maie, Saori Fujii, Lijuan Sun, Yasuhiro Hirano, Takeo Mizoguchi, Yosuke Matsuda
Summary: Leachate from decaying root and leaf litter plays crucial roles in soil biogeochemical processes in forest ecosystems. The chemical composition and microbial community of root litter leachate differ from leaf litter leachate. Understanding organ-specific litter N dynamics is essential for forest ecosystem management.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Mycology
Sergei Polme, Kessy Abarenkov, R. Henrik Nilsson, Bjorn D. Lindahl, Karina Engelbrecht Clemmensen, Havard Kauserud, Nhu Nguyen, Rasmus Kjoller, Scott T. Bates, Petr Baldrian, Tobias Guldberg Froslev, Kristjan Adojaan, Alfredo Vizzini, Ave Suija, Donald Pfister, Hans-Otto Baral, Helle Jarv, Hugo Madrid, Jenni Norden, Jian-Kui Liu, Julia Pawlowska, Kadri Poldmaa, Kadri Partel, Kadri Runnel, Karen Hansen, Karl-Henrik Larsson, Kevin David Hyde, Marcelo Sandoval-Denis, Matthew E. Smith, Merje Toome-Heller, Nalin N. Wijayawardene, Nelson Menolli, Nicole K. Reynolds, Rein Drenkhan, Sajeewa S. N. Maharachchikumbura, Tatiana B. Gibertoni, Thomas Laessoe, William Davis, Yuri Tokarev, Adriana Corrales, Adriene Mayra Soares, Ahto Agan, Alexandre Reis Machado, Andres Arguelles-Moyao, Andrew Detheridge, Angelina de Meiras-Ottoni, Annemieke Verbeken, Arun Kumar Dutta, Bao-Kai Cui, C. K. Pradeep, Cesar Marin, Daniel Stanton, Daniyal Gohar, Dhanushka N. Wanasinghe, Eveli Otsing, Farzad Aslani, Gareth W. Griffith, Thorsten H. Lumbsch, Hans-Peter Grossart, Hossein Masigol, Ina Timling, Inga Hiiesalu, Jane Oja, John Y. Kupagme, Jozsef Geml, Julieta Alvarez-Manjarrez, Kai Ilves, Kaire Loit, Kalev Adamson, Kazuhide Nara, Kati Kungas, Keilor Rojas-Jimenez, Kriss Bitenieks, Laszlo Irinyi, Laszlo Laszlo Nagy, Liina Soonvald, Li-Wei Zhou, Lysett Wagner, M. Catherine Aime, Maarja opik, Maria Isabel Mujica, Martin Metsoja, Martin Ryberg, Martti Vasar, Masao Murata, Matthew P. Nelsen, Michelle Cleary, Milan C. Samarakoon, Mingkwan Doilom, Mohammad Bahram, Niloufar Hagh-Doust, Olesya Dulya, Peter Johnston, Petr Kohout, Qian Chen, Qing Tian, Rajasree Nandi, Rasekh Amiri, Rekhani Hansika Perera, Renata dos Santos Chikowski, Renato L. Mendes-Alvarenga, Roberto Garibay-Orijel, Robin Gielen, Rungtiwa Phookamsak, Ruvishika S. Jayawardena, Saleh Rahimlou, Samantha C. Karunarathna, Saowaluck Tibpromma, Shawn P. Brown, Siim-Kaarel Sepp, Sunil Mundra, Zhu-Hua Luo, Tanay Bose, Tanel Vahter, Tarquin Netherway, Teng Yang, Tom May, Torda Varga, Wei Li, Victor Rafael Matos Coimbra, Virton Rodrigo Targino de Oliveira, Vitor Xavier de Lima, Vladimir S. Mikryukov, Yongzhong Lu, Yosuke Matsuda, Yumiko Miyamoto, Urmas Koljalg, Leho Tedersoo
Summary: The article introduces a database FungalTraits to facilitate functional assignments and ecological interpretation of fungi, discussing the challenges between molecular identification of fungal diversity and knowledge of functional traits. Through the involvement of expert knowledge and tools, researchers reannotated a large number of fungal and Stramenopila genera, summarizing them into 17 lifestyle-related traits suitable for environmental studies.