Lecture 20:Diversity of soils and sediments

A note from Exam III…

http://tylervigen.com/spurious-correlations

Objectives

• What are soils? Sediments?• You should be able to recognize the phyla &

important characteristics (diversity, metabolism & habitat) of some famous example species – phylum Proteobacteria – Gram-positive bacteria (phylum Firmicutes & phylum

Actinobacteria)• What is a biogeochemical cycle?• What is astrobiology?

What is soil?

What is soil?

• A solid matrix that holds plants in the ground• Minerals, organic matter & microbes

What are soils?

• Soils have a vertical profile

• Soils form from parent material (rock)

• Soils change with time, sun, water, wind, ice, and living creatures

What are sediments?

• Sediments are soils that are deposited in aquatic systems

• For example, silt falls out of suspension via sedimentation and forms soil (some of which may eventually become sedimentary rock).

Why should we care about soils?• Soils perform many ecosystem

services • Roles in the environment:

– Recycling system for nutrients and organic waste

– Modifier of the atmosphere– Habitat for soil organisms– Engineering medium– System for water supply and

purification• Soils take thousands of years to

form• Loss from erosion or damage

(pesticide, salt) tends to be permanent

Soils are a microbial habitat• Chemical Factors

– pH– Oxygen– Cation Exchange Capacity (CEC)

• Physical Factors– Soil Texture– Soil pores– Soil Structure– Soil water– Temperature– Soil aggregates

• Biological Factors....

Soils are a microbial habitat

Phylum Proteobacteria

Phylum Proteobacteria

Class Alphaproteobacteria• Includes a wide diversity of organisms, including

– Purple non-sulfur phototrophic bacteria– Heterotrophs– Pathogens– Autotrophic methane oxidizers (methylotrophs)

• Metabolism: Autotrophs fix C by the Calvin cycle• Habitat of this class ranges extensively, but these organisms

dominate in soils and sediments• Examples

– Caulobacter crescentus– Rhizobium etli– Wolbachia spp.– mitochondria

Caulobacter crescentusClass Alphaproteobacteria

• Dimorphic appendage bacteria• Cells are vibroid• Mature cells have a single thin stalk

that is terminal• Cell division is by binary fission, and

just before division is complete, a single flagellum is produced

• They are genomically identical but metabolism of the new swarmer cell is reduced until it finds a surface, adheres and reproduces

• Can be readily isolated from the surfaces of laboratory distilled-water containers

Rhizobium etliClass Alphaproteobacteria

• Nitrogen-fixing plant symbiont, a group informally known as rhizobia

• Has an interesting genome consisting of a single large chromosome and multiple smaller chromosomes, which are the size of plasmids but contain essential genes

• Photo shows root N-fixing nodules, which are terminally differentiated symbiotic associations with plants

Wolbachia pipientisClass Alphaproteobacteria

• Wolbachia are the common intracellular symbionts of arthropods and nematodes

• Up to 60% of all insects are infected with Wolbachia, thought it tends to not infect Aedes aegypti, the mosquito that carries infectious diseases like dengue virus which causes dengue fever

• Mosquitos infected with Wolbachia have a reduced ability to become infected with viruses, including the dengue virus. Fig 10.7. wasp egg infected

with Wolbachia, which are the white dots at the bottom of the image

MitochondriaClass Alphaproteobacteria

• Mitochondria are phylum Alphaproteobacteria, class Rickettsiales

• Has DNA, performs respiration, has an eletron transport system that occurs across membranes, and produces ATP

• thought to have once been a bacterial cell that colonized a eukaryotic cell– This is the endosymbiotic theory– Mitochondria originated as a

symbiosis between separate single-celled organisms

Class Betaproteobacteria• Phylogenetically and functionally diverse• Metabolism

– Most are heterotrophs or chemolithoautotrophs, and include some important pathogens

– Generally aerobic or facultatively anaerobic– Contains members that can degrade

compounds involved in “waste management,” including lignin and phenol

• Habitat: most environments, especially organic-rich soils, sediments, wastewater, and eutrophic aquatic systems

Ralstonia solanacearumClass Betaproteobacteria

• Plant pathogen causing southern bacterial wilt disease in a wide range of crops including tobacco, potato, tomato, pepper, and bananas

• Obligately anaerobic motile rods• Enters the plant through the root

hairs, grows, and is transported around the plant through the xylem

• This pathogen grows in such abundance in plants that the diagnostic test is to dip the cut end of an infected plant in water; the infection can be seen as a milky stream flowing out of the xylem (R)

Rhizosphere• The rhizosphere is the portion of soil directly

influenced by plant roots• Generally has more water, nutrients, stable pH,

microbial biomass and activity compared to bulk soil

Class Gammaproteobacteria• A very large and diverse class• Metabolism

– obligate aerobes, facultative anaerobes, microaerophiles, and obligate anaerobes

– Heterotrophs, chemoautotrophs and photoautotrophs• Habitat

– Pathogens, opportunistic pathogens, and symbionts– Cryophiles, mesophiles, and moderate thermophiles

• Examples– Escherichia coli– Chromatium spp. – Acidothiobacillus ferrooxidans

Escherichia coliClass Gammaproteobacteria

• Discovered in 1885 by Theodor Escherich, a German bacteriologist

• facultative, rod shaped bacteria• commonly found in animal feces, lower

intestines of mammals, and even on the edge of hot springs– Routinely used as a fecal indicator for

contamination in food and water• Opportunistic pathogen

– E. coli O157:H7 is a strain of the bacterium E. coli that produces Shiga-like toxins

– Toxin catalytically inactivate 60S ribosomal subunits of most eukaryotic cells

– enterohemorrhagic

Chromatium spp.Class Gammaproteobacteria

• Purple sulfur bacteria sometimes found in microbial mats

• Accumulates small sulfur globules inside the cells

• Motile by way of polar flagella and grow alone or in small groups

• May use H2 or sulfide (H2S) as an electron donor for reverse electron flow to gain energy (NADH)

• The product of H2S oxidation is elemental sulfur, which accumulates in granules inside of the cell

Chemolithoautotrophs in the class Gammaproteobacteria, living in the Rio Tinto

Bacterial & Archaeal diversity is low in the Rio Tinto communities

Amils et al 2007

Acidithiobacillus ferrooxidans

Acidithiobacillus ferrooxidansClass Gammaproteobacteria

• Iron cycle• can oxidize iron

aerobically and reduce it anaerobically (1,2)

(1) anaerobic activity of Geobacter and Shewanella;(2) aerobic iron oxidation at neutral pH activity is due to specialists, while aerobic and acidic iron oxidation is due to specialists(3) biocorrosion due to Desulfovibrio;(4) Fe3O4 in magnetosomes by magnetotactic bacteria, and Fe2O3 is ferritin which is found in most aerobic bacteria.

• Sulfur cycle• couples

anaerobic sulfide reduction (2,3) to iron oxidation

(1) phototrophic green and purple sulfur bacteria(2) anaerobic bacteria and archaea(3) phototrophic green and purple sulfur bacteria(4) dismutation where four sulfite molecules produce three sulfate molecules and one sulfide (few species)(5) dissimilatory reduction by sulfate-reducing bacteria(6) metabolism by heterotrophic bacteria(7) assimilatory reduction, most microorganisms

Acidithiobacillus ferrooxidansClass Gammaproteobacteria

Acidithiobacillus ferrooxidansClass Gammaproteobacteria

Rio Tinto is a terrestrial analog of Mars

• iron-rich acidic environments are relics of an ancient (Archaean) iron world

• Recent mineralogy (sulfates and iron oxides, “blueberries”) described by the Mars Exploration Rover is compatible with the geomicrobiology existing in the Rio Tinto (@MarsRovers, @SarcasticRover)

• Astrobiology: study of the origin, evolution, distribution, and future of life in the universe

Martian hematite “blueberries”

Class Deltaproteobacteria

• Diversity: most are anaerobic sulfate reducers• Metabolism:– syntrophic hydrogen-generating heterotrophs– Also some aerobic heterotrophs

• Habitat: anaerobic sediments and parasites of other bacteria

• Example species– Myxococcus xanthus– Bdellovibrio bacteriovorans

Myxococcus xanthusClass Deltaproteobacteria

• Gliders with complex life cycles, usually found on bark or decomposing leaves or wood

• Produces simple spheroid fruiting bodies on short stalks

• Is able to swarm and excrete lytic and digestive enzymes that lyse bacteria

Bdellovibrio bacteriovoransClass Deltaproteobacteria

• Swarmer with a single flagellum ensheathed by the outer membrane

• commonly found in soil and fresh water environments

• The attack-phase parasite attaches to the target host and loses its flagellum

• It feeds on the host until nutrients are depleted, growing by elongation

• Finally, it splits into attack cells with flagella and released by lysis of the host

Class Epsilonproteobacteria

• Diversity: narrow phylogenetic group• Habitat: Intestinal symbionts, parasites of other

bacteria, and deep-sea environments, especially hydrothermal vents

• Metabolism: – Microaerophilic or anaerobic heterotrophs– Generally cannont eat carbohydrates

• Example species– Helicobacter pylori

Helicobacter pyloriClass Epsilonproteobacteria

• Microaerophilic curved rod with sheathed flagella

• Common symbiont of the stomach, colonizing ~70% of humans

• Sometimes can cause stomach ulcers, but may also help modulate stomach acidity so important to the human microbiome

Gram-positive bacteria

Phylum Firmicutes

• Large and diverse phylum, aka low G+C Gram positive bacteria

• Metabolism– Almost all Heterotrophs– Anaerobes use substrate-level

phosphorylation rather than anaerobic respiration

• Habitat: abundant in soils, also colonize the skin, mucous membranes & gut

Bacillus cereusPhylum Firmicutes

• Close relative of B. anthracus

• Soils & guts• Produces endospores,

stress-resistant asexual spore that develops inside mother cells

Fig. 11.3. Bacillus cereus

Phylum Actinobacteria• Diversity spans a small phylogenetic

range but includes a large number of families & species

• Metabolism– Generally aerobic respirers– Mostly mesophilic heterotrophs– Known antibiotic producers, including

Streptomycetes and Actinomycetes– These plus Bacillus are the most

common bacterial source of antibiotics• Habitat

– Commonly found in soils & guts– Few animal symbionts and pathogens,

including the notorious Mycobacterium tuberculosis

Fig. 11.11. Mycobacterium ulcerans

Fig. 11.12. Thermoleophilium album

Streptomyces antibioticusPhylum Actinobacteria

• Filamentous growth with specific spatial arrangements

• Used in the industrial production of antibiotics

Fig 11.10. Phase-contrast image overlaid with red (DNA) and green (sporulation septa) fluorescence

Objectives

• What are soils? Sediments?• You should be able to recognize the phyla &

important characteristics (diversity, metabolism & habitat) of some famous example species – phylum Proteobacteria – Gram-positive bacteria (phylum Firmicutes & phylum

Actinobacteria)• What is a biogeochemical cycle?• What is astrobiology?