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Microbial Oceanography

Microbial Oceanography. Lecture 6: 6/5/2014. Many thanks to Drs. Carlson, Chadhain , and Ortmann for many of the slides. What is Microbial Oceanography (Ecology). Study of organisms too small to be seen with the unaided eye

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Microbial Oceanography

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  1. Microbial Oceanography Lecture 6: 6/5/2014 Many thanks to Drs. Carlson, Chadhain, and Ortmann for many of the slides

  2. What is Microbial Oceanography (Ecology) • Study of organisms too small to be seen with the unaided eye • Use a variety of different technologies to see what microbes are doing

  3. Members of the Microbial World • Prokaryotic cells: lack a true membrane-bound nucleus • Bacteria and Archaea • Eukaryotic cells: have a membrane-enclosed nucleus • More complex morphologically and generally larger than prokaryotes • Viruses

  4. How do we determine the identity of prokaryotes if they look so similar? • Culturing studies in ‘traditional’ microbiology • Look at cell shape and morphology • Look at colony shape and morphology • Determine metabolic potential • Molecular biology tools applied to microbiology • Determine the relatedness of gene sequences • Measure change in genes and gene order in genomes http://www.sci.port.ac.uk/ec/_images/CLSMpartner5a.jpg

  5. Culturing has been a major tool for microbiologists for years Benefits of culturing • Isolate of a single species/strain in lab • Determine metabolic potential (test different substrates) • Can carry out range of experiments • Can isolate viruses which infect isolate • More easily manipulate or determine genetics Issues with culturing • May not represent dominant/common species in environment • May grow/behave differently under lab conditions compared to environment • Experiments may be biased due to adaptations to the lab • Viruses may not be ecologically relevant to the isolate • Genetics may not be representative of those in environment

  6. Why can culturing be so unsuccessful? • Lab conditions do not reflect environmental conditions • High nutrient media • High/low temperatures • Different light conditions • Monocultures • Specific trace nutrients missing • Microbial ‘weeds’ are a major problem • Fast growing • dominate/overtake on plates or in liquid media • Consistently end up with these in culture • May not be dominant in the field, or significant

  7. SAR 11, dominated clone libraries but not in any cultures (Rappé et al 2002) • SAR11 (Sargasso Sea) sequences ~26% of total 16S rRNA gene clones • Not seen in any cultures • Isolated (eventually) using a low nutrient dilution to extinction approach • VERY slow growing • Weeks to reach high density

  8. What do living organisms need? • Define a group by how it “solves” some basic problems: • Source of energy (for making ATP) • Source of electrons (NADP(H), reducing power) • Obtaining carbon

  9. Heterotrophic Prokaryotes are not created equal • By definition, use organic C for energy source • Particulate Organic Carbon (POC), by definition organic C > 0.7 µm • Can be ‘worked’ on by microbes • Major source of export (detrital) • Dissolved Organic Carbon (DOC) (< 0.7 µm) can be: • Labile, available to microbes. Lasts hours to days, simple or complex molecules • Semilabile, mostly exported, lasts months to years, composition not known • Refractory, not available. Can last centuries (e.g. CDOM), unknown composition • Microbes convert DOC from mostly labile to refractory • Photodegradation and other abiotic processes also involved

  10. Structure of Marine Ecosystems, Steele 1974 • Large phytoplankton at the base of the food chain • Lost energy dissipates as heat • Lost organic matter recycled by groups of ‘decomposer’ organisms

  11. Effect of the size of primary producer on the biomass at higher trophic levels

  12. Changing Paradigms, Classical view • Classical view The Microbial Loop • Pomeroy 1974 • Observations made prior to advancement of methods

  13. The Microbial Loop (Azam et al. 1983) • Salvage pathway in which bacterioplankton repackage and reincorporate DOC back into the aquatic food web • 60-75% of 1º prod is consumed by organisms <200 µm

  14. DOM production and removal mechanisms • In the open ocean, DOM production is ultimately limited by the level of primary production within a system • Stressed phytoplankton release LOTS of DOM • Nutrient stressed

  15. Where does the PP go? • Phytoplankton release 10-50% of PP as DOM • Almost all is returned to atmosphere by heterotrophic microbes

  16. Bacteria in the Surface Ocean (≤ 200 m) Autotrophs Annual Production Annual Net Marine Primary Production ~50 Pg C Autotrophic BP (~20% of PP) Heterotrophic BP (~15% of PP) 2.9 x 1027 cells ~10 Pg C Heterotrophs Annual Production 3.6 x 1028 cells (0.36 Pg C) 3.6 x 1028 cells ~7.5 Pg C Bacteria are major producers and consumers of organic matter, thereby shaping the composition and concentration of DOM in the ocean.

  17. Microbial Loop: Link or Sink for Carbon? • Link = C passed to higher trophic levels • High growth efficiencies • Sink = C not passed to higher trophic levels, C is respired • Low bacterial growth efficiencies

  18. BCD and BGE: del Giorgio and Cole 1998 • BCD = “bacterial” carbon demand • Total amount of carbon used by the “bacterial” fraction • BCD = Bacterial Prod+Bacterial Respiration (C used for production plus C released by respiration) • BGE = “bacterial” growth efficiency • Efficiency by which bacteria convert organic substrate into biomass • BGE=BP/BCD (fraction of total C used for production)

  19. Why are microbes a sink for Carbon? • Low BGE • 15% in oceans • 35% in estuaries • Lower than lab rat bacteria • Why? • Amount and quality of organic C

  20. Grazer Impact on Bacteria • Most bacteria eaten by small flagellates (<5µm) • Protists most important, especially 2-5 µm heterotrophic nanoflagellates (HNF) • Bacterial production and protistan grazing loss in balance • Protists can grow as fast as bacteria

  21. Viruses • “Agents of microbial mortality” thus play a role in cycling of organic matter in the ocean • Can increase BP…increase remineralization • Can reduce the amount of C to higher trophic levels, “The Viral Shunt” • Abundant: ~108 per ml in productive coastal waters; numbers correlate with system productivity, bacterial numbers and chla; 107 per ml in surface ocean

  22. Diatom Virus Bacteria

  23. Viruses are not pure evil From Breitbart 2012

  24. Bottom Line • May contribute to microbial mortality on scales similar to grazing by zooplankton; but interactions between virus/host, virus/host/grazing are complicated. • Conversion of POC (cells) to DOC may influence removal of C from surface ocean • Quantifying microbial mortality due to viruses is difficult • The real bottom line: • Just because they’re small, we can’t ignore them!

  25. Oceanic Carbon Cycle • Why is C an important element? • Cellular level: essential for macromolecular synthesis • Trophodynamics: important in energy flow between trophic levels • Biogeochemistry: stoichiometry demands ties C to other important nutrient cycles (N,P,Si) • Greenhouse properties

  26. The ability of the ocean to take up atmospheric CO2 is controlled by 2 major pumps • Solubility pump - solubility of CO2 • Biological Pump – photosynthesis and respiration

  27. DOC contours along meridonial transects in the N. Atlantic

  28. What is refractory DOC? % OC as biochemicals

  29. Major DOC classes (Hansell 2013)

  30. Hansell 2013

  31. Why is the Nitrogen cycle important? • N often limits production in many oceanic regimes • N can be used to follow C fluxes. Important even when N is not limiting • N20, a greenhouse gas, is produced during nitrification and denitrification • Uses of N • Biosynthesis (proteins and nucleic acids) • Respiration (electron acceptor) • Energy source (chemolithotrophy)

  32. N-cycle difficult to study • N has numerous oxidation states • Gases, inorganic and organic forms • Results in various forms of N species • Many reactions which alter its form • No convenient radioactive isotope • 13N: radioactive, but half-life of minutes • 14N: stable, most abundant • 15N: stable, 0.366 % of total N

  33. Nitrogen Fixation (N2(gas) to Organic N) • N-fixers (diazotrophs) • Only prokaryotes do it in the ocean • In aquatic systems, mainly cyanobacteria • Marine diazotrophs • Filamentous nonheterocystouscyanos, Trichodesmium • Symbiotic cyanos (Richelia, Calothrix) in diatoms (Rhizosolenia) • Single/unicellular cyanos, Crocosphaera & Cyanthecae relatives

  34. N-fixation cont. • Catalyzed by nitrogenase • Found only in a few species of prokaryotes • High Fe quota • Energetically expensive • Lots of ATP expenditure • Controlled by turbulence, grazing, light, nutrient and trace element availability

  35. Adaptations to low ambient [Fe] • Saito et al. 2010 • Organism of study: Crocosphaerawatsonii • Photosynthesize during the day, fix N at night • Temporal separation • ‘Hot bunking’ technique • Fe used during day then switched over for N-fixation at night • ‘Recycle’ available Fe

  36. Assimilatory and Dissimilatory Nitrate Reduction • N Assimilation • Uptake of NO3- and/or NH4 incorporation into biomass • N Dissimilation • Release/excretion of NH4by microbes and other organisms

  37. Nitrification • Two steps • Ammonium to nitrite, ammonium is oxidized, i.e. it is the e- donor • Nitrite to nitrate, nitrite oxidized further • Carried out by two types of bacteria • Nitrosomonas and Nitrosococcus (step 1) • Nitrobacter and Nitrococcus (step 2)

  38. Denitrification • Two steps • Nitrate nitrite • Nitrite N2 or N2O • Why is it important? • Loss of N from environments • Source of N2O (greenhouse gas)

  39. Anammox • Anaerobic Ammonium Oxidation • Anaerobic oxidation of NH4+ using NO2- as the electron acceptor • Produces N-gas • Anammox bacteria only recently discovered • Planctomyces, a genus in the phylum Planctomycetes • 1st found in sewage treatment plant in Holland • Accounts for “missing” NH4+ in N budgets

  40. Kuypers et al. 2005 • Study site: Oxygen minimum zone (OMZ) in Benguela upwelling system • Found that anammox bacteria are responsible for huge losses of fixed N to N2 gas • 1st time identified and directly linked anammox bacteria to removal of fixed inorganic N in open ocean setting! • Stimulated research to find anammox in other OMZ systems

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