LIU Shuangjiang

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Feb 12, 2013 (4 years and 6 months ago)

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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
)
environme
nts.

Dr. Liu graduated from the
department

of microbial biochemistry at Hebei
University (Baoding) in 1984, and later obtained his
degree
s of master (Ms.A., 1987)
and doctor (Ph.D., 1991) from Zhejiang University (Hangzhou) and Tsinghua
University (Beijing
), respectively.
H
e 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
E
nvironmental

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 postdoc
s (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 mi
crobiology. 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 a
nd
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
demand
s
and the sh
ortage 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 suc
h 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 th
e 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.
M
ore than
thousands

of
bacterial strains were isolated. A few of them have been characterized, some were
identified as novel sp
ecies, 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 in
volved 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 st
rain 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, bec
ause 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
-
chloro
nitrobenzene 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: Choloni
trobenzene 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 w
e 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 occur
rence 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 or
ganism 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 experimen
tal 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 protocat
echuat
e 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 geomochem
ical 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 b
eneficially 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 materia
ls.

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

re
ductase (SOR)
,
involved in oxidation of So during aerobic
cultivation is

studied
.
T
he 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 dete
rmination of SOR activities in
cytoplasmic fraction and membrane fraction, we f
urther discovere
d

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.
R
hodopseudomonas 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. Rhodoci
sta
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 p
roperties 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 Chin
a.
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.
I
nt.
J
.
S
yst.
E
vol.
M
icrobiol
.

54:2091
-
2094.

7.

J. Feng, P. Zhou, Y.
-
G. Zhou, S.
-
J. Liu a
nd 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
Coryneba
cterium
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 alka
noclasticus

to
Planomicrobium

as
Planomicrobium psychrophilum

comb.
nov. and
Planomicrobium alkanoclasticum

comb. nov.
I
nt.
J
.
S
yst.
E
vol.
M
icrobiol.
2005; 55:
699
-

702
.

13.

Zhi
-
Pei Liu, Bao
-
Jun Wang, Ying
-
Hao Liu, and Shuang
-
Jiang Liu
2005.
Novosphingobium
t
aihuense

sp. nov. a new aromatic compound
-
degrading bacterium isolated from Taihu Lake,
China
.
I
nt.
J
.
S
yst.
E
vol.
M
icrobiol.
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
.
I
nt.
J
.
S
yst.
E
vol.
M
icrobiol.
2005; 55: 1239
-

1242
.

15.

Xue
-
Wei Xu, Min Wu, Pei
-
Jin Zhou, Shuang
-
Jiang Liu 2005.
Halobiforma lacisalsi

sp.
N
ov.,
isolated from a solt lake in China.
Int. J. Syst. Evol. Micro
bio
l. 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 Hu
ang 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
Shua
ng
-
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
fr
om 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 mic
robial strains for bioremediation and bioaugumentation will be
strengthened further in the following 3
-
5 years.