The ascomycete phytopathogenic fungus, Colletotrichum scovillei , causes serious yield loss on peppers. However, little is known about molecular mechanisms involved in the development of anthracnose caused by this fungus.

The plant microbiome, the consortium of microbes surrounding a plant, has potential for improving crop productivity and sustainability. Despite the necessity of agriculturally applicable microbiomes, plant microbiome studies have been conducted in noncrop plants because of the relative easiness of research. However, in order to make plant microbiomes useful for agriculture, a crop plant-based model is needed. In parallel, overlooked parts of microbiomes other than the bacteria-centered research need to be considered to expand our understandings on microbiomes to the ecosystem level. Beyond the microbial composition, functional properties of microbiomes over time and space will help us to select appropriate microbes that can support crop plants by providing stage-specific functions. Less explored communities such as fungi and protists also can provide novel insights on compositional and functional dynamics of each community, including interkingdom or multitrophic interactions. Finally, identification of host factors on functional microbiomes using genetic information of both the host and the microbiomes will shift host-centered breeding to parallel breeding of host and microbiome. This review will give basic and collective information on the rice microbiome and foster the establishment of a crop plant-based model to meet agricultural needs.

Sexual plant reproduction depends on the attraction of sperm-cell delivering pollen tubes (PT) by two synergids, followed by their programmed cell death (PCD) in Arabidopsis. Disruption of the mitogen-activated protein kinase 4 (MPK4) by pathogenic effectors activates the resistance protein (R) SUMM2-mediated immunity and cell death. Here we show that synergid preservation and reactive oxygen species (ROS) homeostasis are intimately linked and maintained by MPK4. In mpk4, ROS levels are increased and synergids prematurely undergo PCD before PT-reception. However, ROS scavengers and the disruption of SUMM2, in mpk4, restore ROS homeostasis, synergid maintenance and PT perception, demonstrating that the guardian of MPK4, SUMM2, triggers synergid-PCD. In mpk4/summ2, PTs show a feronia-like overgrowth phenotype. Our results show that immunity-associated PCD and synergid cell death during plant reproduction are regulated by MPK4 underscoring an underlying molecular mechanism for the suppression of plant reproduction during systemic R-mediated immunity.

Vertical transmission of microbes is crucial for the persistence of host-associated microbial communities. Although vertical transmission of seed microbes has been reported from diverse plants, ecological mechanisms and dynamics of microbial communities from parent to progeny remain scarce. Here we reveal the veiled ecological mechanism governing transmission of bacterial and fungal communities in rice across two consecutive seasons. We identify 29 bacterial and 34 fungal members transmitted across generations. Abundance-based regression models allow to classify colonization types of the microbes. We find that they are late colonizers dominating each community at the ripening stage. Ecological models further show that the observed temporal colonization patterns are affected by niche change and neutrality. Source-sink modeling reveals that parental seeds and stem endosphere are major origins of progeny seed microbial communities. This study gives empirical evidence for ecological mechanism and dynamics of bacterial and fungal communities as an ecological continuum during seed-to-seed transmission.

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680 bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely-available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.