Zhisheng Yu

Pyrosequencing analysis of eukaryotic and bacterial communities in faucet biofilms

In order to understand the microbial communities in drinking water biofilms, both eukaryotic and bacterial communities in three faucet biofilms were characterized by 454 pyrosequencing and quantitative PCR approaches. Microbial assemblages of the biofilms were dominated by bacteria, with Sphingomonadales, Rhizobiales, and Burkholderiales comprising the major bacterial populations. Although about 2 years of biofilm development occurred, the microbial community at site WSW still demonstrates the characteristics of a young biofilm community, e.g. low biomass, abundant aggregating bacteria (Blastomonas spp. and Acidovorax spp.) etc. Hartmannella of amoebae was the dominant eukaryotic predator in the biofilms, and correlated closely with biofilm bacterial biomass. Nonetheless, there was no obvious association of pathogens with amoebae in the faucet biofilms. In contrast, residual chlorine seems to be a dominant factor impacting the abundance of Legionella and Mycobacterium, two primary potential opportunistic pathogens detected in all faucet biofilms.

Diversity of bacteria and mycobacteria in biofilms of two urban drinking water distribution systems

In this study, to give insight into the bacterial diversity of biofilms from full-scale drinking water distribution systems (DWDSs), the bacterial community compositions of biofilms from two urban DWDSs (Guangzhou and Beijing, China) were determined using a 16S rRNA gene library technique. Meanwhile, the occurrence and diversity of mycobacteria were also analyzed by a Mycobacterium -specific hsp gene assay. The biofilms from the full-scale DWDSs have complex bacterial populations. Proteobacteria was the common and predominant group in all biofilm samples, in agreement with previous reports. The community structures of bacteria at the three sites in Guangzhou DWDS were significantly different, despite the similar physicochemical properties of portable water. Some abundant and peculiar bacterial phylotypes were noteworthy, including Methylophilus , Massilia, and Planomicrobium , members of which are rarely found in DWDSs and their roles in DWDS biofilms are still unclear. The diversity of Mycobacterium species in biofilm samples was rather low. Mycobacterium arupense and Mycobacterium gordonae were the primary Mycobacterium species in Guangzhou and Beijing biofilms, respectively, indicating that M. arupense may be more resistant to chloride than M. gordonae.

Strain improvement for enhanced production of cellulase in Trichoderma viride.

The filamentous fungi Trichoderma species produce extracellular cellulase. The current study was carried out to obtain an industrial strain with hyperproduction of cellulase. The wild-type strain, Trichoderma viride TL-124, was subjected to successive mutagenic treatments with UV irradiation, low-energy ion beam implantation, atmospheric pressure non-equilibrium discharge plasma (APNEDP), and N-methyl-N′-nitro-N-nitrosoguanidine to generate about 3000 mutants. Among these mutants, T. viride N879 strain exhibited the greatest relevant activity: 2.38-fold filter paper activity and 2.61-fold carboxymethyl cellulase, 2.18-fold β-glucosidase, and 2.27-fold cellobiohydrolase activities, compared with the respective wild-type activities, under solid-state fermentation using the inexpensive raw material wheat straw as a substrate. This work represents the first application of APNEDP in eukaryotic microorganisms.

Enhancement of the Gibberella zeae growth inhibitory lipopeptides from a Bacillus subtilis mutant by ion beam implantation.

Bacillus subtilis JA antagonized the growth of Gibberella zeae. In order to reduce growth of this fungi pathogen to a greater extent, low-energy ion beam implantation was applied in mutant breeding. We studied the effects of different energies and different doses of nitrogen ion implantation. The mutant strain designated as JA026 was obtained showing higher inhibition activity in the screening plate. Its inhibition zone against indicator organism increased by 14.3% compared to the original strain. The electrospray ionization mass spectrometry (ESI/MS) analysis indicated that the antifungal lipopeptides produced by the mutant were identical to those produced by the wild-type strain. The mutant strain exhibited favorable properties including the high yield of antifungal lipopeptides production and faster growth over the parent strain, which suggested that this strain would be a promising biocontrol candidate in agriculture.

Removal of fluoride and arsenic by pilot vertical-flow constructed wetlands using soil and coal cinder as substrate

This study evaluated the performance of soil and coal cinder used as substrate in vertical-flow constructed wetlands for removal of fluoride and arsenic. Two duplicate pilot-scale artificial wetlands were set up, planted respectively with cannas, calamus and no plant as blank, fed with a synthetic sewage solution. Laboratory (batch) incubation experiments were also carried out separately to ascertain the fluoride and arsenic adsorption capacity of the two materials (i.e. soil and coal cinder). The results showed that both soil and coal cinder had quite high fluoride and arsenic adsorption capacity. The wetlands were operated for two months. The concentrations of fluoride and arsenic in the effluent of the blank wetlands were obviously higher than in the other wetlands planted with cannas and calamus. Fluoride and arsenic accumulation in the wetlands body at the end of the operation period was in range of 14.07-37.24% and 32.43-90.04%, respectively, as compared with the unused media.

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

BackgroundToxic compounds present in both the hydrolysate and pyrolysate of lignocellulosic biomass severely hinder the further conversion of lignocellulose-derived fermentable sugars into useful chemicals by common biocatalysts like Zymomonas mobilis, which has remarkable advantages over yeast. Although the extra detoxification treatment prior to fermentation process can help biocatalysts to eliminate the inhibitory environment, it is not environment friendly and cost effective for industrial application. As also reported by previous studies, an ideal and holistic approach to solve this issue is to develop microbial strains with inhibitor tolerance. However, previously engineered strains had the limitation that they could not cope well with the synergistic effect of multiple inhibitors as they are resistant only to a single inhibitor. Hence, understanding the universal cellular responses of Z. mobilis to various inhibitors may guide the designing of rational strategies to obtain more robust engineered strains for biofuel production from lignocellulosic biomass.ResultsQuantitative proteomics and metabolomics approaches were used to determine the cellular responses of Z. mobilis ZM4 to representative biomass-derived inhibitors like formic acid, acetic acid, furfural, 5-hydroxymethylfurfural, and phenol. The differentially expressed proteins identified under the challenge of single and combined inhibitors were involved in cell wall/membrane biogenesis, energy production, DNA replication, DNA recombination, DNA repair, DNA transcription, RNA translation, posttranslational modification, biosynthesis of amino acids, central carbon metabolism, etc. Metabolomics analysis showed that the up- or down-regulation pattern of metabolites was changed consistently with that of relevant proteins.ConclusionFifteen up-regulated proteins (e.g., Isopropylmalate isomerase LeuC, transcription-repair-coupling factor Mfd, and phosphoglucose isomerase PGI) and thirteen down-regulated proteins (e.g., TonB-dependent transporter ZMO1522, transcription termination factor Rho, and S1/P1 nuclease ZMO0127) were identified as candidate proteins related to all the stress conditions, implying that these proteins are potential biomarkers for the improvement of Z. mobilis ZM4 to resist complex biomass-derived inhibitors. These data can be used to generate a database of inhibitor-tolerance biomarkers, which could provide a basis for engineering Z. mobilis that would be able to grow in the presence of multiple inhibitors and directly ferment the biomass-derived sugars into biofuels.

Fermentation of Detoxified Acid-Hydrolyzed Pyrolytic Anhydrosugars into Bioethanol with Saccharomyces cerevisiae 2.399

Pyrolysate obtained from the pyrolysis of waste cotton is a source of fermentable sugars that could be fermented into bioethanol fuel and other chemicals via microbial fermentation. However, pyrolysate is a complex mixture of fermentable and non-fermentable substrates causing inhibition of the microbial growth. The aim of this study was to detoxify the hydrolysate and then ferment it into bio-ethanol fuel in shake flasks and fermenter applying yeast strain Saccharomyces cerevisiae 2.399. Pyrolysate was hydrolyzed to glucose with 0.2 M sulfuric acid, neutralized with Ba(OH)2 followed by treatment with ethyl acetate and activated carbon to remove fermentation inhibitors. The effect of various fermentation parameters such as inoculum concentration, pH and hydrolysate glucose was evaluated in shake flasks for optimum ethanol fermentation. With respect to inoculum concentration, 20% v/v inoculum i.e. 8.0 × 108–1.2 × 109 cells/mL was the optimum level for producing 8.62 ± 0.33 g/L ethanol at 9 h of fermentation with a maximum yield of 0.46 g ethanol/g glucose. The optimum pH for hydrolysate glucose fermentation was found to be 6.0 that produced 8.57 ± 0.66 g/L ethanol. Maximum ethanol concentration, 14.78 g/L was obtained for 4% hydrolysate glucose concentration after 16 h of fermentation. Scale-up studies in stirred fermenter produced much higher productivity (1.32 g/L/h–1) compared to shake flask fermentation (0.92 g/L/h–1). The yield of ethanol reached a maximum of 91% and 89% of the theoretical yield of ethanol in shake flasks and fermenter, respectively. The complex of integrated models of development was applied, that has been successfully tested previously for the mathematical analysis of the fermentation processes.