Transcript 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
• Use a variety of different technologies to see
what microbes are doing
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
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
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
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
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
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
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
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
Effect of the size of primary producer
on the biomass at higher trophic levels
Changing Paradigms, Classical view
• Classical view
Microbial Loop
• Pomeroy 1974
The
– Observations made prior
to advancement of
methods
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
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
Where does the PP go?
• Phytoplankton release 10-50% of PP as DOM
• Almost all is returned to atmosphere by
heterotrophic microbes
Bacteria in the Surface Ocean (≤ 200 m)
Autotrophs
2.9 x
1027
cells
Heterotrophs
Annual Production
~10 Pg C
Annual Net Marine
Primary Production
~50 Pg C
Annual Production
Autotrophic BP
(~20% of PP)
1028
3.6 x
cells
28 cells
(0.36
C)
3.6
x 10Pg
~7.5 Pg C
Heterotrophic BP
(~15% of PP)
Bacteria are major producers and consumers of organic matter,
thereby shaping the composition and concentration of DOM in the
ocean.
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
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)
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
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
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 chl a; 107 per ml in surface ocean
Diatom
Virus
Bacteria
Viruses are not pure evil
From Breitbart 2012
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!
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
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
DOC contours along meridonial
transects in the N. Atlantic
What is refractory DOC?
% OC as biochemicals
Major DOC classes (Hansell 2013)
Hansell 2013
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)
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
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
nonheterocystous cyanos,
Trichodesmium
– Symbiotic cyanos (Richelia,
Calothrix) in diatoms
(Rhizosolenia)
– Single/unicellular cyanos,
Crocosphaera & Cyanthecae
relatives
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
Adaptations to low ambient [Fe]
• Saito et al. 2010
– Organism of study:
Crocosphaera watsonii
• Photosynthesize during
the day, fix N at night
– Temporal separation
• ‘Hot bunking’ technique
– Fe used during day then
switched over for Nfixation at night
– ‘Recycle’ available Fe
Assimilatory and Dissimilatory Nitrate
Reduction
• N Assimilation
– Uptake of NO3- and/or NH4 incorporation into
biomass
• N Dissimilation
– Release/excretion of NH4 by microbes and other
organisms
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)
Denitrification
• Two steps
– Nitrate
– Nitrite
nitrite
N2 or N2O
• Why is it important?
– Loss of N from environments
– Source of N2O (greenhouse gas)
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
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