Bacterial community and dissolved organic matter networks in urban river: The role of human influence.

Human activities have significantly altered the biogeochemical cycles of carbon, nitrogen, and sulfur in aquatic ecosystems, leading to ecological problems.This study utilized 16S rRNA gene high-throughput sequencing and excitation-emission matrix parallel factor analysis (EEM-PARAFAC) to evaluate the bacterial community composition and dissolved organic matter structure in the upstream (less impacted) and downstream (severely impacted) sections of the river, with a focus on the interactions between bacterial diversity and dissolved organic matter (DOM) characteristics.Results indicated significant spatial diversity in bacterial communities, with a higher α-diversity upstream compared to the more polluted downstream sections. Environmental parameters, particularly total phosphorus (TP) and dissolved oxygen (DO), were found to significantly influence the distribution and composition of bacterial phyla through redundancy analysis. The pattern of bacterial community assembly has shifted from predominantly deterministic to predominantly stochastic as a result of human activities. The analysis of DOM through EEM-PARAFAC identified three main fluorescent components, reflecting varied sources and interactions with bacterial communities. Upstream, microbial activities predominantly contributed to autochthonous DOM, while downstream, increased inputs of allochthonous DOM from human activities were evident. Furthermore, the study revealed that through the introduction of various organic pollutants and nutrient loads that shift microbial metabolic functions towards increased degradation and transformation of complex organic compounds downstream. Structural equation modeling (SEM) revealed that upstream human activities primarily affected bacterial communities indirectly by altering DOM properties. In contrast, downstream activities had both direct and indirect effects due to higher pollutant loads and more complex environmental conditions. These interactions underline the profound effect of anthropogenic factors on riverine ecosystems and emphasize the importance of managing human impacts to preserve microbial biodiversity and water quality.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis.

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.

The responding mechanism of indigenous bacteria in municipal wastewater inoculated with different concentrations of exogenous microalgae.

Indigenous bacteria popularly exist in real wastewater. Therefore, the potential interaction between bacteria and microalgae is inevitable in microalgae-based wastewater treatment systems. It is likely to affect the performance of systems. Accordingly, the characteristics of indigenous bacteria is worth serious concerning. Here we investigated the response of indigenous bacterial communities to variant inoculum concentrations of Chlorococcum sp. GD in municipal wastewater treatment systems. The removal efficiency of COD, ammonium and total phosphorus were 92.50%-95.55%, 98.00%-98.69%, and 67.80%-84.72%, respectively. The bacterial community responded differently to different microalgal inoculum concentrations, which was mainly affected by microalgal number, ammonium and nitrate. Besides, there were differential co-occurrence patterns and carbon and nitrogen metabolic function of indigenous bacterial communities. All these results indicated that bacterial communities responded significantly to environmental changes caused by the change of microalgal inoculum concentrations. The response of bacterial communities to different microalgal inoculum concentrations was beneficial for forming a stable symbiotic community of both microalgae and bacteria to remove pollutants in wastewater.

A Parachlorella kessleri (Trebouxiophyceae, Chlorophyta) strain tolerant to high concentration of calcium chloride.

Members of coccoid green algae have been documented in various extreme environments. In this article, a unicellular green alga was found to slowly grow in high concentration (3.6 g/L) and pure calcium chloride solution in the laboratory. It was successfully cultured and a taxonomic study combined approaches of morphological and molecular methods was conducted to determine its classification attribution, which was followed by a preliminary physiology research to explore its unique tolerance characteristics against calcium chloride stress. The strain was identified as Parachlorella kessleri by very similar morphology and the same phylogenetic position. The morphological differences among the three species in genus Parachlorella were then discussed and the characteristic traits of absent or thin mucilaginous envelop and mantel-shaped chloroplast for P. kessleri were supported. In addition, the almost strictly spherical shape of adult cells could further distinguish the P. kessleri from the other two species. The tolerant characteristics to CaCl2  stress for this strain were confirmed and the limit concentration was revealed as between 2000 and 4000 times than the standard BG11 culture concentration. Therefore, this P. kessleri strain is expected to be a good material to explore the mechanism of resistance to calcium ions stress for eukaryotic microbiology.

Comparative morphological, physiological, biochemical and genomic studies reveal novel genes of Dunaliella bioculata and D. quartolecta in response to salt stress.

BACKGROUND: Salinity is an essential abiotic stress in plants. Dunaliella is a genus of high-salt-tolerant microalgae. The present study aimed to compare the characterizations of D. bioculata and D. quartolecta at different levels and investigate novel genes response to salt stress. METHODS AND RESULTS: High chlorophyll contents were detected in D. bioculata on the 35th d of salt stress, while high lipid and carotenoid contents were detected in D. quartolecta via morphological and biochemical analyses. Physiological analysis showed that D. quartolecta cells had a smaller increase in osmotic potential, a smaller decrease in the Na+/K+ ratio and photochemical efficiency (Fv/Fm), and a lower relative conductivity than D. bioculata cells. The genomic lengths of D. quartolecta and D. bioculata were 396,013,629 bp (scaffold N50 = 1954 bp) and 427,667,563 bp (scaffold N50 = 3093 bp) via high-throughput sequencing and de novo assembly, respectively. Altogether, 25,751 and 26,620 genes were predicted in their genomes by annotation analysis with various biodatabases. The D. bioculata genome showed more segmental duplication events via collinearity analysis. More single nucleotide polymorphisms and insertion-deletion variants were detected in the D. bioculata genome. Both algae, which showed a close phylogenetic relationship, may undergo positive selection via bioinformatics analysis. A total of 382 and 85 novel genes were screened in D. bioculata and D. quartolecta, with 138 and 51 enriched KEGG pathways, respectively. Unlike the novel genes adh1, hprA and serA, the relative expression of livF and phbB in D. bioculata was markedly downregulated as salinity increased, as determined by qPCR analysis. The relative expression of leuB, asd, pstC and proA in D. quartolecta was markedly upregulated with the same salinity increase. CONCLUSION: Dunaliella quartolecta is more halophilic than D. bioculata, with more effective responses to high salt stress based on the multiphase comparative data.

Transcriptome Analysis Reveals the Mechanisms of Tolerance to High Concentrations of Calcium Chloride Stress in Parachlorella kessleri.

Salt stress is one of the abiotic stress factors that affect the normal growth and development of higher plants and algae. However, few research studies have focused on calcium stress, especially in algae. In this study, the mechanism of tolerance to high calcium stress of a Parachlorella kessleri strain was explored by the method of transcriptomics combined with physiological and morphological analysis. Concentrations of CaCl2 100 times (3.6 g/L) and 1000 times (36 g/L) greater than the standard culture were set up as stresses. The results revealed the algae could cope with high calcium stress mainly by strengthening photosynthesis, regulating osmotic pressure, and inducing antioxidant defense. Under the stress of 3.6 g/L CaCl2, the algae grew well with normal cell morphology. Although the chlorophyll content was significantly reduced, the photosynthetic efficiency was well maintained by up-regulating the expression of some photosynthesis-related genes. The cells reduced oxidative damage by inducing superoxide dismutase (SOD) activities and selenoprotein synthesis. A large number of free amino acids were produced to regulate the osmotic potential. When in higher CaCl2 stress of 36 g/L, the growth and chlorophyll content of algae were significantly inhibited. However, the algae still slowly grew and maintained the same photosynthetic efficiency, which resulted from significant up-regulation of massive photosynthesis genes. Antioxidant enzymes and glycerol were found to resist oxidative damage and osmotic stress, respectively. This study supplied algal research on CaCl2 stress and provided supporting data for further explaining the mechanism of plant salt tolerance.

Phylogenetic and Morphological Evolution of Green Euglenophytes Based on 18S rRNA.

Green euglenophytes are a group of eukaryotes with ancient origin. In order to understand the evolution of the group, it is interesting to know which characteristics are more primitive. Here, a phylogenetic tree of green euglenophytes based on the 18S rRNA gene was constructed, and ancestral states were reconstructed based on eight morphological characters. This research clarifies the phylogenetic relationships of green euglenophytes and provides a basis for the study of the origin of these plants. The phylogenetic tree, which was constructed by Bayesian inference, revealed that: Eutreptia and Eutreptiella were sister groups and that Lepocinclis, Phacus, and Discoplastis were close relatives; Euglena, Cryptoglena, Monomorphina, and Colacium were closely related in addition to Trachelomonas and Strombomonas; and Euglena was not monophyletic. An ancestral reconstruction based on morphological characters revealed seven primitive character states: ductile surface, spirally striated, slightly narrowing or sharp elongated cauda, absence of a lorica, chloroplast lamellar, shield or large discoid, pyrenoid with sheath, and with many small paramylon grains. However, the ancestral state of the length of the flagellum could not be inferred. Euglena and Euglenaria, which both possessed all of the ancestral character states, might represent the most ancient lineages of green euglenophytes.

Analysis of Adaptive Evolution and Coevolution of rbcL Gene in the Genus Galdieria (Rhodophyta).

To research the adaptive evolution and coevolution of the rbcL gene in the genus Galdieria, 36 sequences were selected. The bioinformatics of proteins encoded by rbcL genes of Galdieria were analyzed, and phylogenetic trees were constructed by the maximum-likelihood method. Then, adaptive evolution and coevolution were analyzed. The phylogenetic tree showed that the inner groups were clustered into four branches, in which the sequences of Galdieria maxima were divided into two small branches, and the posterior probability of each branch is above 94.9%. Eleven reliable positive selection sites were detected in the branched-site model, indicating that the rbcL protein-coding gene of Galdieria underwent adaptive evolution to adapt to extreme environments. Site 269 F is located in the loop 6 domain, while sites 272 D and 273 W are located in the 6-helix structure. Many coevolution pairs were detected, which were closely related to the hydrophobic and molecular weight correlation values of amino acids. The results are helpful to research the evolution process of freshwater red algae, to explore the changes of its essential genes and protein functions to adapt to different environmental pressures, and to understand the close relationship between amino acids in proteins and the molecular mechanism of evolution.

A systems toxicology approach to explore toxicological mechanisms of fluoroquinolones-induced testis injury.

The widespread use of fluoroquinolones (FQs) causes a serious risk to the environment and human health. Here, we evaluated the potential effect to induce testis damage by gatifloxacin (GAT) intragastrically treatment in mice (25, 50, and 100 mg/kg body weight per day for 7 days). We observed testicular weight, serum testosterone, antioxidant enzyme activity, and mRNA levels and pathways. Testicular histopathology indicated that GAT administration induced a dose-dependent spermatogenesis abnormality. At 50 mg/kg, GAT altered gene expression but did not change the weight and the levels of testosterone and antioxidant enzymes. These findings indicate that mRNA levels are more sensitive than weight and testosterone for detecting GAT testicular toxicity. We also found that GAT induced testicular damage by regulating the candidate genes associated with spermatogenesis, germ cell movement, testicular fibrosis, and reproductive axis development. This study enhances our perception of the mechanism of FQs-induced testicular toxicity and environmental effects. However, the molecular mechanism needs to be further researched.

Comparison of the transcriptomes of different life history stages of the freshwater Rhodophyte Thorea hispida.

Thorea hispida exclusively inhabits freshwater environments and is characterized by a triphasic life history. In this study, the organelle genomes and transcriptomes of different life history stages of T. hispida were examined using next generation sequencing. The chloroplast and mitochondrial genomes of the chantransia stage were 175,747 and 25,411 bp in length, respectively. The chantransia stage was highly similar to the gametophyte stage based on comparisons of organelle genomes and phylogenetic reconstruction. Transcriptomic comparisons of two stages found that ribosome-related genes were the most up-regulated in the gametophyte stage of T. hispida. Seven meiosis-specific genes, including SPO11 initiator of meiotic double-stranded breaks(spo11), meiotic nuclear divisions 1(mnd1), RAD51 recombinase(rad51), mutS homolog 4(msh4), mutS homolog 5(msh5), REC8 meiotic recombination protein(rec8), and DNA helicase Mer3(mer3), were differentially regulated between the two life history stages. The organelle genomes and transcriptomes from T. hispida provided in this study will be valuable for future studies of freshwater red algae.

Molecular Mechanism of Lipid Accumulation and Metabolism of Oleaginous Chlorococcum sphacosum GD from Soil under Salt Stress.

The oleaginous microalgae species Chlorococcum sphacosum GD is a promising feedstock for biodiesel production from soil. However, its metabolic mechanism of lipid production remains unclear. In this study, the lipid accumulation and metabolism mechanisms of Chlorococcum sphacosum GD were analyzed under salt stress based on transcriptome sequencing. The biomass and lipid content of the alga strain were determined under different NaCl concentrations, and total RNA from fresh cells were isolated and sequenced by HiSeq 2000 high throughput sequencing technology. As the salt concentration increased in culture medium, the algal lipid content increased but the biomass decreased. Following transcriptome sequencing by assembly and splicing, 24,128 unigenes were annotated, with read lengths mostly distributed in the 200-300 bp interval. Statistically significant differentially expressed unigenes were observed in different experimental groups, with 2051 up-regulated genes and 1835 down-regulated genes. The lipid metabolism pathway analysis showed that, under salt stress, gene-related fatty acid biosynthesis (ACCase, KASII, KAR, HAD, FATA) was significantly up-regulated, but some gene-related fatty acid degradation was significantly down-regulated. The comprehensive results showed that salt concentration can affect the lipid accumulation and metabolism of C. sphacosum GD, and the lipid accumulation is closely related to the fatty acid synthesis pathway.

Harvesting biomass of an oil-rich microalga Parachlorella kessleri TY02 by ferric chloride: Effects on harvesting efficiency, lipid production and municipal wastewater treatment.

Inorganic coagulants have been widely used to harvest microalgal biomass. A great deal of attention has been mainly focused on the response of harvesting efficiency, lipid production and feasibility of the reuse of medium to inorganic coagulants. The physiological state of harvested cells and feasibility of wastewater treatment remain unclear. In this context, the effect of ferric chloride as a conventional inorganic coagulant on the harvesting efficiency, physiological state and lipid content of an oil-rich microalga Parachlorella kessleri TY02 was evaluated. Moreover, the performance of harvested cells for municipal wastewater treatment was also evaluated. When the dosage of iron ions was 0.077 mg/mg dry biomass and the sedimentation time was 5 min, the microalga had good harvesting efficiency and cell viability. As the dosage of iron ions was up to 0.15 mg/mg dry biomass, cell viability notably decreased. Cells harvested by 0.077 and 0.15 mg/mg dry biomass of iron ions showed good wastewater treatment efficiency. It was also found that long sedimentation time (40 min) not only did not promote harvesting efficiency, but also reduced cell viability. Iron ions had no notable effect on lipid content of the microalga. Through comprehensive evaluation of harvesting efficiency, lipid production, physiological state and wastewater treatment efficiency, it indicated that 0.077 mg/mg dry biomass of iron ions could be used to harvest biomass of the microalga.

Graphene Aerogel-Metal-Organic Framework-Based Electrochemical Method for Simultaneous Detection of Multiple Heavy-Metal Ions.

The development of an effective method for detecting heavy-metal ions remains a serious task because of their high toxicity to public health and environments. Herein, a new electrochemical method based on a graphene aerogel (GA) and metal-organic framework (MOF) composites was developed for simultaneous detection of multiple heavy-metal ions in aqueous solutions. The GA-MOF composites were synthesized via the in situ growth of the MOF UiO-66-NH2 crystal on the GA matrix. GA not only serves as the backbone for UiO-66-NH2 but also enhances the conductivity of the composites by accelerating the electron transfer in the matrix. UiO-66-NH2 worked as a binding site for heavy-metal ions because of the interaction between hydrophilic groups and metal cations. The detection performance of the GA-UiO-66-NH2 composite-modified electrodes was determined. The developed electrochemical method can be successfully applied for individual and simultaneous detection of heavy-metal ions, namely, Cd2+, Pb2+, Cu2+,and Hg2+, in aqueous solutions with high sensitivity and selectivity. The method can also be used for simultaneous detection of Cd2+, Pb2+, Cu2+, and Hg2+ in river water and the leaching solutions of soil and vegetable with high accuracy and reliability. This work provides a new approach for simultaneous detection of multiple heavy-metal ions in practical applications.

Long term spatial-temporal dynamics of fluoride in sources of drinking water and associated health risks in a semiarid region of Northern China.

There is a concern about the increasing prevalence of health problems related to the ingestion of fluoride (F-) in the developing world. Drinking water is one important source of F-, and the concentration of F- needs to be known to ensure the safety of drinking water. In this study, F- levels in drinking water were investigated across Taiyuan in Shanxi Province, China. Spatial-temporal distribution characteristics and potential associated health risks were analyzed using GIS. We collected 485 samples from shallow wells without any defluoridation treatments between 2008 and 2016. After analyzing the samples of F- content we found that mean F- levels of urban areas (0.61 ±â€¯0.39 mg L-1), suburban areas (0.70 ±â€¯0.87 mg L-1) and for all of Taiyuan city (0.63 ±â€¯0.56 mg L-1) were in optimum range based on the recommendation by USEPA. However, individual locations within industrial areas (e.g. Gujiao District) had higher F- levels (1.06 mg L-1). A concerning result showed that 12.37% of tested locations had F- concentrations larger than 1.0 mg L-1. We calculated F- Health Risk Indices (HRIsF) and found that highest were associated with suburban areas, especially in the year 2009 and 2010. However, from 2008 to 2016, overall F- levels and HRIsF of the sampled groundwater in Taiyuan City showed a decreasing trend. HRIsF in suburban areas was higher than urban areas, possible due to the heavily prevalent coal mining industry in those areas. Specific policies should be formulated to address HRIsF.

Interactive effects of temperature and nutrients on the phytoplankton community in an urban river in China.

Understanding the relative impact sizes of environmental factors and nutrients on the high annual variation of phytoplankton abundance in eutrophic rivers is important for aquatic ecosystem management efforts. In this study, we used phytoplankton dynamic datasets in the eutrophic Fenhe River to show the variations and drivers of phytoplankton abundance under complex, fluctuating environmental conditions during 2012-2017. The temporal and spatial variations of nutrients in the river depicted that the total phosphorus (TP) concentration was higher in the wet season and in downstream. There were increases in total nitrogen (TN) concentration in the normal season and in upstream. The structural equation model (SEM) showed that the phytoplankton abundance increased during the wet season despite the decrease in the TN:TP ratio and was reduced upstream due to the highest TN:TP ratio. Among the environmental variables, water temperature (WT) was an important predictor and positively correlated temporally and spatially to phytoplankton. The interaction of nutrients with the phytoplankton community at different temperature levels indicated that different phytoplankton groups have different nutrient requirements. We can conclude that enhances in temperature and TP concentration will significantly increase phytoplankton abundance and dominance of cyanobacteria and green algae in the future, whereas there was insignificant effect on diatoms. These data indicated that temperature and TP content were the important abiotic factors influencing the phytoplankton growth of the water body, which could provide a reference for the evaluation of environmental alterations in the future.

Metabolomic Study to Determine the Mechanism Underlying the Effects of Sagittaria sagittifolia Polysaccharide on Isoniazid- and Rifampicin-Induced Hepatotoxicity in Mice.

In this study, a non-targeted metabolic profiling method based on ultra-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) was used to characterize the plasma metabolic profile associated with the protective effects of the Sagittaria sagittifolia polysaccharide (SSP) on isoniazid (INH)-and rifampicin (RFP)-induced hepatotoxicity in mice. Fourteen potential biomarkers were identified from the plasma of SSP-treated mice. The protective effects of SSP on hepatotoxicity caused by the combination of INH and RFP (INH/RFP) were further elucidated by investigating the related metabolic pathways. INH/RFP was found to disrupt fatty acid metabolism, the tricarboxylic acid cycle, amino acid metabolism, taurine metabolism, and the ornithine cycle. The results of the metabolomics study showed that SSP provided protective effects against INH/RFP-induced liver injury by partially regulating perturbed metabolic pathways.

Responses of freshwater algal cell density to hydrochemical variables in an urban aquatic ecosystem, northern China.

In this paper, the algal cell density of cyanobacteria, green algae, and diatoms and their responses to the hydrochemical factors were analyzed to reveal the structural characteristics of water quality in an urban river. A total of nine sampling sites from upstream to downstream was explored in our study. At each site, the density of algae was identified every week during the wet season (June-October) from 2012 to 2017, and in situ detection was used for the relative 11 hydrochemical variables. The temporal and spatial characteristics of 14 variables were analyzed using a heatmap coupled with the cluster analysis method. The trend of each parameter was analyzed using the smoothing method with locally weighted regression. The nonmetric multidimensional scaling method was employed to detect the temporal and spatial similarities among algae along hydrochemical gradients. The responses of algal density to hydrochemical variables were analyzed using a redundancy analysis. The results showed that the water temperature (Wtemp), pH, dissolved oxygen (DO), cyanobacteria, and diatoms exhibited significant declining trends, and significant increasing trends were shown in the permanganate index, chemical oxygen demand, total nitrogen, ammonia nitrogen, and total phosphorus; the cyanobacteria exhibited certain differences with green algae and diatoms in summer and the downstream areas of the river. The temporal-spatial homogeneity of algal to hydrochemical variables showed the key influencing factors of Wtemp for cyanobacteria density, chlorophyll for green algae density, DO, and pH for diatoms. The results presented here are valuable for deepening our understanding of river ecosystem evaluations and effective environmental management, as well as an important reference for the sustainable development of aquatic biological resources.

Microalgal Cultivation in Secondary Effluent: Recent Developments and Future Work.

Eutrophication of water catchments and the greenhouse effect are major challenges in developing the global economy in the near future. Secondary effluents, containing high amounts of nitrogen and phosphorus, need further treatment before being discharged into receiving water bodies. At the same time, new environmentally friendly energy sources need to be developed. Integrating microalgal cultivation for the production of biodiesel feedstock with the treatment of secondary effluent is one way of addressing both issues. This article provides a comprehensive review of the latest progress in microalgal cultivation in secondary effluent to remove pollutants and accumulate lipids. Researchers have discovered that microalgae remove nitrogen and phosphorus effectively from secondary effluent, accumulating biomass and lipids in the process. Immobilization of appropriate microalgae, and establishing a consortium of microalgae and/or bacteria, were both found to be feasible ways to enhance pollutant removal and lipid production. Demonstrations of pilot-scale microalgal cultures in secondary effluent have also taken place. However there is still much work to be done in improving pollutants removal, biomass production, and lipid accumulation in secondary effluent. This includes screening microalgae, constructing the consortium, making use of flue gas and nitrogen, developing technologies related to microalgal harvesting, and using lipid-extracted algal residues (LEA).

Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics.

BACKGROUND: Porphyridium purpureum has been utilized in important industrial and pharmaceutical fields. The identification of microRNAs (miRNAs) in this unique species is of great importance: such identification can help fill gaps in the small RNA (sRNA) studies of this organism and help to elucidate essential biological processes and their regulation mechanisms in this special micro alga. RESULTS: In this study, 254 high-confidence miRNAs (203 conserved miRNAs and 51 novel miRNAs) were identified by sRNA deep sequencing (sRNA-seq) combined with bioinformatics. A total of 235 putative miRNA families were predicted, including 192 conserved families and 43 species-specific families. The conservation and diversity of predicted miRNA families were analysed in different plant species. Both the 100 % northern blot validation rate (VR) of four randomly selected miRNAs and the results of stem-loop quantitative real time RT-PCR (qRT-PCR) assays of 25 randomly selected miRNAs demonstrated that the majority of the miRNAs identified in this study are credible. A total of 14,958 and 2184 genes were predicted to be targeted by the 186 conserved and 41 novel miRNAs. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that some target genes likely provide valuable references for further understanding of vital functions in P. purpureum. In addition, a cytoscape network will provide some clues for research into the complex biological processes that occur in this unique alga. CONCLUSIONS: We first identified a large set of conserved and novel miRNAs in P. purpureum. The characteristic and validation analysis on miRNAs demonstrated authenticity of identification data. Functional annotation of target genes and metabolic pathways they involved in illuminated the direction for further utilization and development this micro alga based on its unique properties.

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

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.