Article
Biology
Jakki J. Mohr, Peter A. Harrison, Jessica Stanhope, Martin F. Breed
Summary: This study explores the potential of genomics in restoring degraded ecosystems and identifies barriers hindering its uptake. The findings reveal varying perspectives among scholars, with experienced scholars emphasizing caution in using genomics and calling for case studies to demonstrate its benefits. Research trends show a significant number of genomics studies in restoration, particularly those using environmental DNA as a monitoring tool.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Melissa Y. Chen, Jordan G. Kueneman, Antonio Gonzalez, Greg Humphrey, Rob Knight, Valerie J. McKenzie
Summary: Ecological community traits of host-associated microbiota can predict infection risk and intensity of pathogenic microbes, with richness and proportion being important predictors.
Review
Biotechnology & Applied Microbiology
Xiangfeng Meng, Yu Fang, Mingyang Ding, Yanyu Zhang, Kaili Jia, Zhongye Li, Jerome Collemare, Weifeng Liu
Summary: Natural products from fungi are important for therapeutic agent development, but many fungal biosynthetic gene clusters (BGCs) are not expressed under laboratory conditions, necessitating the development of new expression platforms. Therefore, increasing heterologous expression of BGCs is a current research focus.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Plant Sciences
Peter Innes, Andre Gossweiler, Scott Jensen, Derek Tilley, Loren St John, Thomas Jones, Stanley Kitchen, Brent S. Hulke
Summary: Common flax is widely grown as a food and fibre crop, while its perennial relative, Lewis flax, shows potential as an oilseed crop and in ecological restoration. A common garden experiment in the Intermountain West region revealed that Lewis flax has key traits that vary according to latitude and climate, which can aid its adaptation. These traits include flowering time, seed mass, and stem number. This study provides valuable information for the use of Lewis flax in both restoration and agriculture, and for its domestication as a high-omega-3 oil source.
Article
Plant Sciences
Paula H. Reyes-Herrera, Eliana Torres-Bedoya, Diana Lopez-Alvarez, Diana Burbano-David, Sandra L. Carmona, Daniel P. Bebber, David J. Studholme, Monica Betancourt, Mauricio Soto-Suarez
Summary: The global banana industry is facing a severe threat from Fusarium wilt of banana, caused by a soilborne fungus called Fusarium oxysporum f. sp. cubense (Foc). A new strain of Foc, known as tropical race 4 (TR4), attacks various banana varieties, including Cavendish clones which account for 99% of banana exports. Genetic analysis reveals that the TR4 isolates from Colombia and Peru are genetically distant, indicating independent incursions of the pathogen to the continent.
Review
Microbiology
Hannah M. Edwards, Massimo Cogliati, Geoffrey Kwenda, Matthew C. Fisher
Summary: Genome sequencing technologies have greatly improved our understanding of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii. These organisms are found ubiquitously as saprotrophs in the environment, posing a risk of cryptococcosis to individuals with compromised immune systems, particularly those living with HIV/AIDS. The study of diverse lineages through genomic analysis has emphasized the importance of enhanced genomic surveillance in their natural environments, especially in Africa, to better understand their ecology, biology, and evolution.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Plant Sciences
Laura S. Bautista-Jalon, Omer Frenkel, Leah Tsror Lahkim, Glenna M. Malcolm, Beth K. Gugino, Sara Lebiush, Marina Hazanovsky, Michael G. Milgroom, Maria del Mar Jimenez-Gasco
Summary: The study analyzed the evolutionary history and genetic differentiation between Verticillium dahliae populations from symptomatic and asymptomatic hosts, finding that asymptomatic weeds and rotational hosts may serve as potential reservoirs for V. dahliae populations of lineage 4B.
Article
Plant Sciences
Ashley Stengel, Rhae A. Drijber, Erin Carr, Thais Egreja, Edward Hillman, Timothy Krause, Samantha Reese, Joshua R. Herr
Summary: Systems of classification are crucial in research and communication. Microbes are traditionally classified as mutualists or pathogens, but there are instances where their behaviors do not fit into these categories. The concept of a continuum of symbiosis suggests that microbial taxa can exhibit mutualistic or pathogenic traits depending on various factors. This commentary introduces an alternative framework based on eco-evolutionary theory to evaluate the continuum of symbiosis using dominant archetypes that define symbiotic ranges.
PHYTOBIOMES JOURNAL
(2022)
Review
Microbiology
Andrew M. Borman, Elizabeth M. Johnson
Summary: Many medically significant fungal species have recently undergone and are likely to undergo further nomenclatural changes as a result of molecular approaches to fungal classification and abandonment of dual nomenclature. This article summarizes the changes affecting key groups of medically important fungi, explaining the taxonomic rationale behind the changes and the clinical relevance of the nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, along with approaches to raise awareness of important changes and minimize potential clinical confusion.
CLINICAL MICROBIOLOGY REVIEWS
(2023)
Article
Genetics & Heredity
Anna Lazar, Ryan M. Mushinski, Gary D. Bending
Summary: The genus Tetracladium is a diverse and widely distributed root colonizing endophyte in the oilseed rape microbiome that positively correlates to crop yield. Crop management practices and soil nutrients are the main drivers of its community composition.
ENVIRONMENTAL MICROBIOME
(2022)
Editorial Material
Multidisciplinary Sciences
Ana S. L. Rodrigues, Marie-Morgane Rouyer
Summary: A global analysis provides evidence that protected areas are slowing down global biodiversity declines, although the effects vary across different groups of species, and what happens outside protected areas also matters.
Article
Immunology
Mohammad Soleimani, Alireza Izadi, Sadegh Khodavaisy, Claudy Oliveira dos Santos, Marlou C. C. Tehupeiory-Kooreman, Roshanak Daie Ghazvini, Seyed Jamal Hashemi, Seyed Amin Ayatollahi Mousavi, Farzad Aala, Mahsa Abdorahimi, Mehdi Aminizadeh, Zohre Abedinifar, Shahram Mahmoudi, Afsaneh Mohamadi, Sara Rezaie, Paul E. E. Verweij
Summary: This study aimed to investigate the clinical features and predisposing factors of fungal keratitis (FK) in Tehran, Iran. The fungal etiology of corneal ulcers was confirmed in 7.23% of cases, with Fusarium spp., Aspergillus spp., and Candida spp. being the predominant species. The study also found that different antifungal agents may be effective in treating FK caused by different fungal species.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Virginia M. Weis
Summary: Biologists have found through careful analysis of nutrient cycling that corals can rely on an unexpected food source to survive in times of food scarcity.
Editorial Material
Multidisciplinary Sciences
Eric J. B. von Wettberg, Azalea Guerra-Garcia
Summary: A high-quality reference genome has been generated for the broad bean (also known as the faba or fava bean), which could be used to identify ways to increase yield, improve pest resistance, and more.
Article
Mycology
M. S. Calabon, K. D. Hyde, E. B. G. Jones, D. F. Bao, C. S. Bhunjun, C. Phukhamsakda, H. W. Shen, E. Gentekaki, A. H. Al Sharie, J. Barros, S. K. U. Chandrasiri, D. M. Hu, V Hurdeal, W. Rossi, L. G. Valle, H. Zhang, M. Figueroa, H. A. Raja, S. Seena, H. Y. Song, W. Dong, T. El-Elimat, W. Leonardi, Y. Li, Y. J. Li, Z. L. Luo, C. D. Ritter, D. B. Strongman, M. J. Wei, A. Balasuriya
Summary: Research on freshwater fungi has yielded a wealth of information in recent decades, including reviews, books, and monographs. With advances in research methodologies and the involvement of many mycologists, our understanding of freshwater fungi has advanced, including new discoveries and insights into their ecology. Given the significant progress made, it is timely to compile an updated account of freshwater fungi to provide a comprehensive overview of their biology. This volume covers topics such as classification, biology, diversity, distribution, and ecological importance, as well as the biotechnological potential and high throughput sequencing methods for freshwater fungal research.
Article
Biochemistry & Molecular Biology
Nicole K. Reynolds, Michelle A. Jusino, Jason E. Stajich, Matthew E. Smith
Summary: Metabarcoding is a useful tool for studying fungal communities, but the choice of DNA marker and methodological biases can greatly impact the recovery of early diverging fungi (EDF) like Zoopagomycota from environmental samples. Different taxonomy assignment methods can yield significantly different results in identifying EDF, and PCR amplification biases are more pronounced in EDF than in Dikarya (Ascomycota + Basidiomycota). Additional techniques, such as phylogenetic reconstruction, may be needed to accurately identify and study EDF in a broader ecological context.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Nicole K. Reynolds, Jason E. Stajich, Gerald L. Benny, Kerrie Barry, Stephen Mondo, Kurt LaButti, Anna Lipzen, Chris Daum, Igor Grigoriev, Hsiao-Man Ho, Pedro W. Crous, Joseph W. Spatafora, Matthew E. Smith
Summary: Improved sequencing technologies have revolutionized the understanding of fungal diversity and evolution on a global scale. A study was conducted using low coverage genome sequencing (LCGS) to analyze 171 Kickxellomycotina fungi and obtain marker genes for phylogenomic reconstruction. The study aimed to evaluate the quality and utility of LCGS data, test relationships among different clades, and compare functional analyses to gain insights into trophic modes.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E. Stajich, Jackie L. Collier, Guangyi Wang
Summary: This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains and investigates their ecological functions from the perspective of organic matter degradation using comparative genomics and biochemical assays. The results show that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems and can actively participate in marine biochemical cycles as decomposers. The study also emphasizes the dual roles of endoglucanase in the process of cellulose degradation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Atul Munish Chander, Marcus de Melo Teixeira, Nitin K. Singh, Michael P. Williams, Anna C. Simpson, Namita Damle, Ceth W. Parker, Jason E. Stajich, Christopher E. Mason, Tamas Torok, Kasthuri Venkateswaran
Summary: NASA's spacecraft assembly facilities are monitored for the presence of bacteria or fungi that can survive in extraterrestrial environments. Fungi show diverse traits to adapt to extreme conditions, and their detection and eradication are necessary to prevent contamination of future missions. Three novel fungal strains were isolated from spacecraft assembly facilities during the Mars 2020 mission, and a polyphasic taxonomic approach supported the proposal for two new genera and one new species. These strains also exhibited unique resistance to ultraviolet-C and possessed specific biosynthetic gene clusters for metabolically active compounds.
Article
Ecology
Zsolt Merenyi, Krisztina Krizsan, Neha Sahu, Xiao-Bin Liu, Balazs Balint, Jason E. Stajich, Joseph W. Spatafora, Laszlo G. Nagy
Summary: Fungi are ecologically important heterotrophs that have evolved from a unicellular opisthokont ancestor to derived multicellular fungi. The genomes of 123 fungi and their relatives reveal the gradual loss of protist genes, major gene turnover, and duplication leading to the evolution of modern traits in filamentous fungi. The taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Chemistry, Multidisciplinary
Bo Yuan, Michelle F. Grau, Ramiro Mendonca Murata, Tamas Torok, Kasthuri Venkateswaran, Jason E. Stajich, Clay C. C. Wang
Summary: Aspergillus melleus IMV 01140, isolated from regions surrounding the Chernobyl nuclear power plant, produces neoaspergillic acid, which inhibits the growth of Candida albicans. However, large-scale production, isolation, and purification pose challenges.
Article
Microbiology
Tania Kurbessoian, Gretchen Heimlich-Villalta, Nichole Ginnan, Flavia Campos Vieira, Philippe E. Rolshausen, M. Caroline Roper, Jason E. Stajich
Summary: The genomes of eighteen Fusarium isolates from diseased and healthy citrus trees were sequenced and confirmed using single marker (TEF1-alpha) phylogenetic assessment. The study of traits and genotypes of plant-associated isolates is crucial for understanding the fungal contribution to citrus phytobiomes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Terrance Shea, Jason T. Mohabir, Tania Kurbessoian, Brittany Berdy, James Fontaine, Andreas Gnirke, Jonathan Livny, Jason E. Stajich, Christina A. Cuomo
Summary: Lichtheimia ornata is an emerging opportunistic Mucorales pathogen that causes fatal infections in immunocompromised individuals. Although environmentally acquired infections of this pathogen have been rarely reported, cases were recently identified in an analysis of COVID-19-associated mucormycosis in India. In this study, we present the annotated genome sequence of the environmental isolate CBS 291.66.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Evolutionary Biology
Julia N. Adams, Merly Escalona, Mohan P. A. Marimuthu, Colin W. Fairbairn, Eric Beraut, William Seligmann, Oanh Nguyen, Noravit Chumchim, Jason E. Stajich
Summary: Acarospora socialis, a pioneer species of ecological significance, has been understudied in terms of genomics. This study presents the first high-quality draft genome of A. socialis, which will be crucial for conservation efforts in California and understanding its adaptability to climate change.
JOURNAL OF HEREDITY
(2023)
Article
Mycology
Cassandra L. Ettinger, Talieh Ostovar, Mark Yacoub, Steven Ahrendt, Robert H. Hice, Brian A. Federici, Jason E. Stajich
Summary: Species of the phylum Blastocladiomycota, including the genus Coelomomyces, are understudied and little is known about their genomics. To address this, researchers generated draft-level genomes and annotations for C. lativittatus and demonstrated their utility in transcriptome analysis. They found that the C. lativittatus transcriptome is complex and dynamic, with differentially expressed genes and enriched GO terms across different life stages. The genomes and transcriptomes reported here provide valuable resources for understanding the biology of early-diverging fungal lineages.
Article
Microbiology
Daniel Murante, Elora G. Demers, Tania Kurbessoian, Marina Ruzic, Alix Ashare, Jason E. Stajich, Deborah A. Hogan
Summary: The identification of MRS4 mutations in Clavispora (Candida) lusitaniae and Exophiala dermatitidis in individuals with cystic fibrosis (CF) highlights a possible adaptive mechanism for fungi during chronic CF lung infections. The findings of this study suggest that loss of function of the mitochondrial iron transporter Mrs4 can lead to increased activity of iron acquisition mechanisms, which may be advantageous for fungi in iron-restricted environments during chronic infections. This study provides valuable information for researchers working toward a better understanding of the pathogenesis of chronic lung infections and more effective therapies to treat them.
Article
Genetics & Heredity
Tania Kurbessoian, Daniel Murante, Alex Crocker, Deborah A. Hogan, Jason E. Stajich
Summary: Individuals with cystic fibrosis are susceptible to chronic lung infections, some of which are caused by slow-growing yeast Exophiala dermatitidis. This study analyzed isolates of E. dermatitidis from two samples collected from the same subject 2 years apart. The isolates were highly similar and exhibited population heterogeneity at the phenotype and genomic levels.
G3-GENES GENOMES GENETICS
(2023)
Review
Microbiology
Andrii P. Gryganskyi, Jacob Golan, Anna Muszewska, Alexander Idnurm, Somayeh Dolatabadi, Stephen J. Mondo, Vira B. Kutovenko, Volodymyr O. Kutovenko, Michael T. Gajdeczka, Iryna M. Anishchenko, Julia Pawlowska, Ngoc Vinh Tran, Ingo Ebersberger, Kerstin Voigt, Yan Wang, Ying Chang, Teresa E. Pawlowska, Joseph Heitman, Rytas Vilgalys, Gregory Bonito, Gerald L. Benny, Matthew E. Smith, Nicole Reynolds, Timothy Y. James, Igor V. Grigoriev, Joseph W. Spatafora, Jason E. Stajich
Summary: The genome of Saccharomyces cerevisiae was the first eukaryotic organism genome sequenced, reported in 1996, but it took over 10 years to sequence any of the zygomycete fungi, which belong to the phyla Mucoromycota and Zoopagomycota. Over 1000 zygomycete genomes have now been sequenced, revealing deep phylogenetic separation between plant-associated saprotrophic Mucoromycota and animal-associated parasites and commensals in the Zoopagomycota. Genomic studies have provided insights into fungal adaptations to living on land, including light and gravity sensing, hyphal growth, and co-existence with terrestrial plants. Genomic data has also facilitated research on genome architecture, pathogenicity genes, secondary metabolites, and endosymbiotic bacteria and viruses.
Article
Microbiology
Kouka Hilaire Kabore, Abalo Itolou Kassankogno, Henri Adreit, Sebastien Ravel, Florian Charriat, Diariatou Diagne, Marc-Henri Lebrun, Didier Tharreau, Jason E. Stajich
Summary: Different fungal species within the Pleosporaceae family can infect rice and cause similar symptoms. Reference genomic sequences are valuable tools for studying the evolution of these species and developing accurate molecular diagnostic tools. In this study, we report the complete genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Theo N. Kirkland, Sinem Beyhan, Jason E. Stajich
Summary: This study compares different gene prediction pipelines on the annotation of the Coccidioides immitis RS genome. Some genes originally predicted were not found in the other pipelines and these genes are more likely to be lineage-specific, poorly expressed, and have RNA-seq support for their structure. Genes predicted only by the Funannotate pipeline have lower functional annotations and expression levels. Genes predicted by multiple pipelines are more likely to have predicted functions and better expression.
