Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa.

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.

Different Amounts of Nitrogen Fertilizer Applications Alter the Bacterial Diversity and Community Structure in the Rhizosphere Soil of Sugarcane.

Sugarcane cropping systems receive elevated application of nitrogen (N) fertilizer for higher production, which may affect production costs and cause environmental pollution. Therefore, it is critical to elucidate the response of soil microbial to N fertilizer inputs in sugarcane soil. A field experiment was carried out to investigate the effects of optimum (N375, 375 kg N/ha) and excessive (N563, 563 kg N/ha) amounts of N fertilizer on soil bacterial diversity and community structure in a sugarcane cropping system by MiSeq high-throughput sequencing; 50,007 operational taxonomic units (OTUs) were obtained by sequencing the 16S rRNA gene amplicons. Results showed that the most abundant phyla in the sugarcane rhizosphere soil were Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, whose ensemble mean accounted for 74.29%. Different amounts of N application indeed change the bacterial diversity and community structures. Excessive application of N fertilizers significantly decreased the pH and increased the available N in soils and unexpectedly obtained a lower yield. Excessive N resulted in a relatively lower bacterial species richness and significantly increased the relative abundance of phyla Proteobacteria, Acidobacteria, and Bacteroidetes and the genera Sphingomonas and Gemmatimonas, while optimum N treatment significantly increased the phylum Actinobacteria and the genera Bacillus and Nitrospira (P < 0.05). N application shifted the N cycle in nitrification, mainly on the Nitrospira, but showed no significant effect on the genera related to nitrogen fixation, methane oxidation, sulfate reduction, and sulfur oxidation (P > 0.05). Overall, the optimum amount of N application might be conducive to beneficial microorganisms, such as Actinobacteria, Nitrospira, and Bacillus and, thus, result in a healthier ecosystem and higher sustainable crop production.

A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China.

Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant-pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families-which include the critical genes for active component biosynthesis-were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.

Effects of supplementary composts on microbial communities and rice productivity in cold water paddy fields.

Cold water paddy field soils are relatively unproductive, but can be ameliorated by supplementing with inorganic fertilizer from animal waste-based composts. The yield of two rice cultivars was significantly raised by providing either chicken manure or cow dung-based compost. The application of these composts raised the soil pH as well as both the total nitrogen and ammonium nitrogen content, which improved the soil's fertility and raised its nitrification potential. The composts had a measurable effect on the abundance of nitrogencycling- related soil microbes, as measured by estimating the copy number of various bacterial and archaeal genes using quantitative real-time PCR. The abundance of ammonia oxidizing archaea and bacteria was markedly encouraged by the application of chicken manure-based compost. Supplementation with the composts helped promote the availability of soil nitrogen in the cold water paddy field, thereby improving the soil's productivity and increasing the yield of the rice crop.

[Wastewater pollution characteristics from typical intensive pig farms in the Pearl River Delta and its ecological risk assessment].

Based on the wastewater quality investigation data from March 2009 to November 2011, wastewater qualities from typical intensive pig farms were assessed in the Pearl River Delta by single and comprehensive pollution index model. The results showed that key pollutants of piggery wastewater were fecal coliform (FC), total phosphorus (TP), chemical oxygen demand (COD) and biochemical oxygen demand (BOD), with their average mass concentrations of 1.98 x 10(9) CFU.L-1, 158.61 mg.L-1, 5 608.68 mg.L-1 and 1984.34 mg.L-1, respectively; key pollutants of biogas slurry were FC, TP, ammonia nitrogen (NH+4 -N) and suspended substance (SS), with their average mass concentrations of 8. 10 x 10(6) CFU.L-1, 81.76 mg.L-1, 476.24 mg.L-1 and 464.58 mg.L-1, respectively. Under the effect of wastewater pollutants, environment surrounding of typical intensive pig farms was seriously polluted, which decreased gradually from piggery wastewater to biogas slurry, and comprehensive pollution indices were 11.41, 6.91, 5.27, respectively. The risk analysis showed that the high-risk wastewater could never be discharged directly and irrigated crops. After the anaerobic treatment, FC, TP, NH+4 -N and SS were still strong factors with the potential ecological risk in the biogas slurry. In the long run, the ecological risk still exists for direct discharge or irrigation of them, and it is necessary to apply further treatment.

The addition of modified attapulgite reduces the emission of nitrous oxide and ammonia from aerobically composted chicken manure.

UNLABELLED: The acceleration of the composting process and the improvement of compost quality have been explored by evaluating the efficacy of various additives, inoculating with specific microorganisms and the application of various biosurfactants. The magnesium-aluminum silicate attapulgite is a low-cost potential composting additive, but its effects on aerobic composting are unknown. This study investigated the effects of attapulgite application on compost production and quality during the aerobic composting of chicken manure. Addition of attapulgite significantly increased the temperature (p < 0.05) while it reduced compost total organic carbon (TOC) and seed germination indices (GIs) throughout the process. Its addition enhanced nitrate concentrations, promoted organic matter degradation, increased seed germination indices, and accelerated the composting process. Interestingly, attapulgite addition did not increase the population of ammonia-oxidizing bacteria. These results suggest that attapulgite is a good additive for the composting industry. IMPLICATIONS: We investigated the addition of two forms of attapulgite during aerobic composting of chicken manure to determine their effects under strict composting environmental parameter control. Our results provides primary evidence that attapulgite may have potential for application in the composting industry. All treatments showed no increase within the first 15 days. However, emissions increased for all treatments within 15-45 days, reaching approximately 6300, 2000, and 4000 mg/m2 from the control, artifactitious attapulgite, and raw attapulgite treatments, respectively.

Improved composting of poultry feces via supplementation with ammonia oxidizing archaea.

Ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. However, the participation of AOA in the composting process has not been established. The addition of AOA to a compost mix was able to speed up both the onset of the hyperthermic phase and the composting time. The composition of the microflora and the relative abundance were determined by using denaturing gradient gel electrophoresis and quantitative real-time PCR, based on the presence of the archaeal amoA genes. The amplicon profiles allowed some of the major AOA species present in the final compost to be identified, and their relative abundance to be estimated from their amplification intensity. The lower pH during the lower temperature phase of compost served to enhance the nitrogen content of the final compost. The addition of AOA resulted in the expanding diversity of microflora species than that of the natural colonization.

[Impact of high salt stress on Apocynum venetum growth and ionic homeostasis].

A pot experiment was conducted in a net room to study the growth responses and related mechanisms of Apocynum venetum treated with different concentrations (100-400 mmol x L(-1)) of NaCl for 30 days. The biomass accumulation, growth rate, root vigor, salt ion content and mineral ion uptake and distribution were measured. Compared with the control, treatment 100 mmol x L(-1) NaCl had lesser effects on the plant dry mass, but decreased the plant fresh mass and growth rate significantly. With increasing NaCl concentration in the medium, the plant dry mass, fresh mass, and growth rate all decreased significantly. The plant root vigor was obviously higher under 100 and 200 mmol x L(-1) NaCl stress, but decreased significantly under 300-400 mmol x L(-1) NaCl stress. With the increase of NaCl concentration in the medium, the Na+ content in A. venetum roots, stems and leaves increased gradually while the K+ content had a slow decrease, the Ca2+ and Mg2+ contents in leaves decreased obviously, and the Ca2+ content in stems and the Mg2+ content in roots increased in different degree. Under NaCl stress, the K+ /Na+, Ca2+/Na+, and Mg2+/Na+ ratios in roots, stems, and leaves decreased markedly, while the selective absorption and transportation of K+ and Ca2+ increased significantly. The stronger ability of salt exclusion and the higher selective absorption and transportation of K+ and Ca2+ were the key adaptive mechanisms of high salt-tolerance of A. venetum.