Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis.

Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein-protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs-MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9-may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities.

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Biochemical characterization of LysVpKK5 endolysin from a marine vibriophage.

Endolysins have been proposed as a potential antibacterial alternative for aquaculture, especially against Vibrio; the bacterial-agents that most frequently cause disease. Although multiple marine vibriophages have been characterized to date, research on vibriophage endolysins is recent. In this study, biochemical characterization of LysVpKK5 endolysin encoded by Vibrio parahaemolyticus-infecting VpKK5 phage was performed. In silico analysis revealed that LysVpKK5 possesses a conserved amidase_2 domain with a zinc-binding motif of high structural similarity to T7 lysozyme (RMSD = 0.107 Å). Contrary to expectations, the activity was inhibited with Zn2+ and was improved with other divalent cations, especially Ca2+. It showed optimal muralytic activity at pH 10, and curiously, no lytic activity at pH ≤ 7 was recorded. As for the thermal stability test, the optimal activity was recorded at 30 °C; the higher residual activity was recorded at 4 °C, and was lost at ≥ 50 °C. On the other hand, increasing NaCl concentrations reduced the activity gradually; the optimal activity was recorded at 50 mM NaCl. On the other hand, the enzymatic activity at 0.5 M NaCl was approx 30% and of approx 50% in seawater. LysVpKK5 endolysin exhibited a higher activity on V. parahaemolyticus ATCC-17802 strain, in comparison with AHPND + strains.

Growth effects in oregano plants (Origanum vulgare L.) assessment through inoculation of bacteria isolated from crop fields located on desert soils.

Bacteria can establish beneficial interactions with plants by acting as growth promoters and enhancing stress tolerance during plant interactions. Likewise, bacteria can develop multispecies communities where multiple interactions are possible. In this work, we assessed the physiological effects of three bacteria isolated from an arid environment (Bacillus niacini, Bacillus megaterium, and Moraxella osloensis) applied as single species or as a consortium on oregano (Origanum vulgare L.) plants. Moreover, we assessed the quorum-sensing (QS) signaling activity to determine the molecular communication between plant-growth-promoting bacteria. The plant inoculation with B. megaterium showed a positive effect on morphometric and physiologic parameters. However, no synergistic effects were observed when a bacterial consortium was inoculated. Likewise, activation of QS signaling in biofilm assays was observed only for interspecies interaction within the Bacillus genus, not for either interaction with M. osloensis. These results suggest a neutral or antagonistic interaction for interspecific bacterial biofilm establishment, as well as for the interaction with oregano plants when bacteria were inoculated in a consortium. In conclusion, we were able to determine that the bacterial interactions are not always positive or synergistic, but they also might be neutral or antagonistic.

An Autophagy-Related Kinase Is Essential for the Symbiotic Relationship between Phaseolus vulgaris and Both Rhizobia and Arbuscular Mycorrhizal Fungi.

Eukaryotes contain three types of lipid kinases that belong to the phosphatidylinositol 3-kinase (PI3K) family. In plants and Saccharomyces cerevisiae, only PI3K class III family members have been identified. These enzymes regulate the innate immune response, intracellular trafficking, autophagy, and senescence. Here, we report that RNAi-mediated downregulation of common bean (Phaseolus vulgaris) PI3K severely impaired symbiosis in composite P. vulgaris plants with endosymbionts such as Rhizobium tropici and Rhizophagus irregularis Downregulation of Pv-PI3K was associated with a marked decrease in root hair growth and curling. Additionally, infection thread growth, root-nodule number, and symbiosome formation in root nodule cells were severely affected. Interestingly, root colonization by AM fungi and the formation of arbuscules were also abolished in PI3K loss-of-function plants. Furthermore, the transcript accumulation of genes encoding proteins known to interact with PI3K to form protein complexes involved in autophagy was drastically reduced in these transgenic roots. RNAi-mediated downregulation of one of these genes, Beclin1/Atg6, resulted in a similar phenotype as observed for transgenic roots in which Pv-PI3K had been downregulated. Our findings show that an autophagy-related process is crucial for the mutualistic interactions of P. vulgaris with beneficial microorganisms.

Silver nanoparticles enhance survival of white spot syndrome virus infected Penaeus vannamei shrimps by activation of its immunological system.

The global aquaculture has shown an impressive growth in the last decades contributing with a major part of total food fish supply. However, it also helps in the spread of diseases that in turn, causes great economic losses. The White Spot Syndrome Virus (WSSV) is one of the major viral pathogen for the shrimp aquaculture industry. Several attempts to eliminate the virus in the shrimp have been addressed without achieving a long-term effectiveness. In this work, we determine the capacity of the commercial non-toxic PVP-coated silver nanoparticles to promote the response of the immune system of WSSV-infected shrimps with or without an excess of iron ions. Our results showed that a single dose of metallic silver in the nanomolar range (111 nmol/shrimp), which is equivalent to 12 ng/mL of silver nanoparticles, produces 20% survival of treated infected shrimps. The same concentration administered in healthy shrimps do not show histological evidence of damage. The observed survival rate could be associated with the increase of almost 2-fold of LGBP expression levels compared with non-treated infected shrimps. LGBP is a key gene of shrimp immunological response and its up-regulation is most probably induced by the recognition of silver nanoparticles coating by specific pathogen-associated molecular pattern recognition proteins (PAMPs) of shrimp. Increased LGBP expression levels was observed even with a 10-fold lower dose of silver nanoparticles (1.2 ng/shrimp, 0.011 nmol of metallic silver/shrimp). The increase in LGBP expression levels was also observed even in the presence of iron ion excess, a condition that favors virus proliferation. Those results showed that a single dose of a slight amount of silver nanoparticles were capable to enhance the response of shrimp immune system without toxic effects in healthy shrimps. This response could be enhanced by administration of other doses and might represent an important alternative for the treatment of a disease that has still no cure, white spot syndrome virus.

Identification of a 'Candidatus Phytoplasma hispanicum'-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball).

The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of 'CandidatusPhytoplasma' (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to 'CandidatusPhytoplasma hispanicum', which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.

Molecular Insights into the Role of Sterols in Microtuber Development of Potato Solanum tuberosum L.

Potato tubers are reproductive and storage organs, enabling their survival. Unraveling the molecular mechanisms that regulate tuberization is crucial for understanding how potatorespond to environmental stress situations and for potato breeding. Previously, we did a transcriptomic analysis of potato microtuberization without light. This showed that important cellular processes like ribosomal proteins, cell cycle, carbon metabolism, oxidative stress, fatty acids, and phytosterols (PS) biosynthesis were closely connected in a protein-protein interaction (PPI) network. Research on PS function during potato tuberization has been scarce. PS plays a critical role in regulating membrane permeability and fluidity, and they are biosynthetic precursors of brassinosteroids (BRs) in plants, which are critical in regulating gene expression, cell division, differentiation, and reproductive biology. Within a PPI network, we found a module of 15 genes involved in the PS biosynthetic process. Darkness, as expected, activated the mevalonate (MVA) pathway. There was a tight interaction between three coding gene products for HMGR3, MVD2, and FPS1, and the gene products that synthetize PS, including CAS1, SMO1, BETAHSD, CPI1, CYP51, FACKEL, HYDRA1, SMT2, SMO2, STE1, and SSR1. Quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the expression analysis of ten specific genes involved in the biosynthesis of PS. This manuscript discusses the potential role of genes involved in PS biosynthesis during microtuber development.

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom.

At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.

Down-regulation of PvTRE1 enhances nodule biomass and bacteroid number in the common bean.

Legume-rhizobium interactions have been widely studied and characterized, and the disaccharide trehalose has been commonly detected during this symbiotic interaction. It has been proposed that trehalose content in nodules during this symbiotic interaction might be regulated by trehalase. In the present study, we assessed the role of trehalose accumulation by down-regulating trehalase in the nodules of common bean plants. We performed gene expression analysis for trehalase (PvTRE1) during nodule development. PvTRE1 was knocked down by RNA interference (RNAi) in transgenic nodules of the common bean. PvTRE1 expression in nodulated roots is mainly restricted to nodules. Down-regulation of PvTRE1 led to increased trehalose content (78%) and bacteroid number (almost one order of magnitude). In addition, nodule biomass, nitrogenase activity, and GOGAT transcript accumulation were significantly enhanced too. The trehalose accumulation, triggered by PvTRE1 down-regulation, led to a positive impact on the legume-rhizobium symbiotic interaction. This could contribute to the agronomical enhancement of symbiotic nitrogen fixation.

Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions.

Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.

Bacterial communities of the psyllid pest Bactericera cockerelli (Hemiptera: Triozidae) Central haplotype of tomato crops cultivated at different locations of Mexico.

Background: The psyllid, Bactericera cockerelli, is an insect vector of 'Candidatus Liberibacter' causing "Zebra chip" disease that affects potato and other Solanaceae crops worldwide. In the present study, we analyzed the bacterial communities associated with the insect vector Bactericera cockerelli central haplotype of tomato crop fields in four regions from Mexico. Methods: PCR was used to amplify the mitochondrial cytochrome oxidase I gene (mtCOI) and then analyze the single nucleotide polymorphisms (SNP) and phylogenetic analysis for haplotype identification of the isolated B. cockerelli. Moreover, we carried out the microbial diversity analysis of several B. cockerelli collected from four regions of Mexico through the NGS sequencing of 16S rRNA V3 region. Finally, Wolbachia was detected by the wsp gene PCR amplification, which is the B. cockerelli facultative symbiont. Also we were able to confirm the relationship with several Wolbachia strains by phylogenetic analysis. Results: Our results pointed that B. cockerelli collected in the four locations from Mexico (Central Mexico: Queretaro, and Northern Mexico: Sinaloa, Coahuila, and Nuevo Leon) were identified, such as the central haplotype. Analyses of the parameters of the composition, relative abundance, and diversity (Shannon index: 1.328 ± 0.472; Simpson index 0.582 ± 0.167), showing a notably relatively few microbial species in B. cockerelli. Analyses identified various facultative symbionts, particularly the Wolbachia (Rickettsiales: Anaplasmataceae) with a relative abundance higher. In contrast, the genera of Sodalis and 'Candidatus Carsonella' (Gammaproteobacteria: Oceanospirillales: Halomonadaceae) were identified with a relatively low abundance. On the other hand, the relative abundance for the genus 'Candidatus Liberibacter' was higher only for some of the locations analyzed. PCR amplification of a fragment of the gene encoding a surface protein (wsp) of Wolbachia and phylogenetic analysis corroborated the presence of this bacterium in the central haplotype. Beta-diversity analysis revealed that the presence of the genus 'Candidatus Liberibacter' influences the microbiota structure of this psyllid species. Conclusions: Our data support that the members with the highest representation in microbial community of B. cockerelli central haplotype, comprise their obligate symbiont, Carsonella, and facultative symbionts. We also found evidence that among the factors analyzed, the presence of the plant pathogen affects the structure and composition of the bacterial community associated with B. cockerelli.

Long-Lasting Defence Priming by ß-Aminobutyric Acid in Tomato Is Marked by Genome-Wide Changes in DNA Methylation.

Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed state, whereby responses to future stress encounters are enhanced. Stress priming can be long-lasting and likely involves epigenetic regulation of stress-responsive gene expression. However, the molecular events underlying priming are not well understood. Here, we characterise epigenetic changes in tomato plants primed for pathogen resistance by treatment with ß-aminobutyric acid (BABA). We used whole genome bisulphite sequencing to construct tomato methylomes from control plants and plants treated with BABA at the seedling stage, and a parallel transcriptome analysis to identify genes primed for the response to inoculation by the fungal pathogen, Botrytis cinerea. Genomes of plants treated with BABA showed a significant reduction in global cytosine methylation, especially in CHH sequence contexts. Analysis of differentially methylated regions (DMRs) revealed that CHH DMRs were almost exclusively hypomethylated and were enriched in gene promoters and in DNA transposons located in the chromosome arms. Genes overlapping CHH DMRs were enriched for a small number of stress response-related gene ontology terms. In addition, there was significant enrichment of DMRs in the promoters of genes that are differentially expressed in response to infection with B. cinerea. However, the majority of genes that demonstrated priming did not contain DMRs, and nor was the overall distribution of methylated cytosines in primed genes altered by BABA treatment. Hence, we conclude that whilst BABA treatment of tomato seedlings results in characteristic changes in genome-wide DNA methylation, CHH hypomethylation appears only to target a minority of genes showing primed responses to pathogen infection. Instead, methylation may confer priming via in-trans regulation, acting at a distance from defence genes, and/or by targeting a smaller group of regulatory genes controlling stress responses.

Habanero pepper (Capsicum chinense) adaptation to water-deficit stress in a protected agricultural system.

Drought is one of the major factors limiting global crop yield. In Mexico, agriculture is expected to be severely affected by drought. The Capsicum genus has several crop species of agricultural importance. In this work, we analysed the Capsicum chinense plant physiological responses and differentially expressed genes under water stress mainly focused on the responses elicited following recovery through repetitive stress. Plants were cultivated in an experimental block. Each block consisted of plants under water deficit and a control group without deficit. Morphometric and functional parameters, and the expression of genes related to resistance to abiotic stresses were measured. Morphological differences were observed. Plants subjected to water deficit showed impaired growth. Nonetheless, in the physiological parameters, no differences were observed between treatments. We selected abiotic stress-related genes that include heat-shock proteins (HSPs), heat-shock factors (HSFs), transcription factors related to abiotic stress (MYB, ETR1 , and WRKY ), and those associated with biotic and abiotic stress responses (Jar1 and Lox2 ). HSF, HSP, MYB72, ETR1, Jar1, WRKYa , and Lox2 genes were involved in the response to water-deficit stress in C. chinense plants. In conclusion, our work may improve our understanding of the morphological, physiological, and molecular mechanisms underlying hydric stress response in C. chinense .

Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs.

Background: Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges. Methods: Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances. Results: The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths. Conclusion: Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports that the sponge microbiome is highly host specific.

Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.).

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N2. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors.

Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico.

BACKGROUND: The begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates. METHODS: The full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed. RESULTS: The SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade. CONCLUSIONS: SLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico.

Improvement of drought tolerance and grain yield in common bean by overexpressing trehalose-6-phosphate synthase in rhizobia.

Improving stress tolerance and yield in crops are major goals for agriculture. Here, we show a new strategy to increase drought tolerance and yield in legumes by overexpressing trehalose-6-phosphate synthase in the symbiotic bacterium Rhizobium etli. Phaseolus vulgaris (common beans) plants inoculated with R. etli overexpressing trehalose-6-phosphate synthase gene had more nodules with increased nitrogenase activity and higher biomass compared with plants inoculated with wild-type R. etli. In contrast, plants inoculated with an R. etli mutant in trehalose-6-phosphate synthase gene had fewer nodules and less nitrogenase activity and biomass. Three-week-old plants subjected to drought stress fully recovered whereas plants inoculated with a wild-type or mutant strain wilted and died. The yield of bean plants inoculated with R. etli overexpressing trehalose-6-phosphate synthase gene and grown with constant irrigation increased more than 50%. Macroarray analysis of 7,200 expressed sequence tags from nodules of plants inoculated with the strain overexpressing trehalose-6-phosphate synthase gene revealed upregulation of genes involved in stress tolerance and carbon and nitrogen metabolism, suggesting a signaling mechanism for trehalose. Thus, trehalose metabolism in rhizobia is key for signaling plant growth, yield, and adaptation to abiotic stress, and its manipulation has a major agronomical impact on leguminous plants.

Down-regulation of PvTRX1h increases nodule number and affects auxin, starch, and metabolic fingerprints in the common bean (Phaseolus vulgaris L.).

The legume-rhizobium symbiotic relationship has been widely studied and characterized. However, little information is available about the role of histone lysine methyltransferases in the legume-rhizobium interaction and in the formation of nitrogen-fixing nodules in the common bean. Thus, this study aimed to gain a better understanding of the epigenetic control of nodulation in the common bean. Specifically, we studied the role of PvTRX1h, a histone lysine methyltransferase coding gene, in nodule development and auxin biosynthesis. Through a reverse genetics approach, we generated common bean composite plants to knock-down PvTRX1h expression. Here we found that the down-regulation of PvTRX1h increased the number of nodules per plant, but reduced the number of colony-forming units recovered from nodules. Genes coding for enzymes involved in the synthesis of the indole-3-acetic acid were up-regulated, as was the concentration of this hormone. In addition, PvTRX1h down-regulation altered starch accumulation as determined by the number of amyloplasts per nodule. Metabolic fingerprinting by direct liquid introduction-electrospray ionization-mass spectrometry (DLI-ESI-MS) revealed that the root nodules were globally affected by PvTRX1h down-regulation. Therefore, PvTRX1h likely acts through chromatin histone modifications that alter the auxin signaling network to determine bacterial colonization, nodule number, starch accumulation, hormone levels, and cell proliferation.

Use of BABA and INA As Activators of a Primed State in the Common Bean (Phaseolus vulgaris L.).

To survive in adverse conditions, plants have evolved complex mechanisms that "prime" their defense system to respond and adapt to stresses. Their competence to respond to such stresses fundamentally depends on its capacity to modulate the transcriptome rapidly and specifically. Thus, chromatin dynamics is a mechanism linked to transcriptional regulation and enhanced defense in plants. For example, in Arabidopsis, priming of the SA-dependent defense pathway is linked to histone lysine methylation. Such modifications could create a memory of the primary infection that is associated with an amplified gene response upon exposure to a second stress-stimulus. In addition, the priming status of a plant for induced resistance can be inherited to its offspring. However, analyses on the molecular mechanisms of generational and transgenerational priming in the common bean (Phaseolus vulagris L.), an economically important crop, are absent. Here, we provide evidence that resistance to P. syringae pv. phaseolicola infection was induced in the common bean with the synthetic priming activators BABA and INA. Resistance was assessed by evaluating symptom appearance, pathogen accumulation, changes in gene expression of defense genes, as well as changes in the H3K4me3 and H3K36me3 marks at the promoter-exon regions of defense-associated genes. We conclude that defense priming in the common bean occurred in response to BABA and INA and that these synthetic activators primed distinct genes for enhanced disease resistance. We hope that an understanding of the molecular changes leading to defense priming and pathogen resistance will provide valuable knowledge for producing disease-resistant crop varieties by exposing parental plants to priming activators, as well as to the development of novel plant protection chemicals that stimulate the plant's inherent disease resistance mechanisms.