Darin M. Eastburn

Bio: Darin M. Eastburn is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Trichoderma harzianum & Verticillium dahliae. The author has an hindex of 22, co-authored 39 publications receiving 1590 citations. Previous affiliations of Darin M. Eastburn include University of California, Davis.

Preserving accuracy in GenBank

Abstract: GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for

Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

Abstract: Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo , and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae. More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts. IMPORTANCE Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.

Influence of atmospheric and climatic change on plant–pathogen interactions

Abstract: Atmospheric change studies conducted in free air concentration enrichment (FACE) systems and open-topped chambers have increased understanding of how factors, such as rising CO2 and O3 levels, impact the development of plant disease epidemics Using these systems, plant scientists have been able to study host/pathogen systems under real-world conditions where variations in multiple environmental parameters impact disease outcomes Results from these studies are useful for evaluating earlier predictions on plant responses to climate-change parameters and the resulting impacts on plant disease epidemics Some of these predictions have been verified, whilst others have yet to be tested Significant interactions among climate-change parameters are highlighting the importance of conducting studies under real-world conditions The development of molecular and gene expression tools is allowing the fine scale mechanisms responsible for the observed reactions to be determined, and should increase the ability to predict plant disease outcomes under future climatic conditions

Preserving accuracy in GenBank

Abstract: GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for

Elevated atmospheric carbon dioxide and ozone alter soybean diseases at SoyFACE

Abstract: Human driven changes in the Earth’s atmospheric composition are likely to alter plant disease in the future. We evaluated the effects of elevated carbon dioxide (CO2 )a nd ozone (O3) on three economically important soybean diseases (downy mildew, Septoria brown spot and sudden death syndrome-SDS) under natural field conditions at the soybean free air concentration enrichment (SoyFACE) facility. Disease incidence and/or severity were quantified from 2005 to 2007 using visual surveys and digital image analysis, and changes were related to microclimatic variability and to structural and chemical changes in soybean host plants. Changes in atmospheric composition altered disease expression, but responses of the three pathosystems varied considerably. Elevated CO2 alone or in combination with O3 significantly reduced downy mildew disease severity (measured as area under the disease progress curve-AUDPC) by 39–66% across the 3 years of the study. In contrast, elevated CO2 alone or in combination with O3 significantly increased brown spot severity in all 3 years, but the increase was small in magnitude. When brown spot severity was assessed in relation to differences in canopy height induced by the atmospheric treatments, disease severity increased under combined elevated CO2 and O3 treatment in only one of the 3 years. The atmospheric treatments had no effect on the incidence of SDS or brown spot throughout the study. Higher precipitation during the 2006 growing season was associated with increased AUDPC severity across all treatments by 2.7 and 1.4 times for downy mildew and brown spot, respectively, compared with drought conditions in 2005. In the 2 years with similar precipitation, the higher daily temperatures in the late spring of 2007 were associated with increased severity of downy mildew and brown spot. Elevated CO2 and O3 induced changes in the soybean canopy density and leaf age likely contributed to the disease expression modifications.

Towards a unified paradigm for sequence-based identification of fungi

Abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

The interaction of plant biotic and abiotic stresses: from genes to the field

Abstract: Plant responses to different stresses are highly complex and involve changes at the transcriptome, cellular, and physiological levels. Recent evidence shows that plants respond to multiple stresses differently from how they do to individual stresses, activating a specific programme of gene expression relating to the exact environmental conditions encountered. Rather than being additive, the presence of an abiotic stress can have the effect of reducing or enhancing susceptibility to a biotic pest or pathogen, and vice versa. This interaction between biotic and abiotic stresses is orchestrated by hormone signalling pathways that may induce or antagonize one another, in particular that of abscisic acid. Specificity in multiple stress responses is further controlled by a range of molecular mechanisms that act together in a complex regulatory network. Transcription factors, kinase cascades, and reactive oxygen species are key components of this cross-talk, as are heat shock factors and small RNAs. This review aims to characterize the interaction between biotic and abiotic stress responses at a molecular level, focusing on regulatory mechanisms important to both pathways. Identifying master regulators that connect both biotic and abiotic stress response pathways is fundamental in providing opportunities for developing broad-spectrum stress-tolerant crop plants.

Food security and food production systems

Abstract: Many definitions of food security exist, and these have been the subject of much debate. As early as 1992, Maxwell and Smith (1992) reviewed more than 180 items discussing concepts and definitions, and more definitions have been formulated since (DEFRA, 2006). Whereas many earlier definitions centered on food production, more recent definitions highlight access to food, in keeping with the 1996 World Food Summit definition (FAO, 1996) that food security is met when “all people, at all times, have physical and economic access to sufficient, safe, and nutritious food to meet their dietary needs and food preferences for an active and healthy life.” Worldwide attention on food access was given impetus by the food “price spike” in 2007–2008, triggered by a complex set of long- and short-term factors (FAO, 2009b; von Braun and Torero, 2009). FAO concluded, “provisional estimates show that, in 2007, 75 million more people were added to the total number of undernourished relative to 2003–05” (FAO, 2008); this is arguably a low-end estimate (Headey and Fan, 2010). More than enough food is currently produced per capita to feed the global population, yet about 870 million people remained hungry in the period from 2010 to 2012 (FAO et al., 2012). The questions for this chapter are how far climate and its change affect current food production systems and food security and the extent to which they will do so in the future (Figure 7-1).