Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.U.S. Department of Energy DE-AC02-05CH1123

Critical Discourse Analysis: Definition, Approaches, Relation to Pragmatics, Critique, and Trends

This chapter introduces the transdisciplinary research movement of critical discourse analysis (CDA) beginning with its definition and recent examples of CDA work. In addition, approaches to CDA such as the dialectical relational (Fairclough), sociocognitive (van Dijk), discourse historical (Wodak), social actors (van Leeuwen), and the Foucauldian dispositive analysis (Jager and Maier) are outlined, as well as the complex relation of CDA to pragmatics. Next, the chapter provides a brief mention of the extensive critique of CDA, the creation of critical discourse studies (CDS), and new trends in CDA, including positive discourse analysis (PDA), CDA with multimodality, CDA and cognitive linguistics, critical applied linguistics, and other areas (rhetoric, education, anthropology/ethnography, sociolinguistics, culture, feminism/gender, and corpus studies). It ends with new directions aiming towards social action for social justice