Unit 7: Diversity of Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).

1. SOILS & SEDIMENTS
Unit 07, 2.25.2021
Reading for today: Brown Ch. 10 & 11
Reading for next class: Brown Ch. 13 & 14
Dr. Kristen DeAngelis
Office Hours by appointment
deangelis@microbio.umass.edu

2. Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast
the microbes living in each. Explain
biogeochemical cycles.
2. Describe the diversity, metabolism &
habitat of the five classes of the phylum
Proteobacteria, including some
common example species.
3. Describe the diversity, metabolism &
habitat of the Gram-positive bacteria
(phylua Firmicutes & Actinobacteria).
2

3. Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast
the microbes living in each. Explain
biogeochemical cycles.
2. Describe the diversity, metabolism &
habitat of the five classes of the phylum
Proteobacteria, including some
common example species.
3. Describe the diversity, metabolism &
habitat of the Gram-positive bacteria
(phylua Firmicutes & Actinobacteria).
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4. What is soil?
• A solid matrix that
supports plant
growth
• Minerals, organic
matter & microbes

5. What is soil?
• "Soils are a medium for plant growth"
• Soil can be divided into two broad
groups:
– Mineral soils = Derived from rock weathering
– Organic soils = Derived from sedimentation in
bogs and marshes
• Soils change with time, sun, water, wind,
ice, and living creatures
• Soils take thousands to millions of years to
form

6. Rhizosphere
• The soil directly influenced by plant roots
• Rhizosphere soils have more water,
nutrients, stable pH, microbial biomass
and activity compared to bulk soil

7. Rhizosphere
• Roots change chemical and physical
properties of soils, so are also a route of soil
formation or transformation
• Root exudates (sugars and amino acids),
secretions (waste), sloughed root cells, and
lysates

8. Rhizosphere-specific microbes
• Plant growth promoting rhizobacteria –
diverse, functionally cryptic other than
promoting plant growth
• Mycorrhizal fungi (shown at right) – not
all plants are capable of making
mycorrhizal associations, but these also
tend to be specific
• Root nodule forming bacteria – N
fixation in symbiosis with plants; can be
specific associations (e.g., the
filamentous Actinobacteria Frankia
which forms nodules on alder trees), or
or non-specific associations
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9. Rhizobium etli
Class Alphaproteobacteria
• N-fixing plant symbiont
– informally known as
rhizobia
– Photo shows root N-fixing
nodules, which are
terminally differentiated
symbiotic associations with
plants

10. Microbial N cycling in soils
• There are 5
movements in the
nitrogen cycle, all
accomplished by
microbes
– Fixation
– Uptake
– Mineralization
– Nitrification
– Denitrification*
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Industrial N2 fixation

11. Microbial N cycling in soils
• Biogeochemical cycles map the transformations
and movements of an element or compound
through the environment.
• Microbes are responsible for all soil N cycling
– Microbes make soil N available to plants
– Plants get ALL of their nutrients (except C) from soils
• N fixation happens naturally by bacteria, but right
now we are industrially fixing N using the Haber-
Bosch process
– As much N enters the atmosphere through industrial
fixation as through biotic routes
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12. Maritan Soils
• There is evidence of water on Mars
• There are iron minerals like on Earth
• No microbes or evidence of them
found on Mars… yet!
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13. Sediments
• Soil transported by
water (fluvial
processes), wind
(aeolian processes)
and ice (glaciers)
– deposition on land
forms soil, which takes
thousands to millions of
years per centimeter
depth.
– may eventually
become sedimentary
rock.

14. Activity for Review of
Unit 07.1
• How are soil and sediment related?
• What is the name for soil influenced by
plant roots?
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15. Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast
the microbes living in each. Explain
biogeochemical cycles.
2. Describe the diversity, metabolism &
habitat of the five classes of the phylum
Proteobacteria, including some
common example species.
3. Describe the diversity, metabolism &
habitat of the Gram-positive bacteria
(phylua Firmicutes & Actinobacteria).
15

16. Phylum Proteobacteria

17. Phylum Proteobacteria

18. Phylum Proteobacteria
• Most of the familiar gram-negative bacteria are
proteobacteria
• This is a “very successful” phylum because of the
tremendous phylogenetic diversity of its members.
– Each of the five classes of proteobacteria (alpha, beta,
gamma, delta and epsilon) is as diverse as any other
bacterial phyla.
• They have a wide range of phenotypes scattered
across the phylogenetic tree.
• They are named for the shape-shifting sea god
Proteus, because these organisms have evolved so
many phenotypes.

19. Class Alphaproteobacteria
• 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
– Wolbachia spp.
– Rhizobium etli
– Mitochondria

20. Wolbachia pipientis
Class Alphaproteobacteria
• Common intracellular
symbiont of arthropods and
nematodes
– Up to 60% of all insects are
infected with Wolbachia
– Maternally transmitted
– tends to not naturally infect
Aedes aegypti, the mosquito
that carries infectious diseases
like dengue virus
• Mosquitos infected with
Wolbachia have a reduced
ability to carry viruses. Fig 10.7. wasp egg infected with
Wolbachia, which are the white
dots at the bottom of the image

21. Mitochondria
Class Alphaproteobacteria
• Order Rickettsiales
• Has DNA, performs
respiration, has an
electron transport system
that occurs across
membranes, and
produces ATP
• endosymbiotic theory
– once was a bacterial cell
that colonized a eukaryote
– Mitochondria originated as
a symbiosis between
separate single-celled
organisms

22. Class Betaproteobacteria
• Large and diverse
• Metabolism
– Chemolithoautotrophs or
heterotrophs, and some pathogens
– Aerobic or facultative anaerobic
– Members can degrade compounds
involved in “waste management,”
including lignin and phenol
• Habitat: most environments,
especially organic-rich soils,
sediments, wastewater, and
eutrophic aquatic systems

23. Ralstonia solanacearum
Class Betaproteobacteria
• Plant pathogen
– Bacterial wilt disease in crops
– tobacco, potato, tomato, pepper,
and bananas
• Obligately anaerobic motile rods
• Infects through the root hairs,
grows, and is transported around
the plant through the xylem
– This pathogen grows in such
abundance 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
(shown at right)

24. 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.

25. Escherichia coli
Class Gammaproteobacteria
• Facultative anaerobe
• Common 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 inactivates the
ribosome of most eukaryotic cells
– enterohemorrhagic

26. Chromatium spp.
Class Gammaproteobacteria
• Purple sulfur bacteria
– microbial mats
• Motile by 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

27. 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

28. Myxococcus xanthus
Class 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

29. 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 cannot eat carbohydrates
• Example species
– Helicobacter pylori

30. Helicobacter pylori
Class 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

31. Helicobacter pylori
• Barry Marshall & Robin Warren won the Nobel prize in 2005 for
establishing the role of H. pylori in stomach ulcers.
• In 1985, Marshall showed that self administration of
Helicobacter pylori causes acute gastritis, and suggested that
chronic colonisation directly leads to peptic ulceration.
• They showed that antibiotic and bismuth salt killed H. pylori
and cured duodenal ulcers.
• This was the first evidence that gastric disorders could be due
to infectious disease.
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32. Activity for Review of
Unit 07.2
• What microbe is an environmental
biocontrol agent for mosquito-transmitted
viral pathogens?
• What microbe is the ancestor of the
mitochondria?
• What microbe is responsible for ulcers?
• What phylum and class do the purple
sulfur bacteria belong to?
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33. Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast
the microbes living in each. Explain
biogeochemical cycles.
2. Describe the diversity, metabolism &
habitat of the five classes of the phylum
Proteobacteria, including some
common example species.
3. Describe the diversity, metabolism &
habitat of the Gram-positive bacteria
(phylua Firmicutes & Actinobacteria).
33

34. Gram-positive bacteria

35. Phylum Firmicutes
• Large & 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

36. Bacillus cereus
Phylum Firmicutes
• Close relative of B.
anthracus
• Soils & guts
• Produces endospores,
stress-resistant asexual
spore that develops
inside mother cells
Fig. 11.3. Bacillus cereus

37. Phylum Actinobacteria
• Diversity spans a small
phylogenetic range but
includes a large number of
families & species
• Metabolism
– Aerobic mesophilic
heterotrophs
– Known antibiotic producers
– These plus Bacillus are the most
common bacterial source of
antibiotics
• Habitat
– Common in soils & guts
– Few animal symbionts and
pathogens
Fig. 11.11. Mycobacterium ulcerans
Fig. 11.12. Thermoleophilium album

38. Streptomyces antibioticus
Phylum 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

39. Mycobacterium tuberculosis
Phylum Actinobacteria
• M. tuberculosis complex (MTC)
– M. africanum, M. bovis, M. canettii,
M. microti, M. tuberculosis (TB).
• Obligate human pathogens with
no environmental reservoir
– One third of people have TB
– Aerosol transmitted
– Treatable with 6 months course of
antibiotics
• MTC’s unique ability to utilize
cholesterol, which is a common
component of human cell
membranes, plays a role in its
persistence

40. Activity for Review of
Unit 07.3 Gram positive bacteria
• For each microbe
listed, name the
phylum it belongs to,
and match it to its
function.
_ Bacillus cereus
_ Mycobacterium
tuberculosis
_ Streptomyces
antibioticus
a. Most common source
of industrial
antibiotics
b. Animal pathogen
with no known
environmental
reservoir
c. Soil microbe that
produces endospores
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41. Unit 7: Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the
microbes living in each. Explain
biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of
the five classes of the phylum Proteobacteria,
including some common example species.
3. Describe the diversity, metabolism & habitat of
the Gram-positive bacteria (phylua Firmicutes
& Actinobacteria).
Next class is Unit 8: Rare & uncultured microbes
Reading for next class: Brown Ch. 13 & 14
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