Three Domains of Life

OCN621: Biological Oceanography- Sediment Microbiology

Guangyi Wang POST 103B [email protected]

Three Domains of Life 1) Unrooted phylogenetic tree constructed based on small-subunit rRNA genes; 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 archaea were collectively called prokaryote that is still commonly used in Slide material courtesy: Craig Smith literature now.

1 Phylogenetic Classification Bergey’s Manual of Systematic Bacteriology - 2nd ed emphasis on 16S rRNA sequence phylogenetic classification

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

Physiological Sediment Microbial Groups -classified based on metabolism (Craig Smith)

(Craig Smith)

1) Light energy - ‘photo’; Chemical energy – ‘chemo’;

2) CO2 as carbon source – ‘auto’; organic compounds Old, but still being commonly used in as carbon source - ‘hetero’; sediment microbiology and biological 3) Inorganic electron donor - ‘litho’; organic electron oceanography!!!! donor - ‘organo’;

2 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7.5 x 1029 (D’Hondt et al, unpublished data) !!

Sediment Microbial Communities (cont’d)

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

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

Organic Matter Remineralization (cont’d)

4 Bioenergy Production from Sediment Microbes

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

Marine Sediment Batteries

Voltage (mM)

1000 800 600 400

Voltage (mM) Voltage 200 0 2.28 3.02 3.03 3.04 3.05 3.06 3.07 3.09 Date

Loi mV Kaneohe mV Keehi mV (S. Lovley) Power-generating capacity of three different types of sediments collected Model SUV powered by marine at Oahu (Wang et al., unpublished geobatteries data)

5 Pharmaceutical Compounds from Marine Sediment Microbes

William Fenical

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)

6 Major Elements of Marine Sediments

A B

C D

• Marine sediments provide good chemical environments for microbial growth

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

7 Features of Sediment Microbial communities • 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.

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)

8 Bacterial Distribution in Marine Sediments • Vertical distribution

800 m

Bacterial populations were determined using the acridine orange direct Why do bacterial populations count (AODA) techniques fluctuate as depth changes? (Teske, 2006, Geobiol. J.)

• Vertical distribution (cont.)

9 Microbial Activities in Deep-sea Sediments • General distribution patterns of dominant prokaryotic microbes 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)

Anaerobic Oxydation of Methane by Microbial Consortium

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

In situ identfication of archaea/SRB aggregates with fluorescently labled CH4 + H2O → CO2+ H2 (red cells) rRNA-targetted oligonucliotide probes; Archaea = red, SRB = -2 - - green, white images are DAPI H + SO → HCO + HS + H 0 (green cells) (DNA) stained. Boetius et a. (2000). 2 4 3 2

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

Linkage between Linkage between bacterial biomass and bioenergetics and carbon production?? microbial growth??

Main Points 1.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.