E Shen

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole.

Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.

Biodegradation of indole by a newly isolated Cupriavidus sp. SHE

Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resources are fairly limited. A bacterial strain designated as SHE was isolated and found to be an efficient indole degrader. It was identified as Cupriavidus sp. according to 16S rRNA gene analysis. Strain SHE could utilize indole as the sole carbon source and almost completely degrade 100mg/L of indole within 24hr. It still harbored relatively high indole degradation capacity within pH4-9 and temperature 25°C-35°C. Experiments also showed that some heavy metals such as Mn(2+), Pb(2+) and Co(2+) did not pose severe inhibition on indole degradation. Based on high performance liquid chromatography-mass spectrum analysis, isatin was identified as a minor intermediate during the process of indole biodegradation. A major yellow product with m/z 265.0605 (C15H8N2O3) was generated and accumulated, suggesting a novel indole conversion pathway existed. Genome analysis of strain SHE indicated that there existed a rich set of oxidoreductases, which might be the key reason for the efficient degradation of indole. The robust degradation ability of strain SHE makes it a promising candidate for the treatment of indole containing wastewater.

Catalytic performance and stability of C-C bond hydrolase BphD immobilized onto single-wall carbon nanotubes

Abstract Single-wall carbon nanotubes (SWCNTs) possess unique mechanical properties and extraordinary thermal conductivity, and were used as the matrix for immobilized biocatalysts. The C-C bond hydrolase BphD was immobilized on SWCNTs by physical adsorption and covalent bonding. The relative activity, stability, and reusability of the immobilized enzyme were investigated. BphD immobilized by physical adsorption retained 52.5% of the activity of free BphD, and BphD thermal stability and denaturant resistance were also improved. Covalently bound BphD exhibited the activity nearly the same as that of free BphD (99.7% of initial activity), but its stability showed no significant improvement over that of free BphD.

Genome Sequence of Sphingomonas xenophaga QYY, an Anthraquinone-Degrading Strain

ABSTRACT Sphingomonas xenophaga QYY is an efficient anthraquinone-degrading strain. Here, we present a 4.2-Mb assembly of the first genome sequence of S. xenophaga. We have annotated 36 coding sequences (CDSs) encoding aromatic catabolism and 216 CDSs responsible for toxic resistance and stress response, which may provide insights into the degradation of complex aromatics.

Tuning the substrate selectivity of meta-cleavage product hydrolase by domain swapping

Abstractmeta-Cleavage product (MCP) hydrolases can catalyze relatively low reactive carbon–carbon bond hydrolysis of products, which are derived from the meta-cleavage of catechols. The strict substrate selectivity of MCP hydrolases attracts an interest to understand the determinants of substrate specificity. Compared with conventional site-directed mutagenesis, domain swapping is an effective strategy to explore substrate specificity due to the large-scale reorganization of three-dimensional structure. In the present study, the hybrid MCP hydrolases BphDLidA and MfphALidD were constructed by exchanging the lid domain of two parental enzymes MfphA and BphD. The residues Gly130/Ala196 (MfphA) and Gly136/Ala211 (BphD) were selected as crossover points according to structural disruption score analysis and molecular dynamics simulations. It was shown that the hybrid enzymes exhibited similar substrate selectivity with the parent enzyme providing the lid domain. Docking studies suggested that the lid domain may play a key role in determining substrate specificity by reshaping the active pocket and modulating the orientation of the substrate.