Analysis of rhizobacterial community associated with the occurrence of Ganoderma basal stem rot disease in oil palm by Illumina next-generation sequencing.

The fungus Ganoderma boninense is a causal pathogen of basal stem rot, a serious disease of oil palm plantation systems. As previously observed, some oil palm trees show no appearance of disease symptoms (asymptomatic oil palm), although they have grown close to a tree that showed severe symptoms of basal stem rot disease (symptomatic oil palm). The microbial community difference between asymptomatic and symptomatic oil palm will help understand disease suppression. Thus, in this study, rhizosphere soil was sampled around asymptomatic (OP - G) and symptomatic (OP + G) oil palm trees in Ganoderma-infected oil palm orchards. Illumina next-generation sequencing (NGS), bioinformatics analysis, bacterial diversity, and soil physicochemical properties were evaluated. The results demonstrated that soil physicochemical properties and species richness around rhizosphere soil of OP - G and OP + G samples were not significantly different. The age of the oil palm trees and oil palm variety showed negligible correlation and were not significant with bacterial diversity. However, the top ten most abundant analysis of the bacterial communities showed that phyla Actinobacteria and Firmicutes were significantly increased in rhizosphere soil around OP - G samples relative to the OP+ G samples. The unique operational taxonomic units (OTUs) of OP - G (2137) were higher than in the OP+ G samples (1747 OTUs). These bacterial communities have been reported as biological control agents and/or plant growth-promoting rhizosphere bacteria that are related to disease suppression. Thus, the data provided are useful for developing suppressive soil to biologically control G. boninense.

Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform.

BACKGROUND: The total bacterial community plays an important role in aquatic ecosystems. In this study, bacterial communities and diversity along the shores of the Upper Gulf of Thailand were first characterized. The association between bacterial communities and types of land use was also evaluated. RESULTS: The bacterial communities and diversity of seawater in the Upper Gulf of Thailand, with regard to types of land use, were first revealed by using Illumina next-generation sequencing. A total of 4953 OTUs were observed from all samples in which 554 OTUs were common. The bacterial communities in sampling sites were significantly different from each other. The run-off water from three types of land use significantly affected the community richness and diversity of marine bacteria. Aquaculture sites contained the highest levels of community richness and diversity, followed by mangrove forests and tourist sites. Seawater physicochemical parameters including salinity, turbidity, TSS, total N, and BOD5, were significantly different when grouped by land use. The bacterial communities were mainly determined by salinity, total N, and total P. The species richness estimators and OTUs were positively correlated with turbidity. The top ten most abundant phyla and genera as well as the distribution of bacterial classes were characterized. The Proteobacteria constituted the largest proportions in all sampling sites, ranging between 67.31 and 78.80%. The numbers of the Marinobacterium, Neptuniibacter, Synechococcus, Candidatus Thiobios, hgcI clade (Actinobacteria), and Candidatus Pelagibacter were significantly different when grouped by land use. CONCLUSIONS: Type of land use significantly affected bacterial communities and diversity along the Upper Gulf of Thailand. Turbidity was the most influential parameter affecting the variation in bacterial community composition. Salinity, total N, and P were the ones of the important factors that shaped the bacterial communities. In addition, the variations of bacterial communities from site-to-site were greater than within-site. The Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia, Euryarchaeota, Planctomycetes, Firmicutes, Deep Sea DHVEG-6, and Marinimicrobia were the most and common phyla distributed across the Upper Gulf of Thailand.

The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana.

Spinicaudatan clam shrimp are a widespread and diverse group of branchiopod crustaceans, yet few mitochondrial genomes have been published for this taxonomic group. Here, we present the mitogenome of Leptestheria brevirostris from a rock pool ecosystem in Botswana. Massively parallel sequencing of a single specimen facilitated the reconstruction of the species' 15,579 bp circularized mitogenome. The reconstructed phylogenetic tree confirms that L. brevirostris forms a monophyletic group with other diplostracan branchiopods, and that these are the sister taxon to Notostraca. The mitogenome reconstructed here is the first to be reported from a leptestherid clam shrimp.

Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil.

The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of ß-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.

Library Preparation for Multiplexed Reduced Representation Bisulfite Sequencing with a Universal Adapter.

Reduced representation bisulfite sequencing (RRBS) is an efficient approach for estimating cytosine methylation and hydroxymethylation at single nucleotide resolution with a focus on CpG sites located in CpG islands. Commonly used methods for multiplexing RRBS libraries involve a different indexed adapter, which is expensive to generate, for each library. Here, we describe a library preparation method that utilizes a universal adapter and labels samples with unique indexed PCR primers, significantly reducing the cost of multiplexed RRBS.

Complete mitochondrial genome of the three Colombian Caribbean loggerhead sea turtles, using next-generation sequencing.

The loggerhead turtle, Caretta caretta (Linnaeus, 1758), is an endangered sea turtle in Colombian Caribbean beach. In the present study was sequenced the complete mitochondrial DNA of three loggerhead turtles using Illumina next-generation sequencing (NGS). The average nucleotide frequency was A: 35% T: 26%, C: 27% and G: 12%. This genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of C. caretta. The sequences were deposited at the GenBank database under the accession number MF554690.1, MF579504.1 and MF579505.1.

Complete mitochondrial genome of the gyrfalcon Falco rusticolus (Aves, Falconiformes, Falconidae).

The complete mitochondrial genome sequence of gyrfalcon (Falco rusticolus), the largest of the true falcons, was characterized using next generation sequencing. The mitogenome was 18 218 bp long, and comprised of 13 protein-coding genes (PCGs), 22 tRNA, 2 rRNA and two non-coding regions; a control region (D-loop) harboring two tandem repeats 80 bp and 56 bp long and a pseudo-control region (ΨD-loop) with a tandem repeat 27 bp long. All genes were encoded on the + strand except ND6 and 8 tRNA genes.

Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario.

Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and comprehensive wildlife rabies control programmes. Better understanding of the mechanisms of spread of rabies virus can play a significant role in guiding such control efforts. To facilitate a detailed molecular epidemiological study of raccoon rabies virus movements across eastern North America, we developed a methodology to efficiently determine whole genome sequences of hundreds of viral samples. The workflow combines the generation of a limited number of overlapping amplicons covering the complete viral genome and use of high throughput sequencing technology. The value of this approach is demonstrated through a retrospective phylogenetic analysis of an outbreak of raccoon rabies which occurred in the province of Ontario between 1999 and 2005. As demonstrated by the number of single nucleotide polymorphisms detected, whole genome sequence data were far more effective than single gene sequences in discriminating between samples and this facilitated the generation of more robust and informative phylogenies that yielded insights into the spatio-temporal pattern of viral spread. With minor modification this approach could be applied to other rabies virus variants thereby facilitating greatly improved phylogenetic inference and thus better understanding of the spread of this serious zoonotic disease. Such information will inform the most appropriate strategies for rabies control in wildlife reservoirs.

Illumina next-generation sequencing reveals the mitochondrial genome of Ducetia japonica (Orthoptera: Tettigoniidae).

Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome (mitogenome) of Ducetia japonica was sequenced in the present study. The mitogenome of D. japonica (Genbank accession no. KU885974) is 16,276 bp in size, had the typical invertebrate mitochondrial gene arrangement and containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and a control region. Except for the control region (868 bp), one novel larger intergenic (616 bp) was found between nad2 and trnW. Phylogenetic results unambiguously support the monophyly of Phaneropterinae, although the gene order of two Sinochlora species different with other Tettigoniidae species. Using Illumina NGS platforms for mitogenome sequencing will provide rather essential and important DNA molecular data for the further phylogenetic analysis across major ensiferan lineages.

16S rRNA gene-based comprehensive analysis of microbial community compositions in a full-scale leachate treatment system.

In this study, we performed a comprehensive analysis of microbial community compositions in leachate and leachate treatment system (14 processes) during dry and rainy seasons (from February to September and from October to January, respectively), at Khanh Son landfill site, Danang City, Vietnam. In this study, raw leachate in dry and rainy seasons was predominated by Arcobacter, Clostridia, Thermotogales, Methanobacteriaceae, and Methanosaeta. During the two seasons, the system had different microbial community compositions. Orders Methanobacteriales, Clostridiales, MBA08 (order-level clone cluster), and Thermotogales predominated the influent, anaerobic pond, and anoxic pond during the dry season, while Campylobacterales and Pseudomonadales orders were predominant in the anaerobic/anoxic systems during the rainy season. In the facultative pond, aerated ponds, sediment tanks, and polishing ponds, predominant orders during the dry season included Actinomycetales, "Saprospirales", Flavobacteriales, Rhizobiales, Rhodospirillales, Burkholderiales, and Alteromonadales; during the rainy season: Sphingobacteriales, Rickettsiales, Sphingomonadales, and Pseudomonadales. In the final post treatment (polishing ponds with vegetation), significant removal of organic matter, total nitrogen, and colour occurred, while nitrogen-fixing and root-associated or related organisms predominated. This suggested that the vegetation in the ponds was essential to achieve the sufficient leachate treatment.