Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Background

High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.

Methods

We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.

Results

Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.

Conclusions

Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.

     

Organic Acid Secretion and Phosphate Solubilizing Efficiency of Pseudomonas sp. PSB12: Effects of Phosphorus Forms and Carbon Sources

Secretion of organic acids is an important mechanism for phosphate solubilizing bacteria (PSB) to dissolve insoluble phosphorus in soil. However, the composition of organic acids produced by PSB in the presence of different phosphorus compounds is poorly known, and little is known about the ability of PSB to degrade pollutants in sediment. In this study, we isolated a strain Pseudomonas sp. PSB12 from the sediment of the Qihe River. PSB12 had maximum phosphate solubilization index (SI) of 3.86 on Pikovskaya's agar medium. The phosphate solubilizing activity was associated with the release of organic acids produced from glucose, while the composition of organic acids produced by PSB12 was dependent on the phosphorus forms. When initial soluble phosphorus was insufficient (in MP1 and MP2 media), gluconic acid was the predominant organic acid. In contrast, formic acid, butyrate, and propanedioic acid were the main organic acids produced when only soluble phosphorus (MP3) was supplied. RT-PCR indicated that the expression of glucose dehydrogenase gene (gcd) of PSB12 was two- to four-fold higher in MP1 than in MP3. PSB12 also possessed the phenol hydroxylase gene (phe) suggesting that phenol could be used as the carbon source to dissolve insoluble phosphorus. PSB12 is a potential candidate for in situ bioremediation and for promoting plant growth in soil contaminated by phenol with low levels of soluble phosphorus.     

Gene markers for exon capture and phylogenomics in ray‐finned fishes

Gene capture coupled with the next‐generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray‐finned fishes. Here, we identified a suite of “single‐copy” protein‐coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and nine orders or higher clades: Acipenseriformes, Lepisosteiformes, Elopomorpha, Osteoglossomorpha, Clupeiformes, Cypriniformes, Gobiaria, Carangaria, and Eupercaria; sensu Betancur et al. 2013). Sorting the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray‐finned fishes at different taxonomic levels. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may greatly enrich the batteries of exon markers for phylogenomic study in ray‐finned fishes.     

Efficient immobilization behavior and mechanism investigation of Pb(II) by Aspergillus tubingensis

Biotechnology Letters - To understand the mechanism of Pb(II) immobilized by Pb(II)-tolerant microbes. Aspergillus tubingensis isolated from the lead-zine mine was investigated through surface...