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Major Concepts 9 Microbes are small, but incredibly abundant and found Marine Microbes everywhere OCN201 Fall 2007 9 Microbes are genetically and physiologically diverse Zackary Johnson Department of Oceanography 9 Micro bes are responsible for most of the energy and http://www.soest.hawaii.edu/oceanography/zij/education.html mass transformations in the ocean

9 Most microbes have never been cultured and in general microbes are poorly understood

Major Concepts What’s in a liter of water? 9 Microbes are small, but incredibly abundant and found 9 Fish none everywhere 9 Copepods 10 Microbes! 9 Microbes are genetically and physiologically diverse 9 Diatoms 10,000 9 Micro bes are responsible for most of the energy and 9 100,000 mass transformations in the ocean 9 Nanoflagellates 1,000,000 9 Most microbes have never been cultured and in 9 Cyanobacterium 100,000,000 general microbes are poorly understood / 1,000,000,000 Viruses 10,000,000,000

Microbes by Epifluorescence Microscopy Microbes are small #/L diameter Fish none >10‐2 m Copepods 10 10‐3 m Diatoms 10,000 10‐4 m Dinoflagellates 100,000 10‐5 m nanoflagellate Nanoflagellates 1,000,000 10‐5 m Cyanobacterium 100,000,000 10‐6 m Archaea/Bacteria 1,000,000,000 10‐7 m Viruses 10,000,000,000 10‐8 m ~1 μl

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Microbes are found everywhere!

•DNA stains (DAPI or Sybr) allow visualization of DNA containing particles (cells) vs. non‐ liv ing partiilcles

•Most microbes are free living, but they can be attached to particles too (particles are concentrated resources or a home)

Distributions of microbes Viruses • Bacteria and Archaea present in significant •Obligate parasites numbers from the surface down to the •No Metabolism bottom of the ocean •No Motility and in the sediments •RNA or DNA viruses • Numbers decrease •Just geneti c i nst ructi ons t o repli cat e, wrapped i n ~exponentially with protective coat depth •A source of mortality (“consumption”) for both • Typically, microbial producers and consumers biomass is about equal to primary •Viruses are about 10X more abundant than all producers other types of microbes (Bacteria/Archaea)

Karner et al. 2001

Viruses Infect All Types of Marine •Marine mammals •Sea Birds •Fish •Crustaceans •Bivalves •Protozoa •Macroalgae (kelp) •Microalgae (phytoplankton) •Bacteria

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Turtle Virus Major Concepts 9 Microbes are small, but incredibly abundant and found everywhere

9 Microbes are genetically and physiologically diverse

9 Micro bes are responsible for most of the energy and Bacterial virus mass transformations in the ocean

9 Most microbes have never been cultured and in general microbes are poorly understood

Attachment > Entry > Synthesis > Assembly > Lysis

Verrucomicrobia 0.05 vadinBE97 Microbes are diverse Major Groups of OP3 WS3 BRC1 Bacteria NKB19 OP9 WS2 OP10 •Highly diverse SC4 NC10 Chlorobi Marine Group A Caldithrix •Not all present in Deferribacteres marine environments, Chrysiogenes arsenatis SBR1093 but no exhaustive OP8 OS-K Nitrospira Termite Group 1 search to date TM6 Synergistes OP5 ABY1 BD1-5 group OP11 WS6 TM7 Guaymas1 WS5 SC3 Deinococcus-Thermus OP1 Coprothermobacter Dictyoglomus Desulfurobacterium Rappé and Giovannoni 2003

Heterotrophic Microbes Microbes do many things •No Mouth - digest food outside of the cell Primary producers (Autotrophic = self feeding): •Digest larger molecules and particles with cell- surface enzymes (swimming stomachs)

Photosynthetic (use sunlight energy): •Take up small molecules through special channels CO2 + H2O Æ CH2O + O2 (porins, transporters) •Important consumers of Chemosynthetic (use chemical energy): dissolved organic matter + - + 2 NH4 + 3 O2 Æ 2 NO2 + 4 H + 2 H2O - - •Many are motile (they move) 2 NO2 + O2 Æ 2 NO3 2+ + 3+ - flagellum 4 Fe + O2 + 4H Æ 4 Fe + 2 H2O - 2- + HS + 2 O2 Æ SO4 + H •Many (use oxygen and sugars) … just like “higher” organisms, but others have unique metabolisms

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Microbes do many things Microbes do many things Consumers: Oxidation of Organic Matter •Conversion of “nutrients” or substrates into different forms - with Different e Acceptors (other than oxygen) “one person’s trash is another person’s treasure”

REACTION ΔGo´ (kcal/mole) CH2O + O2 Æ CO2 + H2O ‐686 ‐ ‐ CO2 + H2O Æ CH2O + O2 5 CH2O + 4 NO3 Æ 4 HCO3 + CO2 + 3 H2O + 2 N2 ‐570 2+ CH2O + 3 CO2 + H2O + 2 MnO2 Æ 4 HCO3‐ + 2 Mn ‐349 CH2O + O2 Æ CO2 + H2O 2+ CH2O + 7 CO2 + 4 Fe(OH)3 Æ 8 HCO3‐ + 3 H2O + 4 Fe ‐114 + - + ‐ 2NH2 NH + 3O3 O Æ 2NO2 NO + 4H4 H + 2H2 H O 2CH2O + SO4 Æ 2 HCO3 + H2S ‐77 4 2 2 2 CH O Æ CO + CH ‐58 - - 2 2 4 2 NO2 + O2 Æ 2 NO3 ΔGo´ (kcal/mole) = free energy released per mole of glucose oxidized •Thus, in addition to producing and consuming energy in CONCEPT: Some energetic transformations are more energetically favorable than others. the environment, microbes are also critical in converting These will usually occur first under natural conditions ‐ i.e., the most energetically different chemical constituents for other organisms favorable terminal electron acceptor (O2) will be used until it is no longer available, then the environment will favor organisms (bacteria) capable of utilizing alternative •The vast majority of these transformations in the ocean electron acceptor to oxidize organic matter. are dominated by microbes

Verrucomicrobia 0.05 vadinBE97 Chlamydiae Major Groups of Bacteria OP3 Major Concepts Planctomycetes WS3 black – cultured BRC1 NKB19 green – uncultured Firmicutes 9 OP9 Microbes are small, but incredibly abundant and found WS2 red – putative identification Cyanobacteria Fusobacteria everywhere OP10 SC4 Actinobacteria NC10 •Not all present in marine Bacteroidetes Chlorobi environments, but no Marine Group A 9 Microbes are genetically and physiologically diverse Caldithrix Gemmatimonadetes exhaustive search to date Fibrobacteres Proteobacteria Deferribacteres • Highly diverse Chrysiogenes arsenatis SBR1093 Acidobacteria 9 Micro bes are responsible for most of the energy and •Most uncultured OP8 OS-K Nitrospira mass transformations in the ocean •More uncharacterized Termite Group 1 TM6 Synergistes OP5 Spirochaetes ABY1 Thus, our understanding of BD1-5 group 9 Most microbes have never been cultured and in OP11 what bacteria are there and WS6 TM7 Guaymas1 general microbes are poorly understood what they are doing is in its WS5 SC3 Chloroflexi infancy. Same thing for Deinococcus-Thermus Thermodesulfobacteria OP1 archaea and microbial Thermotogae Coprothermobacter . Dictyoglomus Aquificae Desulfurobacterium Rappé and Giovannoni 2003

Plate Count Anomaly Major Concepts – redux Direct Counts Plate Counts 9 Microbes are small, but incredibly abundant and found everywhere

9 Microbes are genetically and physiologically diverse

9 Micro bes are responsible for most of the energy and mass transformations in the ocean

9 Most microbes have never been cultured and in general microbes are poorly understood Staley & Konopka, 1985

Only about ~0.1 to 1% of microbes can be cultured!

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