MICROBIAL BIOCHEMISTRY BIOT 309. Dr. Leslye Johnson Sept. 30, 2012

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1 MICROBIAL BIOCHEMISTRY BIOT 309 Dr. Leslye Johnson Sept. 30, 2012

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3 Phylogeny study of evoluhonary relatedness among groups of organisms (e.g. species, populahons), which is discovered through molecular sequencing data and morphological data matrices tree represents a hypothesis of the order in which evoluhonary events are assumed to have occurred

4 Write down 3 things that this tells you? Name/SN

5 TREE OF LIFE Chloroplasts mitochondria

6 BACTERIAL DIVERSITY How do we tell bacterial species apart? Structural Biochemical Environmental Sequence ALL REQUIRE ABILITY TO GROW IN CULTURE

7 STRUCTURAL DIVERSITY: GRAM STAIN DETECTS PEPTIDOGLYCAN G + S. aureus G - E. coli CLASSWORK: List the similarities and differences of Gram and Gram +

8 Pictures from Tortora, Funke and Case, Ch. 4

9 STRUCTURAL DIVERSITY: FLAGELLA

10 STRUCTURAL DIVERSITY: BACTERIAL SHAPE Rod- shaped (bacilli) Coccoid- Shaped Spiral- shaped

11 STRUCTURAL DIVERSITY: COLONY MORPHOLOGY

12 Blog Site h[p://fccljohnson.wordpress.com Intent is two subpages; one for BIOT 412 and the other for BIOT 309 Under the subpage will be posts with the newest post at the top Good Luck Let Dr. Johnson know of any problems or advice.

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15 Sequenced Genomes All Organisms: h[p:// resources/sequenced_genomes/ genome_guide_p1.shtml Microbes: h[p://cmr.jcvi.org/hgr- scripts/cmr/ CmrHomePage.cgi

16 MOST SEQUENCED MICROORGANISMS 173 Escherichia coli 82 Salmonella enterica 78 Staphylococcus aureus 69 Propionibacterium acnes 56 Streptococcus pneumoniae 56 Enterococcus faecalis 45 Bacillus cereus 42 Mycobacterium tuberculosis 36 Vibrio cholerae 29 Pseudomonas syringae 28 Listeria monocytogenes 27 Neisseria meningihdis 27 Helicobacter pylori 27 Enterococcus faecium 27 Acinetobacter baumannii 25 Yersinia peshs 23 Methanobrevibacter smithii 23 Clostridium difficile 23 Burkholderia pseudomallei 22 Campylobacter jejuni

17 SEQUENCING OF MICROORGANISMS Data Summary Complete Draf Totals Bacteria Archaea Viruses Totals

18 SMALL SUBUNIT rrna SEQUENCING Bacteria = 16S (eucaryotes = 18S) copies/cell IdenHfy culturable and non- culturable microorganisms in sample Less expensive than standard microbiological methods and faster Gene encoding SSU rrna is sequenced

19 16S rrna SEQUENCING 1 approach AmplificaHon of DNA by PCR DNA primers recognize conserved region of 16S rrna on the DNA genome generate segment of 16SrRNA gene by PCR Variants of PCR, such as RAPD (randomly amplified polymorphic DNA) uses random mix of six base long primers idenhfies even different strains of same species Sequence PCR fragment and compare with extensive database from ~10,000 species

20 Biochemical Diversity A ClassificaHon Scheme for Life redox * * * *

21 Diversity: Another Schema ClassificaLon Carbon Source Energy Source Electron Donors Photoautotrophs CO 2 Light H 2 O, H 2 S, S, other inorganic compounds Photoheterotrophs Organic compounds Light Chemoautotrophs CO 2 OxidaHon- reduchon reachons Chemoheterotrophs Organic compounds OxidaHon- reduchon reachons Organic compounds Inorganic compounds: H 2, H 2 S, NH 4+, NO 2-, Fe 2+, Mn 2+ Glucose, etc Examples cyanobacteria photosynthehc bacteria Nonsulfur purple bacteria Bacteria : nitrifying, hydrogen, sulfur and iron most microorganisms Note that classification schema are different. ASSIGNMENT: BUILD A TABLE WITH ALL CHARACTERISTICS

22 DIVERSITY EXAMPLE 1 E.coli: Energy from fermentahon or respirahon. RespiraHon Aerobic using - O 2 as final electron acceptor - or Anaerobic, using NO 3 or fumarate as a terminal electron acceptor. Carbon source: uses glucose or lactose and makes all the necessary amino acids, vitamins and nucleohdes

23 DIVERSITY EXAMPLE 2 Rhodospirillum rubrum: Same as E. coli and grows by photoautotrophic, photoheterotrophic or lithotrophic means as long as biohn is in its growth media.

24 MORE DIVERSITY EXAMPLES

25 Blog Site h[p://fccljohnson.wordpress.com Intent is two subpages; one for BIOT 412 and the other for BIOT 309 Under the subpage will be posts with the newest post at the top Good Luck Let Dr. Johnson know of any problems or advice.