Fangru Nan

Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence

Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415–484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.

Nutrients removal from undiluted cattle farm wastewater by the two-stage process of microalgae-based wastewater treatment

Chlorella vulgaris was selected from five freshwater microalgal strains of Chlorophyta, and showed a good potential in nutrients removal from undiluted cattle farm wastewater. By the end of treatment, 62.30%, 81.16% and 85.29% of chemical oxygen demand (COD), ammonium (NH4+-N) and total phosphorus (TP) were removed. Then two two-stage processes were established to enhance nutrients removal efficiency for meeting the discharge standards of China. The process A was the biological treatment via C. vulgaris followed by the biological treatment via C. vulgaris, and the process B was the biological treatment via C. vulgaris followed by the activated carbon adsorption. After 3-5 d of treatment of wastewater via the two processes, the nutrients removal efficiency of COD, NH4+-N and TP were 91.24%-92.17%, 83.16%-94.27% and 90.98%-94.41%, respectively. The integrated two-stage process could strengthen nutrients removal efficiency from undiluted cattle farm wastewater with high organic substance and nitrogen concentration.

Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis

ABSTRACT Eucheuma denticulatum, an economically and industrially important red alga, is a valuable marine resource. Although microRNAs (miRNAs) play an essential role in gene post-transcriptional regulation, no research has been conducted to identify and characterize miRNAs in E. denticulatum. In this study, we identified 134 miRNAs (133 conserved miRNAs and one novel miRNA) from 2,997,135 small-RNA reads by high-throughput sequencing combined with bioinformatics analysis. BLAST searching against miRBase uncovered 126 potential miRNA families. A conservation and diversity analysis of predicted miRNA families in different plant species was performed by comparative alignment and homology searching. A total of 4 and 13 randomly selected miRNAs were respectively validated by northern blotting and stem-loop reverse transcription PCR, thereby demonstrating the reliability of the miRNA sequencing data. Altogether, 871 potential target genes were predicted using psRobot and TargetFinder. Target genes classification and enrichment were conducted based on Gene Ontology analysis. The functions of target gene products and associated metabolic pathways were predicted by Kyoto Encyclopedia of Genes and Genomes pathway analysis. A Cytoscape network was constructed to explore the interrelationships of miRNAs, miRNA-target genes and target genes. A large number of miRNAs with diverse target genes will play important roles for further understanding some essential biological processes in E. denticulatum. The uncovered information can serve as an important reference for the protection and utilization of this unique red alga in the future.

Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis

Chondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117 C. crispus miRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes in C. crispus by constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.

Transcriptome analysis of the typical freshwater rhodophytes Sheathia arcuata grown under different light intensities

The Rhodophyta Sheathia arcuata is exclusively distributed in freshwater, constituting an important component in freshwater flora. This study presents the first transcriptome profiling of freshwater Rhodophyta taxa. A total of 161,483 assembled transcripts were identified, annotated and classified into different biological categories and pathways based on BLAST against diverse databases. Different gene expression patterns were caused principally by different irradiances considering the similar water conditions of the sampling site when the specimens were collected. Comparison results of gene expression levels under different irradiances revealed that photosynthesis-related pathways significantly up-regulated under the weak light. Molecular responses for improved photosynthetic activity include the transcripts corresponding to antenna proteins (LHCA1 and LHCA4), photosynthetic apparatus proteins (PSBU, PETB, PETC, PETH and beta and gamma subunits of ATPase) and metabolic enzymes in the carbon fixation. Along with photosynthesis, other metabolic activities were also regulated to optimize the growing and development of S. arcuata under appropriate sunlight. Protein-protein interactive networks revealed the most responsive up-expressed transcripts were ribosomal proteins. The de-novo transcriptome assembly of S. arcuata provides a foundation for further investigation on the molecular mechanism of photosynthesis and environmental adaption for freshwater Rhodophyta.

The Performance of a Self-Flocculating Microalga Chlorococcum sp. GD in Wastewater with Different Ammonia Concentrations.

The performance of a self-flocculating microalga Chlorococcum sp. GD on the flocculation, growth, and lipid accumulation in wastewater with different ammonia nitrogen concentrations was investigated. It was revealed that relative high ammonia nitrogen concentration (20–50 mg·L−1) was beneficial to the flocculation of Chlorococcum sp. GD, and the highest flocculating efficiency was up to 84.4%. It was also found that the highest flocculating efficiency occurred in the middle of the culture (4–5 days) regardless of initial ammonia concentration in wastewater. It was speculated that high flocculating efficiency was likely related to the production of extracellular proteins. 20 mg·L−1 of ammonia was found to be a preferred concentration for both biomass production and lipid accumulation. 92.8% COD, 98.8% ammonia, and 69.4% phosphorus were removed when Chlorococcum sp. GD was cultivated in wastewater with 20 mg·L−1 ammonia. The novelty and significance of the investigation was the integration of flocculation, biomass production, wastewater treatment, and lipid accumulation, simultaneously, which made Chlorococcum sp. GD a potential candidate for wastewater treatment and biodiesel production if harvested in wastewater with suitable ammonia nitrogen concentration.