7. Environmental Microbiology and Biotechnology PPT

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6 Δεκ 2012 (πριν από 4 χρόνια και 8 μήνες)

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©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Microorganisms in the
Environment and Microbial
Biotechnology

M J Larkin

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

INTRODUCTION


Microorganisms in the environment


Where are they found?


How diverse are they?


Role in geochemical nutrient cycles.



How do they grow and what are their requirements for
growth and biodegradation?


Microorganisms in waste treatment:



Biodegradation and environmental clean up.


Microbial production and products in industry



The genomic


metagenomic

future



DIRECTED READING: Prescot. Ch40 microorganisms as components of the
environment Ch 44 Industrial microbiology and Biotechnology.

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Larkin Lab Research




Biological Sciences and QUESTOR
http://questor.qub.ac.uk



Basic theme is molecular biology and biochemistry of
microorganisms that mediate global processes and remediation
of the environment.



Currently:



Function of
dioxygenases



structure and biochemistry



Bioproducts



chiral

chemicals for pharmaceutical use



Diversity of
biodegradative

genes in environment


evolution from
Archaea



Metagenomic

approaches



Funded by UK government


BBSRC, EC and Industry

Perception:

http://www.qub.ac.uk/mlpage/researchoverview/space.ppt

Overview from keynote lecture at:

http://www.qub.ac.uk/mlpage/researchoverview/overview.ppt

Web of Knowledge


name and address function

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Microorganisms in the environment; Challenging
conventional views of life.


Sagan and
Margulis

(1998) “Garden of Microbial Delights”.


“ALL of the elements crucial to global life
-

oxygen,
nitrogen,phosphorus
,
sulfur
, carbon
-

return to a usable form
through the intervention of microbes… Ecology is based on
the restorative decomposition of microbes and
molds
, acting
on plants and animals after they have died to return their
valuable chemical nutrients to the total living system of life
on earth”



Gould (1996) “Life’s Grandeur” The Power of the Modal
Bacter
.


The first
multicellular

organisms do not enter the fossil
record until about 580 million years ago
-

this is after about
five sixths of life’s history have passed. Bacteria have been
the
stayers

and keepers of life’s history.


©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Where are they found?

Diverse environments



Virtually every environmental niche



Extremes of pH and salinity



Extremes of temperature and pressure



Without air (Anaerobic)



Growth on many chemical substrates



Attached to surfaces in
biofilms



Geothermal vents and subterranean deposits

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Where are they found?

Biomass on the planet.



Most culturing analysis misses over 99% of the microbial
population.



Molecular techniques now reveal hidden diversity



Heterotrophs

-

5
-
20% biomass in sea waters
-

up to 80%
of the primary production



Rich bacterial communities in sub
-
surface strata (600 m
deep)
-

up to 2 x 10
14

tons
-

more than all flora and fauna
-
equivalent to 2 m layer over planet!



see:

http://www.stephenjaygould.org/library/gould_bacteria.html


©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

How diverse are they?



Diverse range of species



Earliest life on the planet



Anaerobic then aerobic



Three Kingdoms



Eukaryote Plants &


Animals



Eubacteria



Archaebacteria



Exteme living bacteria

3 billion years

Eubacteria

Plants &

Animals

Archaea

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

How diverse are they?

Diversity of bacteria in soil

16s rRNA sequences reveal true


diversity in soil DNA

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Genomics and Metagenomics

Chain termination sequencing used
for genomes to date


800 bps per
read

Pyrosequencing “454” direct
sequencing of single strands


300 bps
per read


but rapid.


Use in analysis of RNA transcipts


Use for rapid analysis of ALL DNA in
environment


metagenomics


Screening environment for useful
genes.

Expression requires suitable host

E.Coli
not always suitable


Other hosts more useful


e.g
Rhodococcus



used in many industrial
processes

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.


Microbial genome sequencing links


Sanger Institute UK


http://www.sanger.ac.uk/Projects/



Lists bacterial pathogens sequenced and ongoing


Joint Genome Institute USA


http://www.jgi.doe.gov/


Many environmental microorganisms and
metagenomic

projects

Belfast connection:

Pathogen
Bacteroides fragilis


unprecedented gene switching
mechanisms see:
http://www.sanger.ac.uk/Projects/B_fragilis/


Rhodococcus



analysis of largest bacterial genome at 9.7 mB

Gene rearrangements and adaptation see:

http://www.rhodococcus.ca/

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Role in geochemical nutrient cycles.



Microorganisms play a role as:


PRIMARY PRODUCERS


BIODEGRADERS AND CONSUMERS




Critical role in cycles of many elements;



Carbon and Oxygen cycle


oxygenases

and oxygen fixation



Nitrogen cycle


nitrogenase

-

denitrification



Sulfur cycle


sulphate

reduction



Phosphorus cycle


©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

How do they grow: requirements for
biodegradation?



Nutrients



Carbon, Nitrogen, Phosphorus, Sulfur



Many chemicals supply these



Micronutrients/ trace metals/ vitamins



Electron acceptors
-

usually O
2




Converts / burns carbon substrate to CO
2


Energy and biomass ie GROWTH

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Biodegradation

SINGLE


BACTERIUM

2.0

m

ORGANIC POLLUTANT

AND NUTRIENTS

(C,P,N,O,Fe,S……)

GROWTH
-

CELL DIVISION

INCREASE IN BIOMASS

CO
2

evolved

O
2

consumption

Controlled release of energy

Slow Burning!

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Oxygen and Electron Acceptors: crucial for
Biodegradation reactions in the environment.

SUBSTRATE

METABOLISM

CARBON

ADP

Pi

ATP

H
2
/2e
-

2H
+

O
2

ENERGY

GROWTH/Biomass

H
2
O

CO
2

Electron acceptor

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Role of electron acceptors; rate of
biodegradation

O
2

H
2
O

0.814V

NO
3
-

NO
2
-

N
2

0.741V

SO
4
2
-

H
2
S

-
0.214V

Fe
3
+

Fe
2
+

-
0.185V

FAST

GROWTH

SLOW

GROWTH

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Anaerobic growth and
biodegradation

Organic matter

Fermented

Acetic Acid

H
2

CO
2

+

CH
4

CO
2

H
2
O

Methanogenesis

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Reductase
NAP
(OX)
Reductase
NAP
(RED)
Ferredoxin
NAP
(OX)
Ferredoxin
NAP
(RED)
ISP
NAP
(OX)
ISP
NAP
(RED)
O
H
O
H
O
2
NADH
+ H
+
NAD
+
Further degradation

Cell membrane

Cell Biomass

CO
2

Fixation of oxygen as a first step in
biodegradation


the key step


biodegradion



complex biochemistry

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Biological waste treatment; Managing
microorganisms for environmental cleanup


Municipal waste
-
water treatment


Biodegradation of industrial wastes



petrochemicals, bulk chemical processes



textiles, leathers



metals



Remediation of contaminated land
in situ


10 x 10
6

Chemicals


8 x 10
6

Xenobiotic


1 x 10
6

Recalcitrant


0.4 x 10
6

traded at over 50 tonnes per year


Toxicological/ biodegradative data on only around 5000
-
6000

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Biological waste
-
water treatment: The activated
sludge process.

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Biological waste treatment; Advanced industrial
membrane reactor.

WASTE
-
WATER CONTAINING POLLUTANTS

EFFLUENT FREE OF POLLUTANT

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Cultivation of microorganisms for industrial use.

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Cultivation of microorganisms for industrial use.

Advanced laboratory

fermenters in the

Questor Centre

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Products from Microorganisms: Overview of
range of examples.


Various foods and drinks


Enzymes for varied uses (GM enzymes); biocatalysts


Engineered proteins ( antibodies )


Vaccines and antibiotics (secondary metabolites)


Primary metabolites and bulk chemicals (amino acids
(
glutamic

acid) and organic acids (acetic acid)


Pharmaceuticals and novel
chiral

chemicals


Recovery of metals in bioleaching


Biosensors (use of enzymes to specifically detect chemicals
in medical and )

©
M J Larkin Biological Sciences. The Queen’s University of Belfast.

Microbes are everywhere !


-----

“where the bee sucks, there suck I



in a cowslip’s bell I lie”

------


Ariel in “The Tempest”

proclaiming his ubiquity in all manifestations

of life