Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (<it>Saccharum spp</it>.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.</p> <p>Results</p> <p>In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species <it>S. officinarum </it>and <it>S. spontaneum</it>. Using sugarcane <it>MIR827 </it>as a query, we found a novel <it>MIR827 </it>precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as <it>SsCBP1</it>. <it>SsCBP1 </it>was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of <it>SsCBP1 </it>by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots.</p> <p>Conclusions</p> <p>Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.</p

Characterization and Seasonal Dynamics of Tick Populations in Dairy Cattle Production Systems of Northwestern Colombian Amazon

Cattle ticks are a significant health concern in tropical livestock production due to their hematophagous behavior and potential as vectors for human and animal pathogens. In this study, we investigated the tick population present in dairy cattle production, calves, and grazing areas of livestock systems in the northwestern Colombian Amazon. Identification was based on taxonomic keys and molecular markers. Phylogenetic relationships were established using mitochondrial COX1 and 16S genes. Population structure analysis was performed considering age, racial type (B. indicus vs. B. taurus), and the influence of environmental factors and the geomorphological landscape on tick population dynamics. Our findings revealed the presence of a single tick species, with a unique haplotype identified for each mitochondrial gene assessed. Phylogenetic analysis classified the found species within Clade A of the Rhipicephalus microplus complex. Ticks were more prevalent during periods of low rainfall and high temperature, and B. taurus cows exhibited the highest tick abundance. Thus, these results provide insights into the population characteristics and distribution of the tick species present in dairy cattle production systems in the northwestern part of the Colombian Amazon. This information is fundamental for developing targeted strategies based on seasonal variation and host characteristics to mitigate tick infestation severity in the region

Soil enzyme responses to land use change in the tropical rainforest of the Colombian Amazon region

Soil enzymes mediate key processes and functions of the soils, such as organic matter decomposition and nutrient cycling in both natural and agricultural ecosystems. Here, we studied the activity of five extracellular soil enzymes involved in the C, N, and P-mineralizing process in both litter and surface soil layer of rainforest in the northwest region of the Colombian Amazon and the response of those soil enzymes to land use change. The experimental study design included six study sites for comparing long-term pasture systems to native forest and regeneration practices after pasture, within the main landscapes of the region, mountain and hill landscapes separately. Results showed considerable enzymatic activity in the litter layer of the forest, highlighting the vital role of this compartment in the nutrient cycling of low fertility soils from tropical regions. With the land use transition to pastures, changes in soil enzymatic activities were driven by the management of pastures, with SOC and N losses and reduced absolute activity of soil enzymes in long-term pastures under continuous grazing (25 years). However, the enzyme activities expressed per unit of SOC did not show changes in C and N-acquiring enzymes, suggesting a higher mineralization potential in pastures. Enzymatic stoichiometry analysis indicated a microbial P limitation that could lead to a high catabolic activity with a potential increase in the use of SOC by microbial communities in the search for P, thus affecting soil C sequestration, soil quality and the provision of soil-related ecosystem services.</jats:p

Responses of Soil Phosphorus Fractions to Land-Use Change in Colombian Amazon

Intensive land-use change, the overgrazing of pastures, and the poor soil management in the Amazon region induce significant soil chemical degradation, causing alterations in the soil phosphorus (P) dynamics. Here, we studied the changes in P fractions and availability throughout the soil profile along a chronosequence composed of four study areas representing the typical land-use transition from forest to pasture for extensive cattle ranching in the Colombian Amazon region: (i) Forest—Deforested—Pasture 4 years old and Pasture established &gt;25 years after deforestation. Soil samples collected at 0–10, 10–20, 20–30, and 30–40 cm depth were used for the sequential fractionation of P, determination of acid phosphatase activity and soil organic carbon (C) content, and calculation of C:organic P (Po) ratio and P stocks. Our results showed that the land-use change caused a decrease of 31.1% in the fractions of labile inorganic P, with the mineralization of organic P by phosphatase enzyme playing an essential role in the P availability. Although according to the C:Po ratio of the deeper layer the P seems to be sufficient to satisfy the plant needs of all the land uses assessed, the exploitation of soil nutrients in pastures reduced by 6.1% the moderately and non-labile P stock. Given the role of cattle ranching in the economy of tropical countries, it is imperative to adopt strategies of soil P management to improve P-use efficiency, avoiding the degradation of grazing land resources while ensuring the long-term sustainability of rangeland livestock and decrease further deforestation of the Amazon rainforest.</jats:p

Fresh matter and biochemical characteristics of forest litter layer from Colombian Amazon region.

Fresh matter and biochemical characteristics of forest litter layer from Colombian Amazon region.</p

β-1,4-glucosidase, β-D-cellobiohydrolase, β-D-xylosidase, β-1,4-N-acetylglucosaminidase, acid phosphatase enzymes activities in soil and litter of forest mountain landscape sites over an Andes-Amazon transition in Colombian Amazon region.

Error bars denote standard error. Asterisks indicate that the means values of soil and litter differ significantly between themselves to the level p p p <0.001 (***) for each study site, according to the Student’s Test.</p

Stoichiometry enzymes activity in forest litter and soil in Colombian Amazon region.

Stoichiometry enzymes activity in forest litter and soil in Colombian Amazon region.</p

Specific activity per unit of SOC of soil enzymes β-Glucosidase, β-D-Celobiosidase, β-D-Xylosidase, N-acetyl-β-D-Glucosaminidase, acid phosphatase in pristine forest and pastures located in hills landscape (SVC: San Vicente del Caguan, CTG: Cartagena del Chaira, SLN: Solano) of Colombian Amazon region.

Error bars denote error deviation. The asterisk indicates that the means values of soil and litter differ significantly between themselves (p<0.05) for each study site, according to the Student’s Test.</p

Responses of Soil Phosphorus Fractions to Land-Use Change in Colombian Amazon

Intensive land-use change, the overgrazing of pastures, and the poor soil management in the Amazon region induce significant soil chemical degradation, causing alterations in the soil phosphorus (P) dynamics. Here, we studied the changes in P fractions and availability throughout the soil profile along a chronosequence composed of four study areas representing the typical land-use transition from forest to pasture for extensive cattle ranching in the Colombian Amazon region: (i) Forest&mdash;Deforested&mdash;Pasture 4 years old and Pasture established &gt;25 years after deforestation. Soil samples collected at 0&ndash;10, 10&ndash;20, 20&ndash;30, and 30&ndash;40 cm depth were used for the sequential fractionation of P, determination of acid phosphatase activity and soil organic carbon (C) content, and calculation of C:organic P (Po) ratio and P stocks. Our results showed that the land-use change caused a decrease of 31.1% in the fractions of labile inorganic P, with the mineralization of organic P by phosphatase enzyme playing an essential role in the P availability. Although according to the C:Po ratio of the deeper layer the P seems to be sufficient to satisfy the plant needs of all the land uses assessed, the exploitation of soil nutrients in pastures reduced by 6.1% the moderately and non-labile P stock. Given the role of cattle ranching in the economy of tropical countries, it is imperative to adopt strategies of soil P management to improve P-use efficiency, avoiding the degradation of grazing land resources while ensuring the long-term sustainability of rangeland livestock and decrease further deforestation of the Amazon rainforest