SA

LT

PRESSURE

PH

Extremophiles & Application

Microbial Resource Center

KRIBB

Byoung-Chan Kim

2

• 1991 ~ 1995

• 1995 ~ 1997

• 1997 ~ 2001

• 2001 ~ 2003

• 2003 ~ 2007

• 2007 ~ 2009

• 2009 ~ current

: Bachelor, Department of Food Engineering, Yonsei Univ.

: Master, Department of Food and Biotechnology, Yonsei Univ.

: Ph.D. Department of Biotechnology, Yonsei Univ.

Hyperthermophiles

: Full-time Researcher, Bioproduct Research Center, Yonsei.Univ.

Hyperthermophiles

: Post-doc, Department of Microbiology, Univ. of Mass

Geobacter

: Research Assistant Professor, Department of Microbiology, Univ. of Mass

Geobacter

: Senior Research Scientist, KRIBB

Methanogen

Kim, Byoung-Chan Ph.D.

Origin of Life

종류 특징

Thermophiles

Psychrophile

Alkaliphile

Acidophile

Halophile

Piezophile (=Barophile)

Endloith

Oligotroph

Toxitolerant

Xerotolerant

Radioresistant

Methanogens

55(초고온균 80)에서최적으로생육하는미생물

15 이하에서최적으로생육하는미생물

pH9 이상에서최적으로생육하는미생물

pH3 이하에서최적으로생육하는미생물

0.2M 이상의염농도를생육에필요로하는미생물

고압에서최적으로생육하는미생물

암석안에서자라는미생물

영양성분이낮은상태에서자라는미생물

독성물질의존재하에생육하는미생물

낮은수분의존재하에생육하는미생물

1,000 Gy 이상의방사능에서생육가능한미생물

메탄생성절대혐기성고세균

Extremophiles

5

Hyperthermophiles

Geobacter Methanogen

절대혐기극한미생물

Strict Anaerobic Culture System

cupper gas line (H2, CO2, N2, mix)

Anaerobic Chamber Cupper column for removing oxygen

Gassing Manifold

7

Pressurized Anaerobic Jar System

upperview of the jar underview of the jar

Gas exchanging Gas pressurizing

Process of long-term preservation using capillary

(a) Micropipetting (b) Centering

(c) Sealing (d) Preservation

Long-term preservation for gut methanogens

8

A Map of Sampling Areas in Indonesia

11

2

14

11

1012

13

6

9

8

7

5

315

16 4

1, Pancuran Tujuh; 2, Sileri and Sikidang; 3, Kasulan and Warna pond; 4, shrimp pond;

5, Cipanas and Tanjkuban perahu; 6, cisolok and cikur Dul ;7, Kasulan and ijen crater;

8, Black water; 9, Papandayan and Kamojang ; 10, Lahendong , Tompaso and Langowan ;

11, Karumenga , Ranopaso and Leilem ; 12, Toraget and Kanonag ; 13, Likupang and Moinit

14, Cangar hot spring and Arigek karambia; 15, Rimbo Panti; 16, Padang Ganting and pariarnan

Photos of Sampling Areas in Indonesia

Lagowan area (2001.01)

Merapi area (1997.07) Papandayan area (1999.01)

Manado area (2002.01)

Photos of Sampling Areas in Indonesia

Sikidang area (2002.06)

Likupang area (2002.09)Dieng silery area (2002.06)

Cisolok area (2002.06)

(a)

(b)

60 70 80 90 100

4

8

0

12

16

20

24

26

Temperature (℃)

Ge

ne

rati

on

tim

e (

h)

Morphology & Topt of Hyperthermphile, Thermoproteus javensis

Electron micrographs of the isolate strain KB-2 cultured at 80℃ for 12 hr. SEM(a) and TEM(b) photograph. Bar, 0.5㎛ and 0.2㎛, respectively.

Effect of temperature on the growth of Thermoproteusjavensis. - Maximum growth temperature was 100℃ and

optimum growth tmeperture was 90 ℃

Morphology & Phylogenetic Tree of Thermoanaerobacter yonseiensis

Electron micrographs of the isolate

strain KB-1 cultured at 80℃for 12 hr.

SEM(a) and TEM(b) photograph. Bar,

3㎛ and 0.5㎛, respectively.

C

M

D O

Lipases Produced by Geobacillus thermoleovorans ID-1

Photograph of G. thermoleovorans ID-1

Effect of the temperature on the specific growth rate( ) and lipase production ( ) on 1.5% (v/v) olive oilin modified TYEM medium at different temperaturesand pH 6.0.

0.0

0.5

1.0

1.5

2.0

2.5

3.0

35 40 45 50 55 60 65 70 75 80

Temperature( ℃ )

Sp

ecif

ic g

row

th r

ate

(h－

1)

0

100

200

300

400

500

600

700

800

Lip

ase

acti

vit

y(U

l－

1)

929

996

Thermotoga subterranea DSM 9912T, U22664

1000

Keratinase Produced byFervidobacterium islandicum AW-1

Transmission electron micrograph of strain AW-1

Phylogenetic dendrogram of strain AW-1 and closed related microorganisms

Aquifex pyrophilus DSM 6858T M83548

Thermotoga maritima DSM 3109T, M21774

Thermotoga thermarum DSM 5069T, AB039769

Thermotoga neapolitana DSM 4359T, AB039768

Thermotoga hypogea DSM 11164T, U89768

Thermotoga elfii DSM 9442T, X80790

Fervidobacterium nodosum DSM 5306T, M59177

Fervidobacterium gondwanense DSM 13020T, Z49117

AW-1 (AF434670)

Fervidobacterium islandicum DSM 5733T, M59176

Thermosipho geolei DSM 13256T, AJ272022

Thermosipho melanesiensis DSM 12029T, Z70248

Thermosipho japonicus DSM 13481T, AB024932

Thermosipho africanus DSM 5309T, M83140

1000

1000

1000

1000

997

997

995

664

6530.02

0 day 1 day 2 day

The Degradation of native chicken feather by F. islandicumAW-1 in TF medium: completely hydrolyzed after 2 day-cultivation at 70℃ with native feather.

Uranium Bioremediation & Electricity Generation by

Geobacter

Kim, Byoung-Chan PH.D.

Environmental Biotechnology Center, UMASS (Prof. Derek R. Lovley)

Biological Resource Center, KRIBB

Derek R. Lovley

- University of Connecticut, B.A. (biological sciences)

- Clark University, M.A. (biological sciences)

- Michigan State University, Ph.D. (microbiology), 1982

- U.S. Geological Survey, 1984-1995

- Professor at UMASS, Amherst, since 1995

- Distinguished University Professor

- Director of Environmental Biotechnology Center

- Associate Dean of Natural Resources and the Environment

* Papers

- more than 300 papers (265 papers from PubMed)

- Nature: 12, Science: 10, Nature Reviews: 3, Nature Biotechnology: 2

- Nature Nanotechnology (Aug. 2011)

Nature Nanotechnology 2011 in press (Kim BC as a co-author)

“Tunable metallic-like conductivity in biofilms comprised of microbial nanowires”

http://www.time.com/time/specials/packages/article/0,28804,1934027_1934003_1933965,00.ht

ml

1. Bioremediation

- petroleum (hydrocarbon)

- aromatic compound (benzene, toluene)

- radionuclide (ex. Uranium)

2. Bioenergy

- electricity generation (MFC)

- electrofuel (butanol or octanol by ME)

3. Bioelectronics

- electronic devices (tunable conductive biofilms)

1. Uranium bioremediation by Geobacter

Zone of U(VI) Removal

Acetate

Injection

U(VI)

U(VI)U(VI)

Threatened

Down-Gradient

Water Resource

Geobacter

U(VI)

Acetate2 CO2

Fe(III)Fe(II)

U(IV)

Groundwater

Flow

U(VI)

In situ Uranium Bioremediation StrategyGeobacter species comprise as much as 85% of the microbial

community in the subsurface during the most active phase of in situ

uranium bioremediation.

(R.T. Anderson et al. 2003, Appl Environ Microbiol. 69:5884–5891)

DOE Uranium-Contaminated Groundwater Site at Rifle, Colorado

The Vast Expanse of Subsurface Uranium Contamination at many

Department of Energy Sites Precludes Pump and Treat Remediation; In

Situ Remediation Strategies are Needed

Subsurface Uranium

Contamination Plume

Moving Toward River

Geobacteraceae consistently become significant members of the

community during U(VI) reduction in sediments P

erce

nta

ge

of

Clo

nes

in

16

S r

DN

A L

ibra

ry

Ship

rock

, N

M U

ran

ium

-Min

e T

aili

ngs

Sit

e

20

40

60

80

100

0

Day 0 Day 23

control

Day 23

acetate added

Geobacteraceae

> 40%

-proteobacteria

Gram positive

Holmes, D. E., K. T. Finneran, and D. R. Lovley. 2002. Enrichment of Geobacteraceae associated with stimulation of dissimilatory

metal reduction in uranium-contaminated aquifer sediments. Appl. Environ. Microbiol. 68:2300-2306

2. Electricity generation by Geobacter

“Fuel cell” to separate aerobic and anaerobic processes

Anaerobic chamber Aerobic chamber

e-

+

Can Geobacteraceae conserve energy to support growth with an

electrode serving as the sole electron acceptor?

Flow-Through Potentiostat MFC- high dense electricity generation

- forming conductive biofilms

Hours

mA

High dense electricity generation of wild type

G. sulfurreducens and omcBSTE mutant

Nature Nanotechnology 6: 573-579 2011 Aug. (Kim BC as a co-author)

“Tunable metallic-like conductivity in biofilms comprised of microbial nanowires”

34

Global Affects of Methane - Energy

메탄하이드레이트

셰일가스

메탄생성 고세균 연구의 필요성 - 온실가스

13억 마리/world 1년간 1,105억 kg 메탄가스 방출

전 세계 메탄가스 방출량의 약 25%에 해당

모든 반추동물이 발생시키는 양은 전체의 37%를 차지

소 1마리가 1년간 방출하는메탄양

= 소형차 1대의 1년 배출 CO2와 같은 온실효과

메탄균 억제 사료개발 연구에 대한 관심 증폭 (영양상태 4-12%↑) 35

Hydrogenotrophic Gut Methanogens

36

First isolation of a novel rumen methanogen in Korea

Methanobrevibacter boviskoreani sp. nov. IJSEM 2013

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

IJSEM. 2013. 63:4196-4201

Methanogens isolated from Korean fecal samples--> Methanobrevibacter smithii 99%

Isolation of human(Korean) methanogens

Thank you !