The Complete Genome Sequences of 12 Species of Plants from the Yucatan Peninsula, Mexico.

We present the complete genome sequences of 12 species of plants from Campeche, Mexico and the greater Yucatan Peninsula: Agave americana, Agave angustifolia, Agave fourcroydes, Agave karwinskii, Agave potatorum, Agave tequiliana, Annona squamosa, Cedrela odorata, Pouteria campechiana, Pouteria glomerata, Trichilia hirta and Trichilia minutiflora.

Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation.

As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/-) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI- modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response.

Enhanced Cd-Accumulation in Typha latifolia by Interaction with Pseudomonas rhodesiae GRC140 under Axenic Hydroponic Conditions.

The Typha genus comprises plant species extensively studied for phytoremediation processes. Recently, Pseudomonas rhodesiae GRC140, an IAA-producing bacterium, was isolated from Typha latifolia roots. This bacterium stimulates the emergence of lateral roots of Arabidopsis thaliana in the presence and absence of cadmium. However, the bacterial influence on cadmium accumulation by the plant has not been determined. Moreover, the P. rhodesiae GRC140 effect in Cd phytoextraction by T. latifolia remains poorly understood. In this work, an axenic hydroponic culture of T. latifolia was established. The plants were used to evaluate the effects of cadmium stress in axenic plants and determine the effects of P. rhodesiae GRC140 and exogenous indole acetic acid (IAA) on Cd tolerance and Cd uptake by T. latifolia. Biomass production, total chlorophyll content, root electrolyte leakage, catalase activity, total glutathione, and Cd content were determined. The results showed that Cd reduces shoot biomass and increases total glutathione and Cd content in a dose-dependent manner in root tissues. Furthermore, P. rhodesiae GRC140 increased Cd translocation to the shoots, while IAA increased the Cd accumulation in plant roots, indicating that both treatments increase Cd removal by T. latifolia plants. These results indicate that axenic plants in hydroponic systems are adequate to evaluate the Cd effects in plants and suggest that T. latifolia phytoextraction abilities could be improved by P. rhodesiae GRC140 and exogenous IAA application.

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber.

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.

Phage Therapy for Crops: Concepts, Experimental and Bioinformatics Approaches to Direct Its Application.

Phage therapy consists of applying bacteriophages, whose natural function is to kill specific bacteria. Bacteriophages are safe, evolve together with their host, and are environmentally friendly. At present, the indiscriminate use of antibiotics and salt minerals (Zn2+ or Cu2+) has caused the emergence of resistant strains that infect crops, causing difficulties and loss of food production. Phage therapy is an alternative that has shown positive results and can improve the treatments available for agriculture. However, the success of phage therapy depends on finding effective bacteriophages. This review focused on describing the potential, up to now, of applying phage therapy as an alternative treatment against bacterial diseases, with sustainable improvement in food production. We described the current isolation techniques, characterization, detection, and selection of lytic phages, highlighting the importance of complementary studies using genome analysis of the phage and its host. Finally, among these studies, we concentrated on the most relevant bacteriophages used for biocontrol of Pseudomonas spp., Xanthomonas spp., Pectobacterium spp., Ralstonia spp., Burkholderia spp., Dickeya spp., Clavibacter michiganensis, and Agrobacterium tumefaciens as agents that cause damage to crops, and affect food production around the world.

Resiliencia de la cobertura vegetal en el Suroeste de México ante los efectos del cambio climático / Resilience of vegetation cover in Southwest Mexico to the climate change effects

Resumen El modelado de escenarios de cambios climáticos utilizando sistemas de información geográfica para estimar la resiliencia de la cobertura vegetal es una herramienta útil para proyectar impactos futuros e implementar estrategias de conservación o manejo. En el presente trabajo asociamos espacialmente la biodiversidad de la cobertura vegetal del Suroeste de México con su capacidad para adaptarse a los efectos del cambio climático. Para analizar esta asociación se estimaron índices de riqueza y diversidad de especies, y su relación con escenarios de clima futuro. Se utilizaron los registros geográficos del Inventario Nacional Forestal y de Suelos para ocho comunidades vegetales (arbórea, arbustiva, herbácea, palma, cactus, bejucos, helechos y xerófita) distribuidas entre Guerrero, Oaxaca y Chiapas. La proyección climática fue al 2050, con modelos de circulación global A2 (promedio CCCMA, HADCM3 y CSIRO), 19 variables bioclimáticas y una resolución de 2.5 minutos. Los escenarios de cambio climático se modelaron con el algoritmo MaxEnt y la riqueza de especies, índice de diversidad y regresiones espaciales con el software Diva-GIS v7.5. Los modelos de regresión espacial estimaron que a mayor riqueza y diversidad de especies mayor seria la resiliencia que mostraría el ecosistema. Las comunidades vegetales cactus, palma y xerófita mostraron mayor vulnerabilidad al cambio climático. Las variaciones en la estacionalidad de la temperatura resultó ser el factor que condicionaría su distribución futura. Por lo que, las estrategias de conservación o manejo deberían considerar a la diversidad como un agente del ecosistema que amortiguaría a los efectos negativos del clima futuro.

Abstract The scenarios modeling of climate changes using geographic information systems to estimate the vegetation cover resilience is a useful tool to project future impacts and implement conservation or management strategies. We associate spatially the biodiversity of the vegetation cover of Southwest Mexico with its ability to adapt to the effects of climate change. We analysis this association estimating species richness and diversity indices, and its relationship with scenarios of future climate. Geographical records of the National Forest and Soil Inventory were obtained for eight plant communities (arboreal, shrubby, herbaceous, palm, cactus, vines, ferns, and xerophyte) distributed in Guerrero, Oaxaca, and Chiapas. The climatic projection was to 2050, with global circulation A2 models (CCCMA, HADCM3 and CSIRO average), 19 bioclimatic variables and a resolution of 2.5 minutes. Climate change scenarios were modelled with the MaxEnt algorithm and species richness, diversity index, and spatial regressions with Diva-GIS v7.5 software. The spatial regression models estimated that higher richness and species diversity, the greater resilience that the ecosystem would show. The cactus, palm, and xerophytic plant communities presented greater vulnerability to climate change. Variations in temperature seasonality turned out to be the factor that would condition its future distribution. Therefore, in conservation or management strategies, diversity should be considered as an agent of the ecosystem that cushions the negative effects of future climate.

Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots.

Together with their undeniable role in the ecology of arid and semiarid ecosystems, Agave species are emerging as a model to dissect the relationships between crassulacean acid metabolism and high efficiency of light and water use, and as an energy crop for bioethanol production. Transcriptome resources from economically valuable Agaves species, such as Agave tequilana and A. salmiana, as well as hybrids for fibers, are now available, and multiple gene expression landscape analyses have been reported. Key components in molecular mechanisms underlying drought tolerance could be uncovered by analyzing gene expression patterns of roots. This study describes an efficient protocol for high-quality total RNA isolation from phenolic compounds-rich Agave roots. Our methodology involves suitable root handling and collecting in the field and using saving-time commercial kits available. RNA isolated from roots free of lignified out-layers and clean cortex showed high values of quality and integrity according to electrophoresis and microfluidics-based platform. Synthesis of long full-length cDNAs and PCR amplification tested the suitability for downstream applications of extracted RNA. The protocol was applied successfully to A. tequilana roots but can be used for other Agave species that also develop lignified epidermis/exodermis in roots.

Unravelling Chemical Composition of Agave Spines: News from Agave fourcroydes Lem.

Spines are key plant modifications developed to deal against herbivores; however, its physical structure and chemical composition have been little explored in plant species. Here, we took advantage of high-throughput chromatography to characterize chemical composition of Agave fourcroydes Lem. spines, a species traditionally used for fiber extraction. Analyses of structural carbohydrate showed that spines have lower cellulose content than leaf fibers (52 and 72%, respectively) but contain more than 2-fold the hemicellulose and 1.5-fold pectin. Xylose and galacturonic acid were enriched in spines compared to fibers. The total lignin content in spines was 1.5-fold higher than those found in fibers, with elevated levels of syringyl (S) and guaiacyl (G) subunits but similar S/G ratios within tissues. Metabolomic profiling based on accurate mass spectrometry revealed the presence of phenolic compounds including quercetin, kaempferol, (+)-catechin, and (-)-epicatechin in A. fourcroydes spines, which were also detected in situ in spines tissues and could be implicated in the color of these plants' structures. Abundance of (+)-catechins could also explain proanthocyanidins found in spines. Agave spines may become a plant model to obtain more insights about cellulose and lignin interactions and condensed tannin deposition, which is valuable knowledge for the bioenergy industry and development of naturally dyed fibers, respectively.

Bark water storage capacity influences epiphytic orchid preference for host trees.

PREMISE: Of all orchid species described, 70% live on phorophytes. Trees offer a vital space with characteristics that influence the successful establishment and life cycle of orchids. Field inventory and distribution analysis suggest that phorophyte selection is biased to certain tree species that would serve as better hosts. Phorophyte bark is known as an important factor that influences this preference, but the chemical and physical properties of bark that contribute to creating a favorable space for orchids are still poorly understood. In this work, the effect of bark physical characteristics on phorophyte preference of tropical orchids was studied. METHODS: Orchids and their phorophytes were counted and identified along transects inside two natural reserves in Southeast Mexico. A rhytidome classification was used to describe the bark decoration patterns of the phorophytes. To quantify bark fissuring, we developed a new protocol based on image processing of light micrographs using free-access software. Bark topology characterization was complemented with scanning electronic microscopy. Maximum and minimum water content was also determined. RESULTS: Analyses of bark decorations and bark fissuring were not enough to explain the preference found for some tropical trees. In contrast, a positive relationship was found among water-storage capacity, bark porosity, and phorophyte preference. The host trees preferred by most orchids have bark with higher pore density and higher water retention after draining. CONCLUSIONS: Unexpectedly, the phorophytes preferred by orchids are not those with more fissured bark but those with a higher ability to retain minimum water content after draining, which is a bark property positively correlated with higher pore density. Our data indicate that the bark microenvironment, determined by topology and water storage capacity, has a pivotal role in phorophyte specificity, a key factor that affects orchid diversity and distribution in the world.

PvLOX2 silencing in common bean roots impairs arbuscular mycorrhiza-induced resistance without affecting symbiosis establishment.

The arbuscular mycorrhizal (AM) symbiosis is an intimate association between specific soil-borne fungi and the roots of most land plants. AM colonisation elicits an enhanced defence resistance against pathogens, known as mycorrhizal-induced resistance (MIR). This mechanism locally and systemically sensitises plant tissues to boost their basal defence response. Although a role for oxylipins in MIR has been proposed, it has not yet been experimentally confirmed. In this study, when the common bean (Phaseolus vulgaris L.) lipoxygenase PvLOX2 was silenced in roots of composite plants, leaves of silenced plants lost their capacity to exhibit MIR against the foliar pathogen Sclerotinia sclerotiorum, even though they were colonised normally. PvLOX6, a LOX gene family member, is involved in JA biosynthesis in the common bean. Downregulation of PvLOX2 and PvLOX6 in leaves of PvLOX2 root-silenced plants coincides with the loss of MIR, suggesting that these genes could be involved in the onset and spreading of the mycorrhiza-induced defence response.

APSR1, a novel gene required for meristem maintenance, is negatively regulated by low phosphate availability.

Proper root growth is crucial for anchorage, exploration, and exploitation of the soil substrate. Root growth is highly sensitive to a variety of environmental cues, among them water and nutrient availability have a great impact on root development. Phosphorus (P) availability is one of the most limiting nutrients that affect plant growth and development under natural and agricultural environments. Root growth in the direction of the long axis proceeds from the root tip and requires the coordinated activities of cell proliferation, cell elongation and cell differentiation. Here we report a novel gene, APSR1 (Altered Phosphate Starvation Response1), involved in root meristem maintenance. The loss of function mutant apsr1-1 showed a reduction in primary root length and root apical meristem size, short differentiated epidermal cells and long root hairs. Expression of APSR1 gene decreases in response to phosphate starvation and apsr1-1 did not show the typical progressive decrease of undifferentiated cells at root tip when grown under P limiting conditions. Interestingly, APSR1 expression pattern overlaps with root zones of auxin accumulation. Furthermore, apsr1-1 showed a clear decrease in the level of the auxin transporter PIN7. These data suggest that APSR1 is required for the coordination of cell processes necessary for correct root growth in response to phosphate starvation conceivably by direct or indirect modulation of PIN7. We also propose, based on its nuclear localization and structure, that APSR1 may potentially be a member of a novel group of transcription factors.