Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

Background:Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs.Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3’-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results:Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3’-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3’-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions:The identified IPACs corresponding to novel transcripts, 3’-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants.Funding supports were in part from US National Science Foundation (No. 1541737 to QQL), the Hundred Talent Plans of Fujian Province and Xiamen City (to QQL). This project was also funded by the National Natural Science Foundation of China (Nos. 61201358 and 61174161), the Natural Science Foundation of Fujian Province of China (No. 2012J01154), and the specialized Research Fund for the Doctoral Program of Higher Education of China (Nos. 20120121120038 and 20130121130004), and the Fundamental Research Funds for the Central Universities in China (Xiamen University: Nos. 2013121025, 201412G009, and 2014X0234)

Effects of Liquid Organic Fertilizers on Plant Growth and Rhizosphere Soil Characteristics of Chrysanthemum

Organic fertilizers are generally thought to be an effective way to sustain soil fertility and plant growth. To promote the productivity of chrysanthemum, five sources of liquid organic fertilizers (L1–L5), as well as a chemical fertilizer, were applied at an early stage of the growth cycle to investigate their effects on plant growth. In the short-term pot experiment, the liquid organic fertilizers significantly promoted root and aboveground growth by 10.2–77.8% and 10.7–33.3%, respectively, compared with the chemical fertilizer. The order of growth promotion was: L1 (shrimp extracts) > L2 (plant decomposition) > L4 (seaweed extracts)/L5 (fish extracts) > L3 (vermicompost). Morphological and chemical analyses indicated that, compared with other organic fertilizers, the treatment with shrimp extract (L1) produced the greatest increases in root dry weight, total length, surface area, volume, tips, and thick root length, respectively. Furthermore, the shrimp extract treatment significantly increased the nutrient contents and altered the soil’s functional microbial community at the rhizospheric level compared with the chemical fertilizer treatment. Thus, the shrimp extract liquid organic fertilizer could be part of an effective alternative to chemical fertilization during the early stage of chrysanthemum growth

In-Season Yield Prediction of Cabbage with a Hand-Held Active Canopy Sensor

Efficient and precise yield prediction is critical to optimize cabbage yields and guide fertilizer application. A two-year field experiment was conducted to establish a yield prediction model for cabbage by using the Greenseeker hand-held optical sensor. Two cabbage cultivars (Jianbao and Pingbao) were used and Jianbao cultivar was grown for 2 consecutive seasons but Pingbao was only grown in the second season. Four chemical nitrogen application rates were implemented: 0, 80, 140, and 200 kg·N·ha−1. Normalized difference vegetation index (NDVI) was collected 20, 50, 70, 80, 90, 100, 110, 120, 130, and 140 days after transplanting (DAT). Pearson correlation analysis and regression analysis were performed to identify the relationship between the NDVI measurements and harvested yields of cabbage. NDVI measurements obtained at 110 DAT were significantly correlated to yield and explained 87–89% and 75–82% of the cabbage yield variation of Jianbao cultivar over the two-year experiment and 77–81% of the yield variability of Pingbao cultivar. Adjusting the yield prediction models with CGDD (cumulative growing degree days) could make remarkable improvement to the accuracy of the prediction model and increase the determination coefficient to 0.82, while the modification with DFP (days from transplanting when GDD > 0) values did not. The integrated exponential yield prediction equation was better than linear or quadratic functions and could accurately make in-season estimation of cabbage yields with different cultivars between years

Thermophilic Solid-State Anaerobic Digestion of Corn Straw, Cattle Manure, and Vegetable Waste: Effect of Temperature, Total Solid Content, and C/N Ratio

Thermophilic solid-state anaerobic digestion (SS-AD) of agricultural wastes, i.e., corn straw, cattle manure, and vegetable waste, was carried out in this study. The effects of temperature (40-60°C), initial solid content (ISC, 17.5-32.5%), and C/N ratio (15-32 : 1) on biogas production were evaluated using a Box-Behnken experimental design (BBD) combined with response surface methodology (RSM). The results showed that optimization of process parameters is important to promote the SS-AD performance. All the factors, including interactive terms (except the ISC), were significant in the quadratic model for biogas production with SS-AD. Among the three operation parameters, the C/N ratio had the largest effect on biogas production, followed by temperature, and a maximum biogas yield of 241.4 mL gVS-1 could be achieved at 47.3°C, ISC=24.81%, and C/N=22.35. After 20 d of SS-AD, the microbial community structure under different conditions was characterized by high-throughput sequencing, showing that Firmicutes, Bacteroidetes, Chloroflexi, Synergistetes, and Proteobacteria dominated the bacterial community, and that Firmicutes had a competitive advantage over Bacteroidetes at elevated temperatures. The biogas production values and relative abundance of OPB54 and Bacteroidia after 20 d of SS-AD can be fitted well using a quadratic model, implying that OPB54 and Bacteroidia play important roles in the methanogenic metabolism for agricultural waste thermophilic SS-AD

Comparison of Biochar Materials Derived from Coconut Husks and Various Types of Livestock Manure, and Their Potential for Use in Removal of H2S from Biogas

As a potential adsorbent material, loose, porous livestock manure biochar provides a new approach to livestock manure resource utilization. In this study, coconut husks (CH) and livestock manure, i.e., cow dung (CD), pig manure (PM), and chicken manure (CM) were used as biomass precursors for preparation of biochar via high-temperature pyrolysis and CO2 activation. Characterization technologies, such as scanning electron microscopy, Fourier transform infrared spectroscopy, adsorption–desorption isotherms, and pore size distributions, were used to study the microscopic morphologies and physicochemical properties of unactivated and activated biochar materials. The results showed that CD biochar provides better adsorption performance (up to 29.81 mg H2S/g) than CM or PM biochar. After activation at 650° for 1 h, the best adsorption performance was 38.23 mg H2S/g. For comparison, the CH biochar removal performance was 30.44 mg H2S/g. Its best performance was 38.73 mg H2S/g after 1 h of activation at 750 °C. Its best removal performance is equivalent to that of CH biochar activated at a temperature that is 100 °C higher. Further material characterization indicates that the H2S removal performance of livestock-manure–derived biochar is not entirely dependent on the specific surface area, but is closely related to the pore size distribution