Direct-fed microbials (DFM) are dietary supplements that inhibit gastrointestinal infection and provide optimally regulated microbial environments in the digestive tract. As the use of antibiotics in ruminant feeds has been banned, DFM have been emphasized as antimicrobial replacements. Microorganisms that are used in DFM for ruminants may be classified as lactic acid producing bacteria (LAB), lactic acid utilizing bacteria (LUB), or other microorganisms including species of Lactobacillus, Bifidobacterium, Enterococcus, Streptococcus, Bacillus and Propionibacterium, strains of Megasphaera elsdenii and Prevotella bryantii and yeast products containing Saccharomyces and Aspergillus. LAB may have beneficial effects in the intestinal tract and rumen. Both LAB and LUB potentially moderate rumen conditions and improve feed efficiency. Yeast DFM may reduce harmful oxygen, prevent excess lactate production, increase feed digestibility, and improve fermentation in the rumen. DFM may also compete with and inhibit the growth of pathogens, stimulate immune function, and modulate microbial balance in the gastrointestinal tract. LAB may regulate the incidence of diarrhea, and improve weight gain and feed efficiency. LUB improved weight gain in calves. DFM has been reported to improve dry matter intake, milk yield, fat corrected milk yield and milk fat content in mature animals. However, contradictory reports about the effects of DFM, dosages, feeding times and frequencies, strains of DFM, and effects on different animal conditions are available. Cultivation and preparation of ready-to-use strict anaerobes as DFM may be cost-prohibitive, and dosing methods, such as drenching, that are required for anaerobic DFM are unlikely to be acceptable as general on-farm practice. Aero-tolerant rumen microorganisms are limited to only few species, although the potential isolation and utilization of aero-tolerant ruminal strains as DFM has been reported. Spore forming bacteria are characterized by convenience of preparation and effectiveness of DFM delivery to target organs and therefore have been proposed as DFM strains. Recent studies have supported the positive effects of DFM on ruminant performance.

Small RNAs regulate a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity, in a sequence-specific manner. Accumulating evidence reveals that host endogenous small RNAs and small RNA pathway components play important roles in plant immune responses against various pathogens, including bacteria, fungi, oomycetes, and viruses. Small-RNA-mediated defense responses are regulated through diverse pathways and the components of these pathways, including Dicer-like proteins, RNA-dependent RNA polymerases, Argonaute proteins, and RNA polymerase IV and V, exhibit functional specificities as well as redundancy. In this review, we summarize the recent insights revealed mainly through the examination of two model plants, Arabidopsis and rice, with a primary focus on our emerging understanding of how these small RNA pathway components contribute to plant immunity.

The complete genomes of 30 Soybean mosaic virus (SMV) isolates and strains were sequenced in this study. Together with fourteen previously reported sequences, we analyzed the genetic structure of the SMV population. Analyses of genetic diversity showed that different genomic regions of SMV are under different evolutionary constraints and that there was no significant genetic differentiation between East Asian and North American populations of SMV. Phylogenetic analyses revealed a significant correlation between phylogeny of the cylindrical inclusion (CI) gene of SMV and SMV resistance gene 3 (Rsv3)-relating pathogenicity of SMV, suggesting CI might be a pathogenic determinant in Rsv3-mediated disease response. Interestingly, recombination analyses identified 19 'clear' recombination events in the SMV population. Furthermore, as several resistance-breaking strains were identified as recombinants, it appears that recombination might contribute to overcome host resistance in SMV-soybean pathosystem. Our finding suggests that recombination as well as mutation is an important evolutionary process in the genetic diversification of SMV population.

Effector-triggered immunity (ETI) is an active immune response triggered by interactions between host resistance proteins and their cognate effectors. Although ETI is often associated with the hypersensitive response (HR), various R genes mediate an HR-independent process known as extreme resistance (ER). In the soybean-Soybean mosaic virus (SMV) pathosystem, the strain-specific CI protein of SMV functions as an effector of Rsv3-mediated ER. In this study, we used the soybean (Rsv3)-SMV (CI) pathosystem to gain insight into the molecular signaling pathway involved in ER. We used genome-wide transcriptome analysis to identify a subset of the type 2C protein phophatase (PP2C) genes that are specifically up-regulated in Rsv3-mediated ER. Gain-of-function analysis of the most significantly expressed soybean PP2C gene, GmPP2C3a, showed that ABA-induced GmPP2C3a functions as a key regulator of Rsv3-mediated ER. Our results further suggest that the primary mechanism of ER against viruses is the inhibition of viral cell-to-cell movement by callose deposition in an ABA signaling-dependent manner.