Research Overview of the team of
Environmental Microbiology
Prof. Dr. Shuang-Jiang LIU
Part I. Introduction The research team of Environmental Microbiology, led by Dr. LIU, Shuang- Jiang, focuses on the researches of microbial systems that are related to environmental processes, such as microbial degradation of pollutants, microbial conversion of elemental sulfur, and so on. Also interested are cultivation of new microbes from different environments, including polluted and non-polluted (pristine) environments. Dr. Liu graduated from the department of microbial biochemistry at Hebei University (Baoding) in 1984, and later obtained his degrees of master (Ms.A., 1987) and doctor (Ph.D., 1991) from Zhejiang University (Hangzhou) and Tsinghua University (Beijing), respectively. He worked as an assistant/associate professor at the Institute of Microbiology, Chinese Academy of Sciences (IM/CAS) during 1991- 1995. He worked as postdoc and guest scientist in Germany (University of Muenster), Japan (National Institute of Human Science and Biotechnology, Tsukuba), United States of American (James Madison University, Harrisonburg) during 1995-2001. He joined the team of IM/CAS in Feb. 2001 and took the leadership of environmental microbiology. He is currently editors for “Journal of Biotechnology (China)”, “Journal of Environmental Science (China)”, “Microbes and Environments (Japan)”. Currently, the team has 2 associate professors (Mr. WANG, Baojun, Mr. LIU, Zhipei), 1 assistant professor (Dr. JIANG, Chengying), 1 postdocs (Dr. QI, Suwei), 10 Ph.D. students and 2 graduate students, 2 international students (from Pakistan), and a couple of visiting scholars from other institutions.
Part II. Background and Significance Environmental microbiology is an important branch of microbiology. In the past years, it has been contributed novel knowledge of biodegradation of pollutants and also the improvement of environments by development of new technology for waste (water) treatment and bioremediation. Nowadays, it is becoming more and more important: The sustainable development of human society needs more resources and high quality of environments, and environmental microbiology potentially provides better solution to eliminate the conflict between increasing human demands and the shortage of resources. We deal with various environments and microorganisms, and try to understand the harmony of such systems: What microbes are there, how those microbes fit their ecological roles, and what are the gain and loss of the environments by such microbial activities? Being involved in several national projects of the Natural National Sciences Foundation of China (NSFC) and Ministry of Sciences, we cultivated novel microbial strains from fresh and salty lakes, polluted soils, wastewater treatment facilities, and thermal vents. We investigated the metabolism of aromatic compounds in the newly isolated strains (e.g. Comamonas strain CNB-1, Delftia strain AN-3) as well as in the model strain such as Corynebacterium glutamicum. We also investigated the microbial conversion of sulfur by a thermoacidophilic archaeon, Acidianus tengchongensis, which was isolated from a thermal vent in Yunnan, China.
Part III. Major Achievements 1. Isolation and characterization of new microbes: In the past 4 years, efforts have been made to obtained new microorganisms from various environments, by modification of conventional cultivation techniques. More than thousands of bacterial strains were isolated. A few of them have been characterized, some were identified as novel species, and some others were identified as important strains that degrade various aromatic compounds (Please see the publication list). 2. Degradation of aniline by Delftia strain AN3: Most aniline degraders adopt a strategy that includes hydroxylation the ortho-carbon atom to the ammonium group. Based on our study, Delftia strain AN3 takes a different way: It removes the ammonium group through a dioxygenase that directly attack the carbon atom of which the ammonium group attached. Thus, a novel step that involved in aniline degradation is proposed based on the study of aniline degradation with strain AN3 (The University of Minnesota Biodegradation/Biocatalysis database, http://umbbd.ahc.umn.edu/nb/nb_map). The metabolic pathway of aniline degradation with strain AN3 has been extensively studied at enzymatic and genetic levels. Results indicated that this AN3 took a pathway of 2,3-dioxygenase catalysis. 3. Degradation of chloronitrobenzene: Choloronitrobenzenes are especially resistant to microbial attack, because of the existence of two electron-withdrawing groups, chlorine and nitro-group. Until recently the understanding of microbial degradation of chloronitrobenzene are very poor. We have isolated and identified a Comamonas strain CNB-1, which uses 4-chloronitrobenzene as sole carbon and energy resource, from activated sludge of a wastewater treatment plant. Studies were focused on its degradative pathway, at enzymatic and genetic levels, and results showed that it adopts a partial reductive pathway: Cholonitrobenzene is first reduced by reductase and subsequently converted to 6-aminochlorophenol. This compound is cleaved by an aminophenol 1,6-dioxygenase. The whole gene cluster that involved in cholronitrobenzene degradation has been cloned, sequenced, and we are identifying each ORFs on this gene cluster. 4. Genomic study of aromatic compounds by corynebacterium gluamicum: Many members of Corynebacterium occurred in soil and sediments, and took part in decomposition of aromatic compounds. The universal occurrence and versatile metabolisms of organisms belongs to Corynebacterium make this group of bacteria be ecologically, medically and economically important. As an example, Corynebacterium glutamicum produces several amino acids commercially and is a model organism to study physiology and biochemistry of this group of bacteria. Recently, the entire genome of C. glutamicum ATCC13032 has been sequenced. We investigated the catabolism of aromatic compounds with C. glutamicum by genome data mining and by experimental study. Results indicated that C. glutamicum assimilated different aromatic compounds. Genome data predicted, and enzyme assays confirmed the existence of multiple ring-cleavage pathways for the catabolism of central aromatic intermediates, the protocatechuate and catechol branches of the β-ketoadipate pathway, two similar hydroxyquinol pathways and the gentisate pathway. A novel gene encoding a GSH-independent maleylpyruvate isomerase was identified. 5. Sulfur conversion in thermovents: Biologically geomochemical cycle of sulfur is an essential part of the whole geochemical cycles of various elements. In addition, the bio-oxidation and -reduction of sulfur-containing compounds to sulfite, sulfate, and sulfide etc. are vital to economy: Oxidation of sulfur is beneficially exploited for bioleaching or biomining that becomes more and more important for recovery of high-value metals such as copper and gold from low-graded ores, while reduction of sulfur or sulfate to sulfide causes detrimental corrosions of materials. A thermoacidophilic archaeon, Acidianus strain S5, grows optimally at 70oC and at pH 2.5, oxidizes elemental sulfur (So) to sulfate when cultivated aerobically, or reduces So to sulfide when cultivated anaerobically. The key enzyme, sulfur oxygenase reductase (SOR), involved in oxidation of So during aerobic cultivation is studied. The gene (sor) encoding for the SOR enzyme was cloned and actively expressed in E. coli. An easy procedure to purify the SOR from recombinant E. coli was established. By determination of SOR activities in cytoplasmic fraction and membrane fraction, we further discovered that this SOR locates in the membrane fraction as well in the cytoplasmic fraction.
Publication list:
1. D. Zhang, H. Yang, Z. Huang, W. Zhang, and S. J. Liu. Rhodopseudomonas faecalis sp. nov.,
a phototrophic bacterium isolated from an anaerobic reactor that digests chicken faeces. Int J
Syst Evol Microbiol, 2002; 52: 2055 - 2060.
2. Demin Zhang, Huifang Yang, Wei Zhang, Zhiyong Huang, and Shuang-Jiang Liu. Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater
treatment plant. Int J Syst Evol Microbiol, 2003; 53: 1111 - 1114.
3. Cui-wei Sun, Zhi-wei Chen, Zheng-guo He, Pei-jin Zhou, Shuang-Jiang Liu. 2003.
Purification and properties of the sulfur oxygenase/reductase from the acidothermophilic
archaeon, Acidianus strain S5. Extremophiles 7, 131 - 134
4. J. Feng, P. Zhou, and S.-J. Liu 2004. Halorubrum xingjiangense sp. nov., a novel halophile
isolated from saline lakes in China. Int. J. Syst. Evol. Microbiol. 54:1789-1791
5. X. Shen, Z. Liu, S.-J. Liu 2004. Functional identification of the gene locus (ncg12319) and
characterization of catechol 1,2-dioxygenase in Corynebacterium glutamicum Biotechnol.
Lett. 26:575-580.
6. Y.-T. Hu, P.-J. Zhou, Y.-G. Zhou, Z.-H. Liu and S.-J. Liu 2004. Saccharothrix xinjiangensis
sp. nov., a pyrene-degrading actinomycete isolated from Tianchi lake, Xinjiang, China. Int. J.
Syst. Evol. Microbiol. 54:2091-2094.
7. J. Feng, P. Zhou, Y.-G. Zhou, S.-J. Liu and K. Warren-Rhodes. 2005 Halorubrum
alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China Int.
J. Syst. Evol. Microbiol.; 55: 149-152.
8. J-F Wu, C-W Sun, C-Y Jiang, Z-P Liu, and S-J Liu 2005. A novel 2-aminophenol 1,6-
dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-
1: purification, properties, genetic cloning and expression in Escherichia coli. Arch.
Microbiol. 183:1-8.
9. X-H Shen and S-J Liu 2005. Key enzymes of the protocatechuate branch of the –ketoadipate
pathway for aromatic degradation in Corynebacterium glutamicum. Science in China.
48:241-249.
10. Z-W Chen, C-Y Jiang, Q She, S-J Liu, P-J Zhou 2005. Key role of Cysteine Residues in
catalysis and Subcellular Localization of Sulfur Oxygenase Reductase of Acidianus
tengchongensis. Appl. Environ. Microbiol. 2005 71: 621-628
11. X-H Shen, C-Y Jiang, Y Huang, Z-P Liu, S-J Liu 2005. Functional identification of novel
genes involved in the glutathione-independent gentisate pathway in Corynebacterium
glutamicum. Appl. Environ. Microbiol. 2005 71: 3442-3452
12. X. Dai, Y.-N. Wang, B.-J. Wang, S.-J. Liu and Y. G. Zhou 2005. Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and
Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb.
nov. and Planomicrobium alkanoclasticum comb. nov. Int. J. Syst. Evol. Microbiol. 2005;
55: 699 - 702.
13. Zhi-Pei Liu, Bao-Jun Wang, Ying-Hao Liu, and Shuang-Jiang Liu 2005. Novosphingobium
taihuense sp. nov. a new aromatic compound-degrading bacterium isolated from Taihu Lake,
China. Int. J. Syst. Evol. Microbiol. 2005; 55: 1229 - 1232.
14. Zhi-Pei Liu, Bao-Jun Wang, Shuang-Jiang Liu and Ying-Hao Liu 2005. Asticcacaulis
taihuensis sp. nov., a new stalked bacterium isolated from Taihu Lake, China. Int. J. Syst.
Evol. Microbiol. 2005; 55: 1239 - 1242.
15. Xue-Wei Xu, Min Wu, Pei-Jin Zhou, Shuang-Jiang Liu 2005. Halobiforma lacisalsi sp. Nov.,
isolated from a solt lake in China. Int. J. Syst. Evol. Microbiol. 55,1311-1314
16. Jie Feng, Hong-Can Liu, Jin-Fang Chu, Ji-An Tang, Shuang-Jiang Liu 2005. Genetic cloning
and functional expression in Escherichia coli of an archaerhodopsin gene from Halorubrum
xinjiangense. Extremophiles. (accepted)
17. Xi-Hui Shen, Yan Huang Shuang-Jiang Liu 2005. Genomic analysis and identification of
catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Microbes and
Environments. (accepted)
18. Ying Huang, Xin Dai, Liang He, Ya-Nan Wang, Bao-Jun Wang, Zhi-Heng Liu and Shuang-
Jiang Liu 2005. Sanguibacter marinus sp. nov., isolated from coastal sediment of Eastern
China Sea. Int. J. Syst. Evol. Microbiol. (accepted)
Part IV. Future Research Plan We will continue the work on isolation and characterization of novel microbes from various environments. We will work out the complete pathway of chloronitrobenzene and its regulation. The work on Corynebacterium glutamicum will be expended to develop novel bioprocesses for biotransformation of valued products. Applications of our microbial strains for bioremediation and bioaugumentation will be strengthened further in the following 3-5 years.