OCN621: Biological Oceanography- Sediment Microbiology · OCN621: Biological Oceanography-Sediment...

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OCN621: Biological Oceanography-Sediment Microbiology

Guangyi WangPOST 103B

guangyi@hawaii.edu

Three Domains of Life

Slide material courtesy: Craig Smith

1) Unrooted phylogenetictree constructed based on small-subunit rRNAgenes;

2) Members of all the three domains of (microbial) life are found in Marine sediments;

3) Fungi and protists are commonly present in all types of marine sediment.

4) Bacteria and archaeawere collectively called prokaryote that is still commonly used in literature now.

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Phylogenetic ClassificationBergey’s Manual of Systematic Bacteriology - 2nd edemphasis on 16S rRNA sequence phylogenetic classification

Commonly used in modern microbiology and sediment microbiology!!!!

Physiological Sediment Microbial Groups-classified based on metabolism

1) Light energy - ‘photo’; Chemical energy – ‘chemo’;2) CO2 as carbon source – ‘auto’; organic compounds

as carbon source - ‘hetero’;3) Inorganic electron donor - ‘litho’; organic electron

donor - ‘organo’;

Old, but still being commonly used in sediment microbiology and biological oceanography!!!!

(Craig Smith)

(Craig Smith)

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Marine Sediment Microbial Communities• Significant in number and biomass -1/2-5/6 of earth’s prokaryotic biomass

(Whitman et al. 1998) or 1/10 to 1/3 Earth’s living biomass (Parkes et al. 2000 & Whitman et al. 1998).

50%

90%

7.5 x 1029 (D’Hondt et al, unpublished data) !!

• Diverse microbial morphologies found in marine sediments (material courtesy -Craig Smith)

Sediment Microbial Communities (cont’d)

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Sediment Microbial Communities (cont’d)• Driving forces (bacteria, archaea and fungi) in organic matter

remineralization.

Organic Matter Remineralization (cont’d)

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A. Microbial fuel cell B. Global marine sediments are a “giant microbial fuel cell”

Bioenergy Production from Sediment Microbes

Marine Sediment Batteries

(S. Lovley)

Power-generating capacity of three different types of sediments collected at Oahu (Wang et al., unpublished data)

Model SUV powered by marine geobatteries

Voltage (mM)

0200

400600

800

1000

2.28 3.02 3.03 3.04 3.05 3.06 3.07 3.09

Date

Vol

tage

(mM

)

Loi mV Kaneohe mV Keehi mV

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William Fenical

Pharmaceutical Compounds from Marine Sediment Microbes

Marine Sediments• Cover more than 2-3 times of the earth's surface.• Two basic origins of the particles composing marine sediments

– Created in situ from dissolved compounds– Carried to the oceans from the land, atmosphere, Earth’s inferior, or outer

space• Major types of particles

Distribution of the principal types of marine sediments (Marine Biogeochemistry by R. Chester)

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Major Elements of Marine Sediments

• Marine sediments provide good chemical environments for microbial growth

A B

C D

Bacterial abundance in different sediments

Sedimentary organic carbon content versus microbial cell abundance in three sediment types in Kiel Bight (modified from Meyer-Reil 1986).

Wild et al., 2006

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• Dominant prokaryotes (bacteria & archaea) in sediment microbes

– Larger surface-to-volume ratio than eukaryote & greater impact on overall sediment metabolism (Craig Smith).

– Greater diversity than eukaryotes.– Biomass dominate many marine sediments.

Features of Sediment Microbial communities

Understudied Eukaryotic Microbes• Eukaryote – Fungi, protozoans & others

– Important in plant derived organic matter decomposition.– A few of fungi and protozoans are capable of anaerobic metabolism.

Stratification of fungi and radiolarians in the deep-sea sediment core taken at a depth of 5904m from a trench at the southern extension in the in the Indian Ocean (Raghukumara et al. 2004)

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Bacterial Distribution in Marine Sediments

• Vertical distribution

Why do bacterial populations fluctuate as depth changes?

Bacterial populations were determined using the acridine orange direct count (AODA) techniques (Teske, 2006, Geobiol. J.)

800 m

• Vertical distribution (cont.)

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Microbial Activities in Deep-sea Sediments

a) Sulfate reducing prokaryotes dominates in the sulfate containing upper sediment layer (Bale et al, 1997; Barnes et al. 1998)

b) Methanogenic archaea dominates in the methane-enriched deeper sediment layer (Marchesi et al. 2001)

c) Sulfate-dependent methanotrophic consortia dominate the sulfate-methane transition zone (Boetius et al. 2000; Mechaelis et al. 2002); Teske et al, 2002, 2003) (see anaerobic methane oxidation)

• General distribution patterns of dominant prokaryotic microbes in deep-sea sediments

DeLong, 2000Abundance of archaea/SRB in a sediment core from a Beggiatoa mat. Boetius et al. (2000).

In situ identfication of archaea/SRB aggregates with fluorescently labledrRNA-targetted oligonucliotideprobes; Archaea = red, SRB = green, white images are DAPI (DNA) stained. Boetius et a. (2000).

Anaerobic Oxydation of Methane by Microbial Consortium

CH4 + H2O → CO2+ H2 (red cells)

H2 + SO4-2 → HCO3

-+ HS- + H20 (green cells)

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Sediment Microbial Growth and Biomass

Linkage between bacterial biomass and carbon production??

Linkage between bioenergetics and microbial growth??

Sediment microbes are a very active, but mostly non-growing community (Novitsky, 1987 AEM; modified from Craig Smith’s lecture)

Main Points1.Classification of sediment microbes;2.Significance of marine sediment microbial

communities, particularly, prokaryotes;3.Distribution and metabolic activities;4.Abundance of major marine sediment microbial

communities in different type of sediment;5.Relationship between sediment microbial

communities and sediment biogeochemistry.