BackgroundSmall RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense.ResultsDeep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription.ConclusionOur results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-766) contains supplementary material, which is available to authorized users.

Plants have developed multiple regulatory mechanisms to respond and adapt to stress. Drought stress is one of the major constraints to agricultural productivity worldwide and recent reports have highlighted the importance of plant sRNA in the response and adaptation to water availability. In order to increase our understanding of the roles of sRNA in response to water depletion, cultivars of sugarcane were submitted to treatment of ceasing drip irrigation for 24 hours. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty-eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profiles of eight miRNA were verified in leaf samples from three biological replicates by stem-loop qRT-PCR assay using the cultivars: SP90–1638 - sensitive cultivar- and; SP83–2847 and SP83–5073 - tolerant cultivars. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. Two leaf libraries from individual sugarcane cultivars with contrasting drought-tolerance properties were also analyzed. An enrichment of 22-nt sRNA species was observed in leaf libraries. 22-nt miRNA triggered siRNA production by cleavage of their targets in response to water depletion. A number of genes of the sRNA biogenesis pathway were down-regulated in tolerant genotypes and up-regulated in sensitive in response to water depletion treatment. Our analysis contributes to increase the knowledge on the roles of sRNA in sugarcane submitted to water depletion.

Light is a limiting factor in plant establishment and growth in the understory of forests. In this paper, we assessed acclimation capacity of Siparuna guianensis, an early secondary successional species. We used seedlings and saplings in three regeneration areas with different irradiance regimes to determine the traits that confer photoplasticity. We examined whether these traits differ at different developmental stages. Anatomical characteristics, photochemical efficiency, photosynthetic capacity, and growth were analyzed. Multivariate component analysis revealed the formation of six clusters: three for seedlings (one for each regeneration area) and three for saplings (following the same pattern of seedlings, considering the area). Increased irradiance favored photosynthetic performance, independently of the developmental stage. The same trend was observed for most data on chlorophyll (Chl) a fluorescence and the ratios of net photosynthetic rate/intercellular CO2 concentration (P N /C i ) and P N /PPFD. No parameter indicated photoinhibition stress. The CO 2 -and light-response curve data indicated that seedlings were already acclimated to tolerate variation in irradiance. Anatomical adaptations, such as thickness of leaf blade and of adaxial cuticle, were observed in individuals growing in areas with higher irradiation. Thinning of spongy parenchyma and higher investment into a plant height were observed in seedlings, possibly due to the vertical stratification of CO 2 and light in the understory; because light is a more limiting resource than CO 2 in the lower stratum of the forest. Photoplasticity in S. guianensis is associated with a set of morphological, anatomical, photochemical, and biochemical traits, whereas biochemical performance is best acclimated to variation in irradiance. These traits differed in seedlings and saplings but they were modulated mainly by irradiance in both developmental stages.

Arsenic is a critical contaminant that is released into the environment through geochemical processes and anthropic actions. Two independent hydroponic experiments were performed to evaluate the ecophysiological responses of water hyacinth [Eichhornia crassipes (Mart.) Solms] to As under various stress conditions. In experiment 1, water hyacinth was exposed to As 5+ at concentrations of 0, 0.2, 2.0, and 20 mg L -1 for 0, 2, and 4 d; in experiment 2, water hyacinth was exposed at concentrations of 0, 0.025, 0.05, and 0.1 mg L -1 for 0, 10, and 20 d. In both experiments, As accumulation in plant tissue was proportional to its increase in the nutrient solution; As concentrations were higher in roots than in shoots. Detrimental effects of As on gas exchange were observed and were more pronounced in experiment 1. In experiment 1, at the beginning on the second day of exposure, significant decreases of maximum photochemical efficiency of PSII (F v /F m ), variable chlorophyll fluorescence (F v /F 0 ), and photosynthetic pigment contents were observed in plants exposed to 2.0 and 20 mg(As 5+ ) L -1 . It indicated that damage to the photosynthetic apparatus had occurred. No changes in F v /F m , F v /F 0 , and contents of photosynthetic pigments were observed in the plants grown in the presence of 0.2 mg(As 5+ ) L -1 (in experiment 1) or after any of the treatments in experiment 2, indicating plant tolerance. Elevated nonphotochemical quenching was observed in experiment 2 after 20 d of exposure to As; it was as a part of protection mechanisms of the photosynthetic apparatus in these plants. The results obtained here indicate that the use of water hyacinth for As 5+ removal from highly impacted environments is limited but that it is effective in remediating sites with a low contamination.

Highlights• Early-successional species do not form a homogenous group in responses to stress • Initial restoration conditions can be stressful even in partial shading conditions • The differentiation in species' performances reveals a continuum of adaptive responses