Transcript Lecture 3 Mar 5 Primary production2

1
Main points from last lecture
1. Differences between prokaryotes (Bacteria and
Archaea) and eukaryotes
2. Differences among Bacteria, Archaea, and
Eucarya: organelles, cell walls (peptidoglycan in
bacteria), lipids (ester vs ether linkage)
3. Use of small subunit ribosomal RNA as
phylogenetic marker (16S rRNA for prokaryotes)
Properties
Procaryotes
Eucaryotes
Groups
Eubacteria, archaebacteria*
Algae, fungi, protozoa, plants, animals
Size
Generally small, usually <2 um in diameter
Usually larger, 2 to >100 um in diameter
Nuclear structure and function:
Nuclear membrane
Nucleolus
DNA
Division
Sexual reproduction
Introns in genes
Absent
Absent
Single molecule, not complexed with histones
(other DNA in plasmids)
No mitosis
No meiosis
Rare
Present
Present
Present in several chromosomes, usually
complexed with histones
Mitosis; mitotic apparatus with
microtubular spindle
Meiosis
Common
Cytoplasmic structure and
organization:
Plasma membrane
Internal membranes
Ribosomes
Respiratory system
Photosynthetic pigments
Cell walls
Usually lacks sterols
Relatively simple; limited to specific groups
70S in size
Part of plasma membrane or internal
membranes; mitochondria absent
In organized internal membranes or
chlorosomes; chloroplasts absent
Present (in most) composed of
peptidoglycan and other components
Present (in some)
Present (in some)
Sterols usually present
Complex; endoplasmic reticulum Golgi
apparatus
80S, except for ribosomes of
mitochondria and chloroplasts,
which are 70S
In mitochondria
In chloroplasts
Present in plants, algae, fungi; absent
in
animals, most protozoa; usually
polysaccharide
Absent
Absent
Endospores
Gas vesicles
Forms of motility:
Flagellar movement
Flagella; each flagellum composed of one
flagella rotate
Microtubules
Absent
fiber;
Flagella or cilia; composed of
microtubular elements arranged in
characteristic pattern of nine
outer doublets and two central
singlets; do not rotate
Widespread: present in flagella, cilia, basal
bodies mitotic spindle
apparatus, centrioles
2
a
Main points, conti.
3
4. Dividing up microbes into functional groups
•
source of carbon: autotroph vs. heterotroph
•
source of energy: phototroph vs. chemotroph
Chemoorganotroph= heterotroph
5. Eukaryotic microbes in various functional
groups: primary producers, grazers, and
mixotrophy.
6. Connection between phylogeny (“community
structure”) and function (metabolism—what
microbes do) is a big question in microbial
ecology today.
4
Terms you need to learn (if you don’t know
already)
1. DNA, protein
2. RNA: mRNA, tRNA, and rRNA
3. Ribosomes (proteins + rRNA)
4. Lipids (ester vs. ether)
5. Organelles: Nucleus, chloroplast,
mitochondria
CO2
Fish
20
Macrograzers (mesozooplankton)
Micrograzers (protists)
CO2
Big pools & fluxes
High biomass
Bacteria
+
NH4 , Fe
DOM
Large
Small
Phytoplankton
CO2
Large organic
carbon pool
ca. 50% of primary
production
21
What primary producers are in the oceans?
What are the main types of phytoplankton?
Early emphasis on “net phytoplankton”
Big enough to catch with large nets
Easily visible and distinguishable by light
microscopy (electron microscopy needed
for species level identification)
Identifying features of algae
22
• Shape and Size
• Pigments: many more than in land plants
– All have chlorophyll a (chl a) used to
estimate phytoplankton biomass
– Anoxygenic photosynthesizing bacteria have
bacteriochlorophyll a
– Many (all?) have “accessory pigments”, which
really are main light harvesting pigments
– These pigments can be used to quantitatively
estimate abundance of specific algal groups
22A
Why so many different type of
pigments
Note “attenuation” (shading) at both ends of the spectrum
22B
Very simple guide to photosynthesis
Light
Accessory PigmentsChlorophyll a
Light Reactions
Dark Reactions
ATP and NADH
CO2
CH2O
23
H2O
O2
Some important eukaryotic algal groups: large or net phytoplankton
24
Division
Common
name
Characteristic
Pigments
Chlorophyta
green algae
Chl b
13 Predecessor to chloroplast
Phaeophyta
brown algae
chl c and
fucoxanthin
99 Includes macroalgae (e.g. kelp)
Rhodophyta
red algae
phycobilins
98 produce agar; few microbial
representatives
Chrysophyta
(Bacillariophyceae)**
diatoms
chl c and
fucoxanthin
50 Diatoms have Si in cell walls and
often dominate spring blooms
Chrysophyta
(Coccolithophoridales)
coccolithophorids
chl c and
fucoxanthin
90 Outer covering made of CaCO3
chl c;
xanthophylls;
phycoblins
60 Motility driven by flagella
chl c and
peridinin
93 some heterotrophic; red tide
organisms
Cryptophyta
Pyrrhophyta
dinoflagellates
%
Marine*
Comments
*% marine refers to their abundance in the oceans vs. freshwaters
**There are other members of this division besides diatoms and coccolithophorids.
25
Division
Common name
Chrysophyta
diatoms
(Bacillariophy
ceae)
Characteristic
Pigments
chl c and
fucoxanthin
Comments
Diatoms have Si in
cell walls and
often dominate
spring blooms
Chrysophyta
(Coccolithophoridales)
Coccolithophorids
chl c and
fucoxanthin
Outer covering
made of CaCO3
Pyrrhophyta
dinoflagellates
chl c and
peridinin
some heterotrophic;
red tide
organisms
26
Evidence that the oceans have more than
just “net phytoplankton”
• Lots of chlorophyll and 14CO2 fixation in <1 um
size fraction
• Epifluorescence counts of auto-fluorescencing
cells
• Cells were too small (ca. 1 um) and without
internal structures, i.e. they are bacteria. (But
there are some small eukaryotic phytoplankton—
poorly understood.
27
Coccoid cyanobacteria are abundant and important
in the oceans!
1. Well known in lakes and reservoirs
2.Importance in oceans discovered in 1980
(Synechococcus) and Prochlorococcus (1986)
3.Another important cyanobacterium:
Trichodesmium
29
Some separate Prochlorococcus from
“cyanobacteria” and equate
“cyanobacteria” with Synechococcus, but
not true
Synechococcus and Prochlorococcus are
both cyanobacteria and are distantly related
Selected papers about marine coccoid cyanobacteria
30
Li, W. K. W. and others 1983. Autotrophic picoplankton in the tropical
ocean. Science 219: 292-295.
Chisholm, S. W., R. J. Olson, E. R. Zettler, R. Goericke, J. B.
Waterbury, and N. A. Welschmeyer. 1988. A novel free-living
prochlorophyte abundant in the oceanic euphotic zone. Nature 334:
340-343.
Palenik, B. and others 2003. The genome of a motile marine
Synechococcus. Nature 424: 1037-1042.
Rocap, G. and others 2003. Genome divergence in two
Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature
424: 1042-1047.
Waterbury, J. B., S. W. Watson, F. W. Valois, and D. G. Franks. 1986.
Biological and ecological characterization of the marine unicellular
cyanobacterium Synechococcus, p. 71-120. In T. Platt and W. K. W. Li
[eds.], Photosynthetic Picoplankton. Department of Fisheries and
Oceans.
Schematic of epifluorescence
microscope
31
Excitation
light
Dichroic
mirror
Ocular (10x):
emission
Objective (100X)
Stage with sample
32
33
Sample is excited by lower wavelength light (say
400 nm) and the emitted light (“emission”) is at
a higher wavelength (say 600 nm)
Final magnification= 1000X
34
Autofluorescencing cells = autotrophs= phototrophs
Must have pigment, with few exceptions
Usually chlorophyll, but can excite different pigments with
different wavelenghts of light
Heterotrophic cells (heterotrophic bacteria)
Need to add fluorogenic stain (DAPI and acridine
orange) to stain DNA or other cellular material
35
Red color due to fluorescence from chl a
35A
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Property
Synechococcus
Prochlorococcus
Size
1.0 um
0.7 um
Chlorophyll a
Yes
Modified
Chlorophyll b
No
Yes
Phycobilins
Yes
Less, variable
Visible in microscope? Yes
Difficult
Habitat
Widespread
Open oceans
37
Biomass in North Pacific Gyre
% of total
Mixed Layer
total water column
(mgC/m2)
Het. Bacteria
45
1273
45.4
Prochlorococcus
35
973
34.7
Synechococcus
2
58
2.1
Picoeukaryotes (< 3 um)
14
404
14.1
Large algae
4
98
3.5
Component
Eukaryotes
From Campbell et al. 1994 L&O
Table 3. Comparison of mean abundance estimates and between-station variability for microbial
populations in the HNLC equatorial Pacific, the low nutrient western equatorial Pacific (2°N to
2°S) and the oligotrophic subtropical Pacific (HOT). Abundance estimates are cells ml-1 from 050 m depth. Standard deviations (S.D.) and % coefficient of variations (C.V.) are for the mean
estimates of population abundances averaged for the 0-50 m depth range at individual sampling
stations.
Cells per ml
Region
HNLC Equator
Parameter
Mean
S.D.
C.V.
HBACT
PRO
SYN
PEUK
716,000
126,000
18%
145,000
38,000
26%
9,800
3,400
35%
6,300
1,800
28%
172,000
72,000
42%
2,300
2,600
113%
870
450
51%
183,000
45,000
25%
1,700
1,100
65%
720
360
50%
Western Equator Mean
S.D.
C.V.
HOT
Mean
S.D.
C.V.
444,000
119,000
27%
HBACT=heterotrophic Bacteria; Pro=Prochlorococcus;
Syn=Synechnococcus; PEUK=picoeukaryotes
From Landry and Kirchman, DSR 2002
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Numbers worth remembering
Viruses: 107 ml-1
Heterotrophic Bacteria: 106 ml-1
Cyanobacteria: 105 ml-1
Protists (grazers): 104 ml-1
Large (>3 um) phytoplankton: 103 ml-1
40
In oligotrophic waters, coccoid cyanobacteria
account for >90% of
Phytoplankton biomass (chlorophyll a)
Primary production
41
Global estimates:
Roughly 50% of total marine primary
production
If marine is 50% of total production--->
Cyanobacteria account for about 25% of global
primary production!!
42
From Madigan et al. “Brock Biology of Microorganisms”
43
Another main type of cyanobacteria:
Trichodesmium
(formally known as Oscillatoria)
Filaments of several cells, common in Sargasso Sea
Can form macroscopic tuffs of cells
Do NOT have heterocysts
More about Tricho and heterocysts when we talk
about N2 fixation.
Other algae: note the weird and
wonderful shapes!
Not all algae are “nice”