MIKROBA YANG BERPERAN DALAM BIOMETALURGI & …

MIKROBA YANG BERPERAN DALAM BIOMETALURGI & METABOLISMENYA

Oleh

Siti K ChaerunGeomicrobiology-Biomining & Biocorrosion Laboratory, Microbial Culture Collection Laboratory,

Biosciences & Biotechnology Research Center (BBRC)Department of Metallurgical Engineering, Faculty of Mining & Petroleum Engineering

Institut Teknologi [email protected]; [email protected]

Cell phone: 087878590709 (WhatsApp)

Di alam semesta ini ada 3 domain makluk hidup berdasarkan filogenetika molekuler (dari gen rRNA) yaitu: Bacteria, Archaea dan Eucarya

No protein coat

No DNA or RNA

Molecular PhylogenyMolecular phylogenetics is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.

Phylogeny: the development or evolution of a particular group of organisms

Systematics: the study of systems and the principles of classification and nomenclature

Prokaryotic vs. Eukaryotic Cells

Makluk hidup di alam semesta dibagi 2 kelompok/grup berdasarkan struktur sel

Chromosome

Gene

DNA Nucleotides

Nitrogenous baseDeoxyribose (pentose sugar)Phosphate group

Chromosome: A circular strand of DNA in bacteria and archaea that contains the hereditary information necessary for cell life.

Gene: the functional unit of genetic informationAll life forms contain genes

Nucleosome: Any of the repeating subunits of chromatin found in eukaryotes, consisting of a DNA chain coiled around a core of histones.

Histone: Any of several basic proteins found in association with the DNA in the chromatin of eukaryotes.

Chromatin: the part of the nucleus that consists of DNA and proteins, forms the chromosomes,

Level Taksonomi(Klasifikasi, Identifikasi dan nomenklatur)

PROKARIOT• Domain: Bacteria• Phylum: Firmicutes• Class: Bacilli• Order: Bacillales• Family: Bacillaceae• Genus: Bacillus• Species: B. subtilis

EUKARIOT• Domain: Eucarya• Kingdom: Fungi• Phylum: Ascomycota• Subphylum: Pezizomycotina• Class: Eurotiomycetes• Order: Eurotiales• Family: Trichocomacease• Genus: Aspergillus• Species: A. niger

The classification and naming of organisms in an ordered system that is intended to indicate natural relationships, especially evolutionary relationships.

Structure of a prokaryotic cell

plasmid – extra-chromosomal DNA

Cellular Structures of Bacterial Cells

Plasmids

S-layer

: penentu bentuk sel & pendukung struktur

Gram + vs. Gram – Cell Walls

A: A TEM image of a Bacillus subtilis cell wallB: Representation of the overall structure of a Gram-positive bacterium

A: A TEM image of a Synechococcus PCC7942 cell wall B: Representation of the overall structure of a Gram-negative bacterium

15

A comparison of the detailed structure of a gram-positive and gram-negative cell walls

Gram Positive Gram Negative

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Cell membrane

-same structure as eukaryotic cells. -three main components:

1) bilayer of phospholipid

2) proteins

3) carbohydrates (CHO)-attached to the protein or the lipid as:

a] glycoproteins - membrane proteins with short pieces of CHO attached

b] glycolipids - phospholipids with short pieces of CHO attached

18Phospholipids - Membrane molecules

19From Black 2002

3. Cell Membrane

A general comparison of prokaryotic and eukaryotic cells and viruses

Overall macromolecular composition of an average E. Coli cell

Bacteria Archaea• Lipid nya mengandung

fatty acid yang terhubung dengan glycerol dg “ester bond”.

• Lipid nya pada umumnya adalah bilayer.

• Ada yang “lack of wall” yaitu genus Mycoplasma

• Kebanyakan cell wall nya mengandung peptidoglycan YANG tersusun dari muramic acid.

• Bisa juga punya S-layer, tapi S-layer ini bukan sbg struktur cell wall satu-satunya.

• Lipid nya mengandung “isoprenoid side chains” yang terhubung dengan glycerol dg “ether bond”.

• Lipid nya bbrp adalah monolayer yang mengandung glycerol tetraethers.

• Ada yang “lack of wall” yaitu genus Thermoplasma.

• Sebagian kecil cell wall nya mengandung peptidoglycan YANG TIDAK tersusun dari muramic acid, dimana polimer peptidoglycannya berbeda dari polimer peptidoglycan bakteri.

• Punya S-layer sbg pengganti peptidoglycan dan S-layer ini dapat sbg struktur cell wall satu-satunya.

• S-layer adalah monolayer yg merupakan protein tunggal yg berfungsi sbg shape dan integritas struktur sel.

S-layer: : terdiri dari protein dan glycoprotein dengan BM 24,000~150,000dan mempunyai asam amino lengkap kecuali cysteine dan methionine kandungannya sangat sedikit.

TEM image of the cyanobacterium Synechococcusstrain GL24 showing the S-layer as its outmost surface layer.

Sleytr et al., 2011

Glycoproteins: polysaccharides + proteinGlycolipids: polysaccharides + lipids

Berperan penting dalam cell membranes sebagai cell surface receptor molecules

Energy source

sunlight photo-

-troph

Preformed molecules chemo-

Electron donor

organic compound organo-

inorganic compound litho-

Carbon source

organic compound hetero-

inorganic compound auto-

Classification of organisms based on their metabolism

Nutrisi:The chemicals from the environment of which a cell is builtLitho: stone -troph: Of, relating to, or characterized by a specified kind of nutritionHeterotroph: (different) An organism that is dependent on complex organic substances for nutrition because it cannot synthesize its own food.Autotroph: (Self) An organism capable of synthesizing its own food from inorganic substances, using light or chemical energy.

Acidithiobacillusthiooxidans

Metabolisme Mikroba Biometalurgi• Nutrisi: the chemicals from the environment of which a cell is built

– Nutrients are taken up into the cell and are changed into cell constituents

• Anabolism/Biosynthesis: The process by which a cell is built up from the simple nutrients obtained from its environment .– An energy-requiring process– Each cell must thus have a means of obtaining energy.– Energy source is obtanied from the environment (sources: light

and oxidation of chemicals)• Catabolism: the process by which chemicals are broken down and

energy released– Chemicals used as energy sources are broken down into simpler

constituents and as this breakdown occurs, energy is released– Cell also needs energy for other cell functions, such as cell

movement (motility) and transport of nutrients.

A simplified view of the major features of cell metabolism

A typical growth curve for a bacterial population. Compare the difference in the shape of the curves in the death phase (colony-forming units versus optical density)

Fase-fase pertumbuhan mikroba

CO2

CO2

BiosynthesisOther organic compoundsSO4

-2NO3-

O2

Inorganic compounds CO2

O2

CO2

H2, H2S, NH3

Metabolisme bakteri heterotrofik secara aerob

Metabolisme bakteri heterotrofik secara anaerob

Aerobic (blue) or anaerobic (red) mineralization of an organic compound

Aerobic respiration

Fermentasi: microbes perform internally balanced oxidation-reduction reactions of organic compounds with the release of energy

-only partial oxidation of the C atoms of the organic compound occurs and thus only a small amount of the potential energy available is released.

Red form

Red forme.g., NADH

ox form

Summary of the various toxic influences of metals on the microbial cell demonstrating the ubiquity of metal toxicity. Metal toxicity generally inhibits cell division and

metabolisms. As a result of this ubiquity, microorganisms have to develop “global” mechanisms of resistance that protect the entire cell from metal toxicity.

Translation: The process by which messenger RNA directs the amino acid sequence of a growing polypeptide during protein synthesis.

In response to metal toxicity, many microorganisms have developed unique mechanisms to resist and detoxify harmful metals. These mechanisms of resistance may be intracellular or extracellular

and may be specific to a particular metal, or a general mechanisms able to interact with a variety of metals.

E. pumps: (A flowing outward.) An active transport system for the removal of some antibiotics (such as tetracyclines, macrolides, and quinolones) from bacterial cells

Metallothionein (MT) is a family of cysteine-rich, low molecular weight (MW ranging from 500 to 14000 Da) proteins.

Cysteine(abbreviated as Cys or C) is an α-amino acid with the chemical formulaHO2CCH(NH2)CH2SH.

Jenis-jenis aktivitas mikroba alami dalam men-detoksifikasi logam toksik dan senyawa radioaktif (sbg

komponen mineral)

Prinsip & mekanisme biomineralisasi Biologically induced biomineralizationBiologically controlled biomineralizationBIB & BCB

TEM images of the attractive network formation of bacterial cells consisting of short and long rod-shaped bacteria and spherical bacteria attached to the edges of hexagonal kaolinite (a) and tubular halloysite (b) in R2 after 64 days of incubation.

Chaerun et al., 2004

• Chemolithotrophs• Chemoorganotrophs• Mixotrophs

• Pengoksidasi Fe• Pengoksidasi S• Asidofilik• Tahan terhadap metal• Produksi

biosurfaktan/EPS• Produksi asam

organik