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POKOK BAHASAN PENDAHULUAN PENGGOLONGAN MIKROORGANISME STRUKTUR DAN FUNGSI SEL MIKROORGANISME PERTUMBUHAN MIKROORGANISME GENETIKA MIKROORGANISME BIOENERGETIKA MIKROORGANISME PENGENDALIAN PERTUMBUHAN MIKROORGANISME INTERAKSI DAN PENYEBARAN MIKROORGANISME PERANAN MIKROORGANISME

02. PENGGOLONGAN MIKROORGANISME POKOK BAHASAN PENDAHULUAN EVOLUSI DAN KERAGAMAN MIKROBA TINGKATAN TAKSONOMI SISTEM KLASIFIKASI KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI FILOGENI MIKROBA DIVISI UTAMA ORGANISME BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT

02. PENGGOLONGAN MIKROORGANISME PENDAHULUAN Taksonomi adalah ilmu klasifikasi biologis Klasifikasi adalah penataan organisme ke dalam kelompok-kelompok (taksa) Nomenklatur adalah pemberian nama untuk kelompok-kelompok taksonomi Identifikasi adalah penentuan isolat tertentu pada takson tertentu Peranan taksonomi mikroba: Memungkinkan ilmuwan mengorganisasikan sejumlah besar pengetahuaannya Memungkinkan ilmuwan membuat prediksi dan kerangka hipotesis tentang organisme Menempatkan organisme dalam kelompok-kelompok bermakna dengan memberi nama secara tepat, jadi akan mempermudah komunikasi ilmiah. Penting untuk identifikasi mikroorganisme secara tepat. http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Sistematik adalah kajian ilmiah organisme dengan tujuan akhir untuk mengkarakterisasi dan menempatkan organisme dengan cara yang teratur Taksonomi mikroba saat ini sedang memasuki perode perubahan besar yang disebabkan oleh penggunaan teknik molekuler http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

02. PENGGOLONGAN MIKROORGANISME POKOK BAHASAN PENDAHULUAN EVOLUSI DAN KERAGAMAN MIKROBA TINGKATAN TAKSONOMI SISTEM KLASIFIKASI KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI FILOGENI MIKROBA DIVISI UTAMA ORGANISME BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT

02. PENGGOLONGAN MIKROORGANISME EVOLUSI DAN KERAGAMAN MIKROBA Bumi berumur kira-kira 4,6 milyar tahun dan sisa-sisa fosil sel prokariotik berumur 3,5-3,8 milyar tahun terdapat dalam stromatolit dan batuan sedimen Stromatolit adalah batuan berlapis yang dibentuk dari penggabungan sedimen mineral menjadi hamparan mikroba (microbial mats) Prokariot pertama mungkin bersifat anaerob. Sianobakteri aerobik mungkin muncul 2,5-3,0 milyar tahun yang lalu. http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Hasil penelitan Carl Woese dan kawan-kawan menyarankan bahwa organisme dibagi dalam tiga domain: Eukaria-meliputi seluruh organisme eukariotik Bakteria-terdiri dari organisme prokariotik yang mempunyai rRNA bakterial and lipid membran terutama berupa diasil gliserol eter Archaea-terdiri dari organisme prokariotik yang mempunyai rRNA archaeal dan lipid membran terutama berupada isoprenoid gliseral dieter atau turunan diglesrol tetraeter. http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

The Three-Domain System

Sel eukariotik modern yang muncul kurang lebih 1,4 milyar tahun yang lalu berasal dari prokariot Hipotesis I: perkembangan kloroplast dan mitokondria merupakan pelipatan (invaginasi) membran plasma dan kemudian membentuk ruang- ruang (compartmentalization) dengan fungsi tertentu http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Hipotesis II (hipotesis endosimbiotik) menyarankan sebagai berikut: Proses pertama pembentukan sel eukariot adalah pembentuk nukleus (mungkin fusi bakteri dan archaea purba) Kloroplast dibentuk ketika bakteri fotosintetik yang hidup bebas bersimbiosis dengan sel eukariotik primitif (sianobakteria dan proklron disarankan sebagai kandidat yang paling kuat) Mitokondria mungkin terbentuk melalui proses yang sama (tetua Agrobacterium, Rhizobium, dan riketsia menjadi kandidatnya) Hopotesis endosimbiotik mendapat dukungan kuat dari penemuan sianobakterium yang berendosimbiotik dengan protista biflagelata (Cyanophora paradoxa); sianobakterium berfungsi sebagai chloroplast Cyanophora paradoxa; endosimbiotik ini dikenal sebagai sianel (cyanelle) http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

02. PENGGOLONGAN MIKROORGANISME POKOK BAHASAN PENDAHULUAN EVOLUSI DAN KERAGAMAN MIKROBA TINGKATAN TAKSONOMI SISTEM KLASIFIKASI KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI FILOGENI MIKROBA DIVISI UTAMA ORGANISME BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT

02. PENGGOLONGAN MIKROORGANISME TINGKATAN TAKSONOMI Tingkatan taksonomi (dari bawah ke atas) adalah: spesies, genus, famili, ordo, klas, kerajaan (kingdom); Namun, ahli mikrobiologi seringkali menggunakan nama seksi (suatu pengelompokan yang kurang formal) yang bersifat deskriptif untuk kelompok-kelompok organisme tertentu, seperti metanogen, purple bacteria, bakteri asam laktat, dan lain-lain. http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Biovar – berbeda secara biokimiawi atau fisiologis Galur adalah populasi organisme yang dapat dibedakan dari sekurang-kurang beberapa pupulasi lain dalam suatu kategori taksonomik, galur dianggap berasal dari organisme tunggal atau isolat kultur tunggal. Biovar – berbeda secara biokimiawi atau fisiologis Morfovar – berbeda secara morfologi Serovar – berbeda sifat antigenik Galur tipe (Type strain) adalah galur suatu spesies yang dikaji pertama kali (yang paling rinci dikarakterisasi), galur ini tidak harus anggota yang paling mewakili. Genus adalah kelompok spesies (satu atau lebih) yang telah ditentukan dengan sangat baik yang secara jelas terpisah (berbeda) dari genera lain http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Dalam sistem nomenklatur binomial yang diajukan oleh Carl von Linne (Carolus Linnaeus), huruf pertama nama genus ditulis dengan huruf besar dan epitet spesifik ditulis dengan huruf kecil pada huruf pertamanya (e.g., Escherichia coli); dalam artikel ilmiah, huruf pertama genus dapat disingkat setelah ditulis lengkap pada penulisan sebelumnya, contoh, E. coli http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

02. PENGGOLONGAN MIKROORGANISME POKOK BAHASAN PENDAHULUAN EVOLUSI DAN KERAGAMAN MIKROBA TINGKATAN TAKSONOMI SISTEM KLASIFIKASI KARAKTERISTIK UTAMA YANG DIGUNAKAN DALAM TAKSONOMI FILOGENI MIKROBA DIVISI UTAMA ORGANISME BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY GARIS BESAR FILOGENI DAN KERAGAMAN PROKARIOT

02. PENGGOLONGAN MIKROORGANISME SISTEM KLASIFIKASI Klasifikasi Alami (Natural classification) – penataan organisme ke dalam kelompok-kelompok yang anggota-anggotanya mempnyai banyak kesamaan sifat dan mencerminkan sebanyak mungkin sifat biologis organisme. http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Sistem (Phenetic systems) adalah mengelompokkan organisme didasarkan atas kesamaan secara keseluruhan Seringkali berupa suatu sistem alami yang didasarkan atas kesamaan karakter Tidak tergantung pada analisis filogenetik Menggunakan “unweighted traits” Sistem terbaik jika membandingkan sebanyak mungkin sifat (attributes) http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Taksomi Numerik (Numerical taxonomy) Informasi sifat suatu organisme dikonversikan ke bentuk yang sesuai untuk analisis numerk dan dibandingkan menggunakan komputer. Ada atau tidaknya sekuran-kurangnya 50 (sebaiknya beberapa ratus) karakater dibandingkan; karakter tersebut di antaranya karakter morfologi, biokimiawi, dan fisiologi) Koefisien asosiasi ditentukan di antara karakter-karakter yang dimiliki oleh dua organisme http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Koefisien kesesuaian sederhana (Simple matching coefficient) – proporsi yang sesuai (match) baik untuk karakter yang ada maupun tidak ada Koefisien Jaccard (Jaccard coefficient) – mengabaikan karakter-karakter yang tidak ada pada kedua organisme Nilai-nilai tersebut diatur untuk membentuk matriks kesamaan (similarity matrix); organisme dengan kesamaan tinggi dikelompokkan bersama dalam fenon (phenons) Perbedaan (significance) fenon tidak selalu jelas terlihat tetapi fenon dengan kesamaan 80% seringkali dianggap satu spesies (bakteri) http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Sistem (Phenetic systems) adalah mengelompokkan organisme didasarkan atas kesamaan secara keseluruhan Seringkali berupa suatu sistem alami yang didasarkan atas kesamaan karakter Tidak tergantung pada analisis filogenetik Menggunakan “unweighted traits” Sistem terbaik jika membandingkan sebanyak mungkin sifat (attributes) http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

Sistem filogenetik (filetik) {Phylogenetic (phyletic) -pengelompokan organisme didasarkan pada hubungan evolusioner Untuk prokariot adalah sulit untuk mengetahui hubungan evolusi karena kekurangan catatan fosil yang baik Pembandingan langsung materi genetik dan produk gen seperti rRNA dan protein dapat digunakan untuk mengatasi kesulitan tersebut di atas http://www.microbialworld.com/Microbes/microbes.htm. DIAKSES 17-3-06 The classification of microorganisms is based on their major characteristics which are as follows. Morphological characteristics: Cell shape, size and structure; cell arrangement; occurance of special structure and developmental forms; staining reactions; and motility and flagellar arrangement. Chemical composition: The vasrious chemical constituents of the cell Cultural characteristics: Nutritional requirementa and physical conditions required for growth, and the manner in which growth occurs. Metabollic characteristics: The way in which cells obtain and use their energy, carry out chemical reactions, and regulate these reactions Antigenis characteristics: Special large chemical components (antigens) of the cell, distinctive for certain kinds of microorganisms Genetic characteristics: Characteristics of the hereditary material of the cell (DNA); and occurance and function of other kinds of DNA that may be present, such as plasmids Pathogenicity: The ability to cause disease in various plants or animals or even other microorganisms Ecological characteristics: Habitat and the distribution of the organism in nature and interactions between and among species in natural environments

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