Vol 1, No 1 (2016)

Table of Contents


539 Views, 237 PDF Downloads
Ji-Dong Gu




Biodegradation Microbiology

3561 Views, 327 PDF Downloads
Honghong Chen, Hui Wang, Tongtong Wang, Songren Huang, Xiaoxia Zang, Shunpeng Li, Jiandong Jiang


Chlorothalonil hydrolytic dehalogenase (Chd) is one of two reported hydrolytic dehalogenases for halogenated aromatics, and its catalysis is independent of coenzyme A and ATP. Earlier studies have established that the catalytic activity of Chd requires zinc ions. In this study, the metal center of Chd was systematically investigated. The metal content of Chd was determined by inductively coupled plasma-atomic emission spectrometry (ICP-AES), and there were 2.14 equivalents of zinc/mol of protein, indicating that Chd contains a binuclear (Zn2+-Zn2+) center. It was found that other divalent cations, such as cobalt (Co2+) and cadmium (Cd2+), could substitute zinc (Zn2+) leading to relative activities of 91.6% and 120.0%, whereas manganese (Mn2+) and calcium (Ca2+) could substitute Zn2+ leading to relative activities of 29.1% and 57.0%, respectively. The enzymatic properties of these different metal ion-substituted Chd variants were also compared. Error-prone PCR and DNA shuffling methods were applied to directly evolve Chd to generate variants with higher catalytic efficiencies of chlorothalonil. Enhanced Chd variants were selected based on the formation of clear haloes on Luria-Bertani plates supplemented with chlorothalonil. One variant, Q146R/N168Y/S303G, exhibited a 4.43-fold increase in catalytic efficiency, showing the potential for application in the dehalogenation and detoxification of chlorothalonil contaminated-sites.

1713 Views, 748 PDF Downloads
Ji-Dong Gu


Biodegradation tests have been conducted for testing the degradation of environmental pollutants for at least half a century, but little innovations and new information have been made available from the more recent efforts. In this context, substrate, microorganisms, enrichment and degradation are discussed critically to summarize the essential approaches for biodegradation testing and also the new directions in this area of research. The information intends to pro-vide some essential assistance to individuals working on this topic in their research and applications.

659 Views, 225 PDF Downloads
Guojun Wu, Menghui Zhang, Chaochun Wei, Yun Wang, Xiangyu Yao, Liping Zhao, Xiaojun Zhang


The draft genome sequence of Thauera sp. DTG was reconstructed from a metagenome of a denitrifying quinoline degrading microbial consortium. The organism is most closely related to Thauera aminoaromatic S2 and Thauera sp. MZ1T and is a facultative anaerobe. It is predicted to take the central role for quinoline denitrifying degradation.

643 Views, 293 PDF Downloads
Xuejiao Zhu, Minsheng Huang, Qiuzhuo Zhang, Varenyam Achal


The biodegradation ability of Citrobacter sp. FL5 on fluorene was investigated in the present study. The bac-terial isolate was identified based on biochemical test, physiological and 16S rDNA sequence analysis. Fluorene biodegradation was studied in the liquid media at the initial concentration of 50 mg L−1 fluorene at different pH values (6, 7, 8 and 9) and temperatures (25, 30, 37 and 45°C). Citrobacter sp. FL5 showed maximum performance of fluorene degradation ability at pH 7 and 30°C where it degrades 98% fluorene in liquid media. Furthermore, the isolate degrades 97.5% and 96% of 100 and 150 mg L–1 fluorene respectively at 168 hrs. The possible metabolic pathway for fluorene biodegradation by Citrobacter sp. FL5 was deduced by identification of metabolites through Gas Chromatography Mass Spectrometry (GC-MS) technique. 5 types of metabolites that were detected and identified were dibenzofuran, 9-fluorenylmethanol, methyl benzilate, piperonylic acid and catechol. This study was the first to report and describe the ability of Citrobacter sp. in detail for degradation of higher fluorene concentrations at various pH and temperatures ranges.

646 Views, 264 PDF Downloads
Karen Choi-Wan Yip, Ji-Dong Gu


A bacterial strain, designated as MPKc, was isolated from the mudflat sediment of Mai Po Inner Deep Bay of Hong Kong Mai Po Nature Reserve by enrichment culturing with 2-methylindole as the sole source of carbon and energy. The microorganism was a Gram-negative, rod-shaped (0.4–0.6 μm × 1.0–2.2 μm) and aerobic bacterium. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain MPKc should be assigned as a novel bacterium, at least, at the species level. The 16S rDNA sequence most similiar to that of strain MPKc was Azoarcus evansii (94%) from available 16S rDNA sequences of the GenBank, indicating that strain MPKc was a member of the β-subclass of the Proteobacteria. Biochemical tests showed that strain MPKc was able to reduce nitrate to nitrogen. Carbon sources utilized by this strain included adipic acid, malate, citrate and phenylacetic acid although it only grew weakly on glucose, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose and gluconate. Strain MPKc showed no growth on capric acid. Its optimal growth occurred at 30°C, pH 6.5–7.5 and salinity 5–10‰. Strain MPKc was capable of degrading 80 μM 2-methylindole in 7 days under aerobic conditions. The possible chemical pathway for 2-methylindole degradation is through oxidation at 3-position or/and 2-position of the pyrrole ring.


Gut Microbiology

5709 Views, 324 PDF Downloads
Hao Fang, Wen Chen, Baojun Wang, Xiaojuan Li, Shuang-Jiang Liu, Hong Yang


The complex symbiotic relationship between wood-feeding termites and microorganisms inhabiting their intestinal tracts is a fascinating phenomenon in nature. To understand the physiological functions of symbiotic micro-organisms, bacteria were isolated from the gut homogenate of Reticulitermes chinensis with different media and culture conditions. Under aerobic conditions, 105 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified basal mineral medium, MM-4. Most dominant isolates were bacteria in the genera Bacillus (27.6%) and Lactococcus (21.9%). Under anaerobic conditions, 60 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified Peptone-Yeast medium. The predominant isolates were bacteria in the genus Enterobacter (41.7%) and Citrobacter (33.3%). Many of these bacterial isolates shared high sequence similarity (>98%) in 16S rRNA genes to bacterial clones obtained from the same termite and the other wood-feeding termites or cockroaches. Several bacterial species such as Deinococcus and Gryllotalpicola were isolated from termite gut for the first time. Characterization of these isolates showed that (i) most of Enterobacteriaceae and Lactococcus strains were able to hydrolyze uric acid; and (ii) many of the Bacillus and Streptomyces strains presented endo-β-1,4-glucanase activity. The preliminary results of this work gave us hints of possible functions of symbiotic bacteria in nitrogen recycling and cellulose degradation in the gut of wood-feeding termites

848 Views, 285 PDF Downloads
Ho Wang Chan, Han Meng, Ji-Dong Gu


Anammox bacteria serve an important ecological role in the global nitrogen cycle, enabling the coupling of ammonium and nitrite to yield dinitrogen gas (N2) under anoxic conditions. Based on PCR amplifications of genomic DNA and analysis of the 16S rRNA gene sequence, anammox bacteria was found in intestinal tracts of two types of fish, Siganus fuscescens and Mugil cephalus. Anammox bacteria identified in these fish belonged to the genera Brocadia and Kuenenia, suggesting that the living conditions of S. fuscescens and M. cephalus were under significant influence of wastewater pollution. Our results showed an association between the existence of anammox bacteria in fish intestinal tracts and sediment- or mud-eating habits of the fish involved. The presence of anammox bacteria in an animal system would provide a more comprehensive understanding on ecophysiological characteristics and distribution of anammox bacteria. This discovery might also provide useful information about the living conditions of fish, serving as an environmental indicator of anthropogenic pollution.

983 Views, 177 PDF Downloads
Meng Li, Ji-Dong Gu


Neanthes are one of the most important groups of polychaete in coastal sediments, which play an important role on the nutrient cycling in coastal sediments. Here we report on the existence of anammox bacteria in the gut of polychaete Neanthes glandicincta based on the analysis of 16S rRNA gene and fluorescence in situ hybridization (FISH). Three distinct clusters of anammox bacteria are found in different gut sections of N. glandicincta, and one of them is considered as a novel, gut specific anammox bacteria after comparing with the anammox bacteria recovered from surrounding pre-digested sediment. The uniform axial distribution of anammox bacteria in different gut sections of N. glandicincta is also found in present study. These results extend our knowledge of microbial ecology of anammox bacteria in the natural environments.


Phytoremediation and Antibiotics

669 Views, 207 PDF Downloads
Xiao-Zhang Yu, Xing-Hui Feng


This paper presents an investigation of the effects of trivalent chromium on biomass growth (RGR), water use efficiency (WUE) and distribution of nutrient elements in young rice seedlings (Oryza sativa L. cv. XZX 45) exposed to chromium nitrate (Cr(III)) hydroponically. Results indicated that phytotoxicity of Cr(III) to rice seedlings was apparent, showing an linear decrease in both RGR and WUE with increasing Cr(III) concentrations. Using the Leven-berg-Marquardt Algorithm, the effective concentrations (EC) obtained from the RGR were always smaller than these from WUE, indicating that the former was more sensitive to change of Cr(III) application than the latter. Although a dose-dependent total accumulation rate of Cr in plant materials was observed, the translocation of Cr into shoots was a restricted process during phytotransport of Cr within plant materials. Results also showed that the effect of Cr(III) application on uptake and distribution of nutrient elements in rice seedlings was variable. In conclusion, the toxic response of young rice seedlings to Cr(III) was obvious and inhibitory effects were highly dependent on the total accumulation rate of Cr in plant materials.

736 Views, 220 PDF Downloads
Jian Wang, Haiqing Pu, Lin Ye, Liangyan Chen, Xuxiang Zhang


Antibiotic resistance genes (ARGs), a potential threat to the health of humans and animals, have been widely detected in various environments. However, not much information about ARGs in freshwater lakes have been recorded. In this study, we investigated the occurrence of 17 kinds of ARGs and three types of integronase genes in Taihu Lake (China), an important drinking water source for local residents. Fecal coliforms were also isolated from the water and sediments for antimicrobial susceptibility tests and related ARGs detection. Results showed that tetracycline resistance gene tetC, sulfanilamide resistance genes sul1 and sul2, and class 1 integronase gene int1 were present in all water and sediment samples. TetG was present in all water samples but was mainly distributed in sediment samples from the northern region of Taihu Lake. β-Lactam resistance gene blaOXA-1 was present in all water samples but was absent in the sediment samples. TetM and tetO were found present in water and sediment samples from the western area of the lake. Remarkably, 95% of isolated fecal coliforms were resistant to trimethoprim and multi-drug resistant isolates were also observed. Sul1 and tetC genes were found to be carried by isolates resistant to corresponding antibiotics. This study provided baseline information about the occurrence of ARGs and integronase genes in Taihu Lake and the results may extend our knowledge about antibiotic resistance of microbial communities in the lake.


Tree Disease and Diagnosis

1190 Views, 464 PDF Downloads
Yong-Feng Wang, Han Meng, Victor W. Gu, Ji-Dong Gu


Phellinus noxius (P. noxius) is an important pathogen that causes brown root rot of trees in tropical and sub-tropical areas and has led to severe damage to trees. A quick and accurate diagnostic technique is essential to the timely confirmation of the pathogen and possible treatment. In this study, a fast, sensitive and accurate approach of molecular technique was used to diagnose the brown root rot pathogen on trees and in soils of subtropical Hong Kong. Two pairs of specific PCR primers were used to amplify the target rDNA internal transcribed spacer (ITS) region through polymerase chain reaction (PCR) for both tree tissues and soil samples. The amplified ITS fragments were then sequenced and analyzed phylogenetically for the diagnostic identification of the pathogen P. noxius. The results showed that 13 of 38 suspected trees in Hong Kong were infected with P. noxius through molecular detection. The pathogen showed no specific preference to any particular tree species. Quantitative PCR was applied to soils grown with trees identified both positive and negative for P. noxius, but the soils with healthy trees were also found positive for P. noxius. For the first time, P. noxius was reported to infect a wide range of tree species in Hong Kong and widely presented in soils, probably serving as a reservoir for the pathogen. Through this study, it is proposed that P. noxius is a soil-borne pathogen, which increases its infectivity when trees start to grow in the soil as a means in addition to the previously proposed root-to-root contact.


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