ocn621: biological oceanography- microbial ecology vi · 2006. 2. 1. · chlamydiae op3...
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OCN621: Biological Oceanography-Microbial Ecology VI
Zackary JohnsonMSB614
<http://www.soest.hawaii.edu/oceanography/zij/ocn621.html>
Three Domains of Life
Plate Counts Direct CountsPlate Count Anomaly
Staley & Konopka, 1985
Major Groups of Bacteria
black – culturedgreen – unculturedred – putative identification
Not all present in marine environments, but no exhaustive search to date
Highly diverseMost unculturedMore uncharacterized
Thus, our understanding of what bacteria are there and what they are doing is in its infancy
VerrucomicrobiavadinBE97
ChlamydiaeOP3
PlanctomycetesWS3BRC1
NKB19Firmicutes
OP9WS2
CyanobacteriaFusobacteria
OP10SC4
ActinobacteriaNC10
BacteroidetesChlorobi
Marine Group ACaldithrix
GemmatimonadetesFibrobacteres
ProteobacteriaDeferribacteresChrysiogenes arsenatis
SBR1093Acidobacteria
OP8OS-K
NitrospiraTermite Group 1
TM6Synergistes
OP5Spirochaetes
ABY1BD1-5 group
OP11WS6
TM7Guaymas1
WS5SC3
ChloroflexiDeinococcus-Thermus
ThermodesulfobacteriaOP1
ThermotogaeCoprothermobacter
DictyoglomusAquificae
Desulfurobacterium
0.05
Rappé and Giovannoni 2003
Major Groups of BacteriaAlpha proteobacteria-Anoxygenic Aerobic Phototrophs (AAPs) -Mitochondria-Nitrite Oxidizers: Nitrobacter-Plant symbionts, Nitrogen Fixers: Azospirillum, Rhizobium-Methanotrophs: Methylosinus, Methylocystis-members include: SAR11 (most abundant group of bacterioplankton,
Pelagobacter), Roseobacter (AAP, DMSP degradation)
Gamma proteobacteria-“Typical” marine plankton. i.e. Alteromonas, Oceanospirillum,
Photobacterium, Shewanella, Vibrio, Pseudomonas, etc. etc.-Grow in Marine Broth-Enteric flora (Escherichia coli, Salmonella, etc)-Methanotrophs: Methylomonas, Methylobacter-Sulfur associated Anaerobic Phototrophs: Chromatium and relatives-Ammonia and Nitrite Oxidizers: Nitrosococcus oceani, Nitrococcus-Sulfur oxidizing: Beggiatoa, Thioploca, vent symbionts-Most (cultivated members) aerobic or facultative anaerobic
chemoorganotrophs
Major Groups of Bacteria (cont)Delta Proteobacteria
unknown metabolismdepth dependent distributions
Actinobacteriaunknown metabolismlow percentage of total
Marine Group A (uncultivated)Exhibit depth dependent distributionCorrelated with chlorophyll at surface at BATS stationUnknown metabolism
CyanobacteriaPrimary producersProchlorococcus, Synechococcus
BacteroidetesMost Isolated using rich mediaCommon groups: Cytophaga, Cellulophaga, Flexibacter Polaribacter, Most are aerobic organotrophs; high ectoenzyme activity: degrade polymeric molecules such as cellulose and chitincoastal
Beta Proteobacteriametabolism unknown
ArchaeLarge percentage of ‘bacterio’plankton in oceanic and nearshore environsBelow the euphotic zone: taxon-specific counts can be as high as 39%Abundance increases with depth, peaking between 100-300 m
Two Groups:
Crenarchaeota- Large proportion of the summer and early spring microbialcommunity in the euphotic zone of Antarctic coastal waters, and negatively correlated to chlorophyll-a (Murray et al. 1998)- Out-competed by other prokaryotes under higher primary, and secondary production conditions?Cold temperature adaptation: DNA polymerases of a close relativeand endosymbiont of the sponge Axinella (Schleper et al. 1997)
Euryarchaeota (less abundant)
Take Home Messages- although Bacteria and Archae can be counted, this is a highly
cosmopolitan community whose taxonomic composition is poorly described
- few representatives are in culture
- little is known about their physiology, distributions or ecology
- extreme diversity in metabolism
- thus, bacteria can not be lumped together into one ‘box’ and there is much to do to understand this “group”
Methods of estimating bacterialbiomass and production
Biomass (mg C L-1)
•ATP•Muramic Acid•Cell abundance•Cell volume•LPS
Production (mg C L-1 d-1)Δbiomass/time
•FDC•3H-thymidine•3H or 14C-leucine•3H-adenine•Bromodeoxyuridine
Note: none of these are direct measures of biomass or productivity (i.e. carbon)
Bacterial Abundance and ProductionBacterial Abundances
~10X phytoplankton abundance(but much smaller in size/volume)
concentrations decrease ~exponentially with depth
<0.01 × 106Deep Sea
0.5-1.0 × 106Open ocean
1-5 × 106Coastal
>5 × 106Estuaries
Cell Density (cells/ml-1)Habitat
Bacterial Abundance and ProductionBacterial Abundances
~equal to phytoplankton biomass
-Bacterial biomass constitutes a large pool of livingcarbon in marine ecosystems
-Significant variability between biomes
0.960.6264%
14431740120%
64110516%
MeanSD
%CV
0.581248724Arabian Sea
1.7447750Station ALOHA
1.2447571North Pacific
0.114500500North Atlantic
1.2573659Sargasso Sea
BB:PBPhytoplankton Biomass(mg C m-2)
Bacterial Biomass(mg C m-2)
Location
Bacterial Abundance and ProductionBacterial Production
concentrations decrease ~exponentially with depth
Bacterial Abundance and ProductionBacterial Production
~20% of phytoplankton primary production- mean growth rate ~0.25 d-1
- significant variability between biomes
15310569%
257
106
56
275
70
Bact. Prod. (mg C m-2 d-1)
7653344%
1165
486
629
1083
465
Prim. Prod.(mg C m-2 d-1)
0.180.0635%
0.22
0.22
0.09
0.25
0.15
BP:PP
0.250.2079%
64110516%
MeanSD
%CV
0.35724Arabian Sea
0.14750Station ALOHA
0.1571North Pacific
0.55500North Atlantic
0.11659Sargasso Sea
BP:BB(d-1)
Bact. Biomass(mg C m-2)
Location
Molecular Approaches to Bacterial Abundance-all Bacteria and Archae (and Eukaryotes) have ribosomal RNA (rRNA) – 16S-universality makes comparisons possible between distantly related organisms-rRNA sequence is ‘unique’ to individual species, but related species have sequences that are more similar than unrelated species-range of rRNA sequence can be assessed using clone libraries-specific or groups of rRNA sequence can be quantified (qPCR, probes)-shotgun/BAC sequencing to identify novel and informative genes
http://users.ugent.be/~avierstr/principles/pcrani.html
extract DNA
sequence
clone
ID
qPCR-use specific primers to amplify only groups (or “species”) of interest-monitor amplification in real time and compare unknowns to standard curve to back calculate the original unknown concentration
FISH -Fluorescence In situ Hybridization (FISH) -use targeted fluorescent probes (DNA) and microscopy to count cells that have a specific sequence
DAPI Hybridized
Shotgun/BAC sequencing-sequence random short (~700bp) or intermediate (~30kb) fragments
-no a priori information required – useful for identifying new organisms or genes
DAPI Hybridized
-use sequence information combined with database (NCBI –GenBank) of genes of known function to infer composition and processes occurring in the ocean
DeLong 2005