ocn621: biological oceanography- microbial ecology vi · 2006. 2. 1. · chlamydiae op3...

OCN621: Biological Oceanography-Microbial Ecology VI

Zackary JohnsonMSB614

zij@hawaii.edu

<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