Download Biological process and Bioremediation

Biological process and
Bioremediation
Metabolisme Mikroorganisme
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Sistem energi mikroorganisme
Reaksi redoks dalam proses metabolisme
Klasifikasi mikroorganisme
Konsorsium mikroorganisme
Enzim
Sistem energi mikroorganisme
•ATP : bentuk penyimpanan energi yang
dapat digunakan secara biologis dalam
metabolisme mikroorganisme dan
disimpan di dalam sel
•Terbentuknya ATP melalui proses
katabolisme
•Hidrolisa ATP menghasilkan energi untuk
tumbuh dan reproduksi dalam proses
anabolisme
•Mineralisasi : konversi dari suatu unsur
dari bahan organik menjadi suatu
keadaan anorganik sebagai akibat proses
dekomposisi oleh mikroba
Metabolisme Mikroorganisme
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Sistem energi mikroorganisme
Reaksi redoks dalam proses metabolisme
Klasifikasi mikroorganisme
Konsorsium mikroorganisme
Enzim
Akseptor elektron dan pendonor elektron
•Dalam kaitan dengan degradasi kontaminan, secara konseptual,
dapat ditulis sebagai berikut :
Kontaminan + Xoks
Produk + Xred
Contoh soal
Reaksi redoks dalam proses metabolisme
a. Akseptor elektron dan pendonor elektron
b. Fosforilasi dan kemiosmotis
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Fosforilasi pada tingkat substrat dilakukan oleh mo yang tumbuh
dan hidup dalam kondisi anaerob
Mekanisme transpor proton dan elektron melewati dinding sel
yang bersifat sebagai membran
c. Urutan penggunaan elektron penerima dalam reaksi
redoks
Urutan akseptor elektron : O2 > NO3 > Mn > Fe > SO4 > CO2
d. Reaksi generik degradasi senyawa organik
Metode prakiraan berdasarkan pendekatan stoikiometrik berbasis
reaksi redoks dilakukan untuk perkiraan perbaikan tanah dan
pertimbangan biaya operasi. Untuk itu reaksi generik antara
kontaminan sebagai pendonor elektron dan akseptor elektron
dalam bentuk reaksi redoks dapat digunakan untuk
memperkirakan jumlah akseptor elektron yang diinginkan. Lihat
halaman 197-200 buku Pencemaran Tanah dan Air Tanah oleh
Suprihanto Notodarmojo.
Reaksi penting yang dimediasi
mikroorganisme
• Reaksi transformasi biotis
- reaksi hidrolisa
- Reaksi cleavage (pemecahan atau pemutusan rantai)
- Reaksi oksidasi reduksi
- Reaksi dehidrogenasi
- Reaksi dehidrohalogenasi
- Reaksi substitusi
• Jalur proses dalam transformasi biotis
Langkah pertama dalam proses degradasi oleh metabolisme
mikroorganisme adalah bagaimana molekul target atau substrat
masuk ke dalam sel membran melalui mekanisme difusi
Selanjutnya reaksi di sitoplasma untuk menguraikan senyawa organik
dan keberadaan elektron donor dan elektron akseptor
Degradasi Hidrokarbon
- PAH (polyciclic aromatic hydrocarbon)
- Metabolisme didahului oleh white rot fungi
dan alga hijau
Degradasi Pestisida
DDT menjadi
perhatian karena
sifat persistensi dan
sifat racunnya
Ada dua jalur yaitu
aerob dan anaerob
Faktor faktor yang mempengaruhi
proses biologis dalam tanah
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Mikroorganisme sebagai pelaku
Substrat dan nutrien
Penerima elektron (akseptor elektron)
Faktor lingkungan : kelembaban tanah,
temperatur, pH tanah dan kandungan garam
Interaksi mikroorganisme dengan
logam
• Spesies logam dan bioavailability
Spesies logam dalam tanah dipengaruhi oleh kondisi redoks, pH dan kekuatan
ion
Mikroorganisme mempunyai kemampuan mempengaruhi potensial redoks
(mengubah spesies logam dalam larutan tanah), misal kehaidran bakteri
Desulfovibrio yg dalam kondisi tereduksi mereduksi sulfat menjadi sulfida.
Logam terbentuk endapan yang non toxic.Dalam kondisi teroksidasi
hampir semua logam terlarut dalam bentuk ion bebas. pH akan turun
karena aktivitas thiobacillus thioooxidans yang mengoksidasi belerang
menjadi asam sulfat. pH rendah kelarutan logam meningkat.
Bioavailability merupakan spesies logam yang terlarut, yang tidak terikat atau
tersorpsi oleh partikel padat tanah.
Toksisitas logam terhadap mo tgt bioavailability logam. Semakin tinggi
kelarutan , maka semakin tinggi bioavailability dan toksisitas semakin
tinggi
Interaksi logam dengan
mikroorganisme
• 3 proses utama yang menyebabkan interaksi antara
mikroorganisme dengan logam”
1. oksidasi-reduksi
Contoh Pseudomonas spp. dapat mengoksidasi arsenite menjadi
arsenate
2. Kompleksasi. 2 mekanisme komplekasi logam oleh bakteri :
Logam ikut aktif dalam pengikatan (non specific binding) pada
permukaan dinsing sel, lapisan lendir atau pada bagian luar sel
lainnya (extracelullar matrix)
Logam mungkin masuk ke bagian dalam sel dan terikat
3. Metilasi
Penambahan metil atau gugus alkil pada logam membentuk metil
logam. Metilasi logam membentuk senyawa yang mudah
menguap, selain itu logam termetilasi akan meningkatkan
kemampuan menembus membran biologis sel
BIOREMEDIATION
Bioremediation Defined
• Any process that uses microorganisms, fungi, green plants or their
enzymes to break down harmful chemicals and pollutants in order
to return the environment to its original natural condition.
• “Bioremediation is not only about genetics and enzymology but
also about physiology and ultimately ecology.”—de Lorenzo V:
Systems biology approaches to bioremediation. Curr Opin
Biotechnol 2008, 19:579-589.
Alleviating Pollution
• Ex situ or in situ intervention
– Natural attenuation
• Example: phytoremediation (hyperaccumulators) store
heavy metals in vacuoles
– Sebertia acuminata 20% dry weight is nickel.
– Plants on side of freeways are taking up lead from gas exhaust
– Bio-stimulation
• Add nutrients (nitrate/sulfate) that cause blooms of
naturally occurring microbial bioremediators.
– Example: bacteria that metabolize polycyclic aromatic
hydrocarbons or polychlorinated biphenyls
– Bio-augmentation
• Genetically Modified Bioremediators
– Alter organisms to manufacture proteins for desired
metabolism
» Yellow poplar tree given enzyme mercuric reductase
thrives in mercury soil, cadmium, TCE
» Bacteria gene breaks down TNT is linked to jellyfish gene
that glows. Bacteria spread on soil glows green near
explosives
» Chakrabarty first patented oil eater bacterium. Combined
4 plasmids in one bacterial cell gave it the ability to
degrade four components of crude oil.
Why do we even need it?
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We can’t seem to stop polluting
– Inorganics
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Uranium, technicium, sulfur, slfuric acid
– Explosives
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RDX, TNT
– Polyaromatic hydrocarbons
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creosote
– Chlorinated hydrocarbons
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Trichlorethylene, PCBs, pentachlorophenol
– Petroleum hydrocarbons
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Gas, gas additives (MTBE), deisel
From mid-1980’s up to 90’s numerous
attempts were made to design GMO for
environmental release for pollutants and
heavy metals (USGS).
– Failures to program: bacteria doesn’t behave in
a predictable fashion from the lab.
Case Study 1
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Most failures at bioremediation are due to failure of introduced organisms to
thrive in the natural environment or a failure to access the contaminant. This could
be due to:
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Lack of nutrients
Predation or parasitism
Competition (GEM’s tend to compete poorly with indigenous populations).
Immobility of introduced bacteria
Contaminant concentrations below threshold for organism survival
Organisms may feed on alternative substrates (E. coli and Pseudomonas diverge genetically
from initial inoculum in field trials).
A few examples of failed bioremediation attempts:
– Inoculation of soil with aliphatic hydrocarbon degrading bacteria did not enhance degradation
of fuel oil
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Venosa AD, Wrenn BA (1996) Selective enumeration of aromatic and aliphatic hydrocarbon degrading
bacteria by a most-probable number procedure. Can. J. Microbiol.42: 252-258
– A Pseudomonas sp. shown in lab cultures to degrade 1,4-dichlorophenol failed to degrade the
compound when added to surface soils
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Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms for
bioremediation processes. Curr Opin Biotechnol 11:286-289
Case study 2:
degradation of crude oil by halophilic Archaea
Defining bioremediation by natural attenuation
– what is the environment? what is the pollutant?
– are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?
– what conditions (nutrient, temperature, pH, salt etc) are necessary for
that activity?
Defining bioremediation by natural attenuation:
hydrocarbon degradation in the Arabian Gulf hypersaline coast
– what is the environment? what is the pollutant?
• the hypersaline coast of the Arabian coast
• crude oil (hydrocarbons)
West, Ian. 2008. Qatar - sabkhas, evaporites and some other
desert features: an introduction.
http://www.soton.ac.uk/~imw/Qatar-Sabkhas.htm
Defining bioremediation by natural attenuation:
hydrocarbon degradation in the Arabian Gulf hypersaline coast
– what is the environment? what is the pollutant?
• the hypersaline coast of the Arabian coast
• crude oil (hydrocarbons)
– are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?
2 Haloferax strains
1 Halobacterium strain
1 Halococcus strain
environmental samples
grow on minimal mineral plates
with crude oil vapor as
sole
carbon/energy
source
(Al-Mailem et al., 2010 Extremophiles)
Defining bioremediation by natural attenuation:
hydrocarbon degradation in the Arabian Gulf hypersaline coast
– are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?
C18 hydrocarbon
autoclaved control
Haloferax isolate
Halobacterium isolate
Halococcus isolate
gas-liquid chromatography to measure
hydrocarbon degradation
(Al-Mailem et al., 2010 Extremophiles)
Defining bioremediation by natural attenuation:
hydrocarbon degradation in the Arabian Gulf hypersaline coast
– what conditions (nutrient, temperature, pH, salt etc) are necessary for
that activity?
• increased salt increased hydrocarbon degradation
Haloferax isolate
Haloferax
Haloferax isolate
isolate
Halococcus isolate
Halobacterium isolate
(Al-Mailem et al., 2010 Extremophiles)
How could this hydrocarbon degradation activity by Haloarchaea
be improved?
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General strategies for improving microbial bioremediation: stimulation or augmentation
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Some existing bio-engineering tools
– University of Minnesota Biocatalysis/Biodegradation
Database (UMBBD): enzymes, pathways, reactions,
compounds from hundreds of bacterial species of interest
(Gao et al., 2010)
– MetaRouter: tracks possible breakdowns from a starting point
using all possible reactions (Pazos et al., 2005)
– in silico modeling of altered strains: ex. Optstrain (Pharkya et
al. 2004), DESHARKY (Rodrigo et al. 2008)
How could this hydrocarbon degradation activity by Haloarchaea
be improved?
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How could systems level knowledge help design stimulation or augmentation strategies?
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need to know network topology of the pathway being added or altered as well as the
influence of the environment on that pathway
understand coupling of pathways to better integrate the engineered or altered pathway into
the rest of the host system
understand demands created by the new flux on resources needed for growth/survival:
energy, carbon, redox balance, transcriptional and translation capacity
is it possible to compensate by altering regulation by TFs etc, or by adding or deleting other
pathways?
understand effect of environment on pathway flux
understand role of noise in pathway regulation
if cooperation between multiple microbial species is used, then systems analysis can
evaluate impact of biodegradative flux on the multispecies consortia