Illumina High-throughput Sequencing Technology Research Articles

Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (Acanthopagrus schlegelii).

Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy-Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.

The complete mitochondrial genome of the Yellow-rumped Flycatcher (Ficedula zanthopygia) from Maorshan, China

The Yellow-rumped Flycatcher (Ficedula zanthopygia) is a secondary cavity nesting bird and widely distributed in China, Mongolia, Russia and Korea. In this study firstly sequenced the mitotic genome of the Yellow-rumped Flycatcher (Ficedula zanthopygia) gathered at Maorshan, China, using Illumina high-throughput sequencing technology, and then annotated the assembly. The total length of the complete mitochondrial genome is 16,730 bp and it consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 control region (CR). The CR is 1148 bp in length. The nucleotide composition is 29.59% A, 14.75% T, 32.13% G, 23.54% C. The result of phylogenetic analysis showed that there is close genetic relationship among Ficedula zanthopygia and Ficedula hyperythra.

Structural and Dynamic Analysis of Leaf-Associated Fungal Community of Walnut Leaves Infected by Leaf Spot Disease Based Illumina High-Throughput Sequencing Technology.

Leaf-associated microbiota is vital in plant-environment interactions and is the basis for micro-ecological regulation. However, there are no studies on the direct differences in microbial community composition between disease-susceptible and healthy walnut leaves. This study collected five samples of healthy and infected leaves (all leaves with abnormal spots were considered diseased leaves) from May to October 2018. Differences in fungal diversity (Chao1 index, Shannon index, and Simpson index) and community structure were observed by sequencing and analyzing diseased and healthy leaf microbial communities by Illumina HiSeq sequencing technology. The main fungal phyla of walnut leaf-associated were Ascomycota, Basidiomycota, and Glomeromycota. Diversity indices (Shannon and Chao1 index values) of healthy leaves differed significantly in the late stages of disease onset. The results showed that the fungal species that differed considerably between the healthy and infected groups differed, and the fungal species that differed significantly between the healthy and infected groups changed with the development of the leaf disease. Critical control time points were determined by analyzing the population dynamics of pathogenic fungi. Leaf-associated microorganisms are abundant and diverse, and fungal identification and diversity studies are helpful for developing more appropriate walnut management strategies.

Effect of nitrate and sulfate coexistence on hydrogen autotrophic reduction of antimonate (Sb(V)) and microbial community structures

Hydrogen autotrophic bioreduction of antimonate (Sb(V)) to antimonite (Sb(III)) is an alternative approach for removing antimony (Sb) from water. This study investigated Sb(V) reduction kinetics and the effects of various parameters on the Sb(V) removal performance in a hydrogen autotrophic reaction system (HARS). Sb(V) reduction in the HARS was well fitted to the Michaelis-Menten model, showing a positive correlation between the reaction rate and biomass. The maximum specific substrate removal rates were 0.29–4.86 and 6.82–15.87 mg Sb(V)/(g·VSS·h) at initial Sb(V) concentrations of 500 μg/L and 10 mg/L, respectively. Coexisting nitrate significantly inhibited Sb(V) reduction, and the inhibition intensified with increasing nitrate concentration. However, coexisting sulfate had a positive effect on Sb(V) reduction, and the sulfate effectively enhanced total antimony (TSb) removal performance by generating sulfide from sulfate reduction. Illumina high-throughput sequencing technology was used to determine the changes in microbial community structure during different periods in the HARS, revealing the effects of co-existing ions on the dominant Sb(V) reducing bacteria. In the HARS, Longilinea and Terrimonas were the dominant genera in the presence of nitrate, and Longilinea was the dominant genus in the presence of sulfate, at initial Sb(V) concentration of 500 μg/L. When the concentration of Sb(V) was 10 mg/L, Longilinea and Thauera were the dominant genus in the HARS for treating water co-polluted with nitrate and sulfate, respectively. These results provide a theoretical basis of the application of HARS for the bio-remediation of Sb(V) contaminated water.

Appropriate crop rotation alleviates continuous cropping barriers by changing rhizosphere microorganisms in Panax notoginseng

Crop rotation is the most sustainable way to solve the CCO which is the main problem restricting the development of Chinese herbal medicine. In this study, we used Illumina high-throughput sequencing technology to study the effects of different interval years on rhizosphere microorganisms of Panax notoginseng at 1, 2 and 3 years intervals. The results showed that the number of beneficial bacteria increased while the pathogenic bacteria decreased during crop rotation. We also found that choosing the suitable crop is more effective than extending the rotation cycle duration. Phylogenetic analysis results showed that the preceding crop plays a decisive role in the rotation. Indicator, Random forest and Network all showed that crop rotation is to increase Trichoderma to combat CCOs. Our study indicated that job's tears is more suitable as the preceding crop of P. notoginseng. T. asperellum play a key role in crop rotation.

The complete chloroplast genome sequence of Clerodendrum cyrtophyllum from Guangzhou, China

Clerodendrum cyrtophyllum is a well-known medicinal plant in southern China. Here, we presented the complete chloroplast (cp) genome of C. cyrtophyllum using Illumina high-throughput sequencing technology. The C. cyrtophyllum cp genome size is 152,004 bp with 38.13% GC content, including a pair of inverted repeat regions (IR, 51,592 bp) separated by a large single copy (LSC, 86,480 bp) and a small single copy region (SSC, 18,425 bp). It possesses 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis fully shows that C. cyrtophyllum is closely related to Clerodendrum bungei and Clerodendrum lindleyi. Overall, the complete cp genome sequence of C. cyrtophyllum provides a valuable resource for genetic diversity, phylogenetic relationship, and species identification.

The complete chloroplast genome of the Egyptian henbane (Hyoscyamus muticus L., Solanaceae)

Egyptian henbane (Hyoscyamus muticus L. Mant. Pl. 1767) is an important medicinal plant of the family Solanaceae. Its complete chloroplast (cp) genome was assembled using Illumina high-throughput sequencing technology to contribute to its conservation genetics studies. Here, we report the complete sequence of the chloroplast genome of H. muticus. The cp genome was 156,271 bp in length with an asymmetric base composition (30.9% A, 18.9% C, 18.6% G and 31.6% T). It encodes 132 genes comprising 87 protein-coding genes, 29 tRNA genes, and 8 rRNA genes. The overall GC content of the H. muticus chloroplast genome was 37.5%, and the corresponding values in the large single-copy (LSC), the small single-copy (SSC), and the inverted repeat (IR) regions were 35.5%, 31.5%, and 43.0%, respectively. The complete chloroplast genome sequence was deposited to the GenBank (NCBI, Accession number: MZ450974). The maximum likelihood phylogenetic analysis showed that the H. muticus and H. niger were clustered into one clade with strong support values, indicating their closer relationship.

Rice washing drainage (RWD) embedded in poly(vinyl alcohol)/sodium alginate as denitrification inoculum for high nitrate removal rate with low biodiversity

Immobilization technology with low maintenance is a promising alternative to enhance nitrate removal from water. In this study, washing rice drainage (RWD) was immobilized by poly(vinyl alcohol)/sodium alginate (PVA/SA) to obtain RWD-PVA/SA gel beads as inoculum for denitrification. When initial nitrate concentration was 50 mg N/L, nitrate was effectively removed at rates of 50–600 mg/(L∙d) using acetate as carbon source (C/N = 1.25). Arrhenius activation energy (Ea) of nitrate oxidoreductase was 28.64 kJ/mol for the RWD-PVA/SA gel beads. Temporal and spatial variation in microbial community structures were revealed along with RWD storage and in the reactors by Illumina high-throughput sequencing technology. RWD-PVA/SA gel beads has a simple (operational taxonomic units (OTUs) 〈100). Dechloromonas, Pseudomonas, Flavobacterium and Acidovorax were the most four dominant genera in the denitrification reactors inoculated with RWD-PVA/SA gel beads. This study provides an inoculum for denitrification with high nitrate removal performance and simple microbial community structures.

Analysis of Bacterial Community Composition and Ecological Function during Soft Rot Process in Pitaya (Hylocereus spp.) Stems

The soft rot in pitaya (Hylocereus spp.) stems seriously affected the harvest of pitaya fruits, but the dynamic change characteristics of bacterial community in pitaya stems during soft rot stages had not been revealed. In this study, we analyzed the bacterial community composition of different soft rot stages and visualized functional annotations of the core bacterial community in five soft rot periods via the Illumina high-throughput sequencing technology, MetaCoMET online network platform, and FAPROTAX database. The results showed that the dominant bacteria in healthy and diseased pitaya stems were Proteobacteria and Firmicutes. Pseudomonas, Enterobacter, Sphingomonas, and Sphingobacterium were the core bacteria microbiomes during the infection stages. Meanwhile, the ecological function analysis results showed that the Enterobacter and Pseudomonas bacteria may play an important role in causing soft rot of pitaya stems. Therefore, the results shown in this paper could provide a useful reference for the study on microecological mechanism of soft rot of pitaya stems.

The complete chloroplast genome of Solanum sisymbriifolium (Solanaceae), the wild eggplant

Solanum sisymbriifolium is a critical wild eggplant resource with resistance to many serious diseases that affect eggplant production. In this study, the chloroplast genome of S. sisymbriifolium was successfully sequenced using Illumina high-throughput sequencing technology. The length of the complete chloroplast genome is 155,771 bp, and its GC content is 37.76%. There is a large single-copy region (86,404 bp), a small single-copy region (18,525 bp), and a pair of inverted repeat regions (25,421 bp) in the chloroplast genome. A total of 128 coding genes were annotated in the entire chloroplast genome, including 83 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The phylogenetic tree of 17 complete chloroplast genomes shows that S. sisymbriifolium is closely related to Solanum wrightii.

Transcriptomic analysis identifies candidate genes for shell colour formation in the Venus clamCyclina sinensis

ABSTRACTSome bivalves are important in fisheries and aquaculture, and provide significant economic benefits to humans. The diversity in shell colour among bivalves has received attention due to its potential in breeding and its relevance to the study of speciation and adaptation. In this study, the relationship between whole-genome-scale gene expression and shell coloration in the clam Cyclina sinensis was analysed using high-throughput Illumina sequencing technology. A total of 15,367 annotated genes and 4,425 novel genes were detected based on transcript assembly. The results of the transcriptome analysis show that 49 genes were differentially expressed in the outer mantle fold tissue of purple- vs white-shelled specimens. These genes include three lipoprotein receptor genes, low-density lipoprotein receptor gene (ldlr), low-density lipoprotein receptor-related protein 4 (lrp4) and scavenger receptor cysteine-rich protein gene (srcr). These genes may be involved in the transport of carotenoid pigments. Moreover, as shown by the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, several receptor activity terms and a glycosphingolipid biosynthesis pathway were detected, and these might be involved in shell coloration. Together with the analyses of differentially expressed genes, our results suggest a possible molecular mechanism governing the selective transport of carotenoids in the mantle of purple-shelled clams and shell colour formation. The results of this study may help to elucidate the colour formation mechanism in clam shells.

Community Structure of Eukaryotic Phytoplankton in Wetland of Golmud River and Its Lower Reaches and Relative Environmental Factors

Identification of the community structure of phytoplankton is an important link in studying the structure and function of aquatic ecosystems. However, research on the community structure of phytoplankton in the Golmud area is very scarce at present. To explore the composition of phytoplankton in the Golmud area, eukaryotic phytoplankton and environmental parameters were sampled in September 2020. The composition and diversity of the eukaryotic phytoplankton community were determined by microscopic observation and Illumina high-throughput sequencing technology. The results showed that a total of 40 species of eukaryotic phytoplankton from 4 phyla were identified by microscopic observation, and 154 species of eukaryotic phytoplankton from 7 phyla were obtained by high-throughput sequencing, mainly Bacillariophyta and Chlorophyta. The dominant species were Dunaliella sp., Teleaulax sp., Parvodinium mixtum, and Lindavia radiosa. The eukaryotic phytoplankton density in summer was 0.09–12.08 × 105 cells/L, the total biomass was 0.002–0.55 mg/L, and the concentration of chlorophyll-a was 0.00–0.91 μg/L. Multiple α diversity indices showed that the diversity of water in different salinities was in the order of freshwater &gt; brackish &gt; saline. The β diversity results showed that the eukaryotic phytoplankton community composition was more similar in water with the same salinity. The redundancy analysis results of water with different salinities showed that environmental factors susc as salinity, total phosphorus concentration, and dissolved oxygen affected the eukaryotic phytoplankton community structure, among which salinity had the greatest influence.

The complete chloroplast genome of Ananas comosus var. erectifolius (L.B. Smith) Coppens & Leal

Ananas comosus var. erectifolius (L.B. Smith) Coppens & Leal, a tropical plant from Bromeliaceae family, has immense applications, especially for fiber production of excellent quality. The lack of available chloroplast (cp) genome information limits its breeding and application. Here, we assembled its complete cp genome using Illumina high-throughput sequencing technology. The cp genome size is 159,983 bp, with 37.4% GC content, including a large single copy region (LSC) of 87,787 bp, a small single copy region (SSC) of 18,606 bp, and a pair of inverted repeat regions (IRs) of 26,795 bp. It encodes 89 protein-coding, 38 tRNA and 8 rRNA genes. Phylogenetic analysis showed that A. comosus var. erectifolius was close to Ananas comosus. The complete cp genome sequences could provide valuable information for variety breeding and genetic analysis of agronomic and economic traits in A. comosus var. erectifolius.

Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.

Tetraploid Robinia pseudoacacia L. is a difficult-to-root species, and is vegetatively propagated through stem cuttings. Limited information is available regarding the adventitious root (AR) formation of dark-pretreated micro-shoot cuttings. Moreover, the role of specific miRNAs and their targeted genes during dark-pretreated AR formation under in vitro conditions has never been revealed. The dark pretreatment has successfully promoted and stimulated adventitious rooting signaling-related genes in tissue-cultured stem cuttings with the application of auxin (0.2 mg L−1 IBA). Histological analysis was performed for AR formation at 0, 12, 36, 48, and 72 h after excision (HAE) of the cuttings. The first histological events were observed at 36 HAE in the dark-pretreated cuttings; however, no cellular activities were observed in the control cuttings. In addition, the present study aimed to uncover the role of differentially expressed (DE) microRNAs (miRNAs) and their targeted genes during adventitious root formation using the lower portion (1–1.5 cm) of tetraploid R. pseudoacacia L. micro-shoot cuttings. The samples were analyzed using Illumina high-throughput sequencing technology for the identification of miRNAs at the mentioned time points. Seven DE miRNA libraries were constructed and sequenced. The DE number of 81, 162, 153, 154, 41, 9, and 77 miRNAs were upregulated, whereas 67, 98, 84, 116, 19, 16, and 93 miRNAs were downregulated in the following comparisons of the libraries: 0-vs-12, 0-vs-36, 0-vs-48, 0-vs-72, 12-vs-36, 36-vs-48, and 48-vs-72, respectively. Furthermore, we depicted an association between ten miRNAs (novel-m0778-3p, miR6135e.2-5p, miR477-3p, miR4416c-5p, miR946d, miR398b, miR389a-3p, novel m0068-5p, novel-m0650-3p, and novel-m0560-3p) and important target genes (auxin response factor-3, gretchen hagen-9, scarecrow-like-1, squamosa promoter-binding protein-like-12, small auxin upregulated RNA-70, binding protein-9, vacuolar invertase-1, starch synthase-3, sucrose synthase-3, probable starch synthase-3, cell wall invertase-4, and trehalose phosphatase synthase-5), all of which play a role in plant hormone signaling and starch and sucrose metabolism pathways. The quantitative polymerase chain reaction (qRT-PCR) was used to validate the relative expression of these miRNAs and their targeted genes. These results provide novel insights and a foundation for further studies to elucidate the molecular factors and processes controlling AR formation in woody plants.

Characteristic Analysis of nirS Denitrifying Bacterial Community in Lijiahe Reservoir During Stratification

To explore the composition of the nirS denitrifying bacterial community during stratification in spring(March to May) in a drinking water reservoir and its relationship with water quality, the water quality and relative abundance and structure of the denitrifying bacterial community were analyzed using in-situ monitoring coupled with Illumina high-throughput sequencing technology in the Lijiahe Reservoir. The results showed that:① through high-throughput sequencing, 4 phyla and 13 genera were identified. The dominant bacterial phylum was Proteobacteria, and its relative abundance was between 52.5% and 70.6%. The overall trend of the relative abundance of Proteobacteria decreased on the time scale (P<0.05), and its relative abundance in the surface and middle layers was higher than that of the bottom layer on the spatial scale (P<0.05). There was no difference in the proportion of Proteobacteria between the surface and middle layers (P>0.05), and the abundance of its bottom layer was relatively stable; eight genera of bacteria with denitrification function were identified, among which the dominant bacterial genera (relative abundance>1%) were Dechloromonas and Pseudomonas. The relative abundance of Dechloromonas showed a trend of first decreasing and then increasing on the time scale, whereas the relative abundance of Pseudomonas showed a trend of increasing first and then decreasing on the time scale. There were no differences on the spatial scale between these two genera (P>0.05); the changes in bacterial diversity and abundance were basically similar, with a trend of first increasing and then decreasing on the time scale. The highest diversity and abundance of the bacterial community gradually increased with increasing depth on the spatial scale. ② ρ(TN) of the reservoir during stratification was 2.35-2.91 mg·L-1, and the nitrogen pollution was more serious. In March and April, ρ(TN) on the vertical scale was basically similar and showed a decreasing trend. In May, the content of total nitrogen was higher than that in March and April, and the highest value of total nitrogen content occurred in the surface layer. ③ Redundancy analysis showed that water temperature, dissolved oxygen, nitrate, and ammonia nitrogen were the main driving factors, and ammonia nitrogen showed a significantly negative correlation with Dechlormonas. In summary, the study of nirS-type denitrification communities and related influencing factors will contribute to analyzing the characteristics of denitrifying bacterial community changes in a micro-polluted drinking water reservoir and provide a theoretical research basis for the biological remediation of nitrogen pollution in such reservoirs in the future.

Ploidy level enhances the photosynthetic capacity of a tetraploid variety of Acer buergerianum Miq.

BackgroundPolyploidy plays an important role in plant breeding and has widespread effects on photosynthetic capacity. To determine the photosynthetic capacity of the tetraploid variety Acer buergerianum Miq. ‘Xingwang’, we compared the gas exchange parameters, chloroplast structure, chlorophyll contents, and chlorophyll fluorescence parameters between the tetraploid Acer buergerianum ‘Xingwang’ and the diploid ‘S4’. To evaluate the effects of genome duplication on the photosynthetic capacity of Acer buergerianum ‘Xingwang’, the transcriptomes of the autotetraploid ‘Xingwang’ and the diploid ‘S4’ of A. buergerianum were compared.MethodsThe ploidy of Acer buergerianum ‘Xingwang’ was identified by flow cytometry and the chromosome counting method. An LI-6800 portable photosynthesis system analyzer was used to assess the gas exchange parameters of the tetraploid variety ‘Xingwang’ and diploid variety ‘S4’ of A. buergerianum. We used a BioMate 3S ultraviolet-visible spectrophotometer and portable modulated fluorometer to measure the chlorophyll contents and chlorophyll fluorescence parameters, respectively, of ‘Xingwang’ and ‘S4’. Illumina high-throughput sequencing technology was used to identify the differences in the genes involved in the photosynthetic differences and determine their expression characteristics.ResultsThe single-cell DNA content and chromosome number of the tetraploid ‘Xingwang’ were twice those found in the normal diploid ‘S4’. In terms of gas exchange parameters, the change in stomatal conductance, change in intercellular CO2 concentration, transpiration rate and net photosynthetic rate of ‘Xingwang’ were higher than those of the diploid ‘S4’. The chlorophyll contents, the maximal photochemical efficiency of PSII and the potential photochemical efficiency of PSII in ‘Xingwang’ were higher than those of ‘S4’. The chloroplasts of ‘Xingwang’ contained thicker thylakoid lamellae. By the use of Illumina sequencing technology, a total of 51,807 unigenes were obtained; they had an average length of 1,487 nt, and the average N50 was 2,034 nt. The lengths of most of the unigenes obtained ranged from 200–300 bp, with an average value of 5,262, followed by those longer than 3,000 bp, with an average value of 4,791. The data revealed numerous differences in gene expression between the two transcriptomes. In total, 24,221 differentially expressed genes were screened, and the percentage of differentially expressed genes was as high as 46.75% (24,224/51,807), of which 10,474 genes were upregulated and 13,747 genes were downregulated. We analyzed the key genes in the photosynthesis pathway and the porphyrin and chlorophyll metabolism pathway; the upregulation of HemB may promote an increase in the chlorophyll contents of ‘Xingwang’, and the upregulation of related genes in PSII and PSI may enhance the light harvesting of ‘Xingwang’, increasing its light energy conversion efficiency.

Insights into plastome of Fagonia indica Burm.f. (Zygophyllaceae): organization, annotation and phylogeny

The enhanced understanding of chloroplast genomics would facilitate various biotechnology applications; however, the chloroplast (cp) genome / plastome characteristics ofplants like Fagonia indica Burm.f. (family Zygophyllaceae), which have the capability to grow in extremely hot sand desert, have been rarely understood. The de novo genome sequence of F. indica using the Illumina high-throughput sequencing technology determined 128,379 bp long cp genome, encode 115 unique coding genes. The present study added the evidence of the loss of a copy of the IR in the cp genome of the taxa capable to grow in the hot sand desert. The maximum likelihood analysis revealed two distinct sub-clades i.e. Krameriaceae and Zygophyllaceae of the order Zygophyllales, nested within fabids.

Differences between male and female leaves of Schisandra sphenanthera: based on RNA-Seq

Schisandra sphenanthera is dioecious and only the fruits of female plants can be used as medicine and food. It is of great significance for the cultivation and production of S. sphenanthera to explore the differences between male and female plants at the non-flowering stage and develop the identification markers at non-flowering or seedling stage. In this study, the transcriptome of male and female leaves of S. sphenanthera at the non-flowering stage was sequenced by Illumina high-throughput sequencing technology and analyzed based on bioinformatics. A total of 236 682 transcripts were assembled by Trinity software and 171 588 were chosen as unigenes. Finally, 1 525 differentially expressed genes(DEGs) were identified, with 458 up-regulated and 1 067 down-regulated in female lea-ves. The down-regulated genes mainly involve photosynthesis, photosynthesis-antenna protein, carbon fixation in photosynthetic or-ganisms, and other pathways. Real-time quantitative PCR(qPCR) identified two genes between male and female leaves and one of them was a HVA22-like gene related to floral organ development and abscisic acid(ABA). Enzyme linked immunosorbent assay(ELISA) was applied to determine the content of ABA, auxin, gibberellin, and zeatin riboside(ZR) in leaves of S. sphenanthera. The results showed that the content of ABA and ZR in male leaves was significantly higher than that in female leaves. The involvement of down-regulated genes in female leaves in the photosynthesis pathway and the significant differences in the content of endogenous hormones between male and female leaves lay a scientific basis for analyzing the factors affecting sex differentiation of S. sphenanthera.

Community Distribution of the Rhizospheric and Endophytic Bacteria of Phragmites australis and Their Limiting Factors in Iron Tailings

The composition of the rhizospheric and endophytic bacteria Phragmites australis in spring and summer around the Qiananling iron tailings reservoir in the Huairou District of Beijing was studied using Illumina high-throughput sequencing technology. Sequencing identified 40 phyla, and Proteobateria and Actinobacteria were the dominant phyla in all samples, accounting for more than 80% of the sequences in all samples. At the genus level, Pseudoarthrobacter was dominant. α-diversity analysis showed that species richness(Sobs, Chao) and species diversity indexes(Shannon, PD) of the rhizosphere soil microorganisms were significantly higher than those of endophytes. The maximum and minimum differences of the Sobs, Chao, Shannon, PD indexes were 1336, 1582.24, 6.48, and 81.18, respectively. β-diversity analysis indicated that there were significant differences in the community compositions of rhizosphere soil microorganisms and root endophytes, while now notable differences were observed between samples in different seasons. In addition, the dominant strains in each sample(such as Pseudomonas, Arthrobacter, and Streptomyces) were highly resistant to heavy metals. Among the 774 genera, a total of 250 genera coexisted in four types of samples, indicating that the microbial community composition of different samples had some degree of similarity. Correlation analysis between soil physical and chemical properties showed that Ni, Fe, available phosphorus, effective sulphur, and organic matter were significantly related to the microbial communities. Through the prediction of COG function, it was found that the microbial metabolic functions(i.e., energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, inorganic ion transport, and metabolism) were abundant.

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.

Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.