Unit 5: Everything is everywhere? LECTURE LEARNING GOALS 1. State the Baas Becking hypothesis, and describe the environmental traits are the strongest drivers of microbial community. 2. Explain how to measure community dissimilarity. Explain why the Baas Becking hypothesis continues to be tested today. 3. Describe methods to link taxonomic or community structure to function.

1. EVERYTHING IS EVERYWHERE…?
Unit 05, 2.16.2021
Reading for today: Brown Ch. 22 & 23
Reading for next class: Brown Ch. 8 & 9
Dr. Kristen DeAngelis
Office Hours by appointment
deangelis@microbio.umass.edu
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2. Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and
describe the environmental traits are the
strongest drivers of microbial community.
2. Explain how to measure community
dissimilarity. Explain why the Baas
Becking hypothesis continues to be
tested today.
3. Describe methods to link taxonomic or
community structure to function.
2

3. Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and
describe the environmental traits are the
strongest drivers of microbial community.
2. Explain how to measure community
dissimilarity. Explain why the Baas
Becking hypothesis continues to be
tested today.
3. Describe methods to link community to
function.
3

4. 4
Baas Becking Hypothesis
"Everything is everywhere, but the environment selects”
Translated from the original Dutch:
"Alles is overal: maar het milieu selecteert”
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5. Baas Becking Hypothesis
• Lourens Baas Becking was a Dutch
botanist and microbiologist
– published in the 1930s
• ‘everything is everywhere’ = dispersal
capability of microbes is so enormous
that they erase the effects of past
evolutionary and ecological events
• ‘the environment selects’ = different
contemporary environments maintain
distinctive microbial assemblages
• Emphasis on “BUT”…
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6. Simulated concentration (103 m−3) of 1 µm bacteria in near-surface air
based on an adjusted general circulation model (Burrows et al. 2009a).
Ann M. Womack et al. Phil. Trans. R. Soc. B 2010;365:3645-3653
Biogeography

7. Biogeography
• The study of patterns of species
distribution across geographical areas
• “...like plant and animal distributions,
microbial distributions can be the result of
both deterministic (environmental) and
stochastic (dispersal) processes.”
– Environment
– Life history eg., dispersal limitation, past
conditions
• Figure from Womack, Bohannan and Green 2010, Figure
1: Simulated concentration (103 m −3) of 1 µm bacteria
in near-surface air based on an adjusted general
circulation model (Burrows et al. 2009a). 7

8. Salinity
• the strongest
driver of
microbial
community
structure
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9. Salinity
• Samples (n=202) derive from a range ‘‘normal’’
environments such as soil, seawater, and sediments
plus environments at the extremes of temperature
(hot springs, hydrothermal vents, marine ice), salinity
(hypersaline basins, lakes and mats), acidity (acidic
springs and rocks, alkaline lakes), and nutrient
availability (oligotrophic caves)
• Red circles indicate nonsaline environments, green
triangles indicate saline environments, and blue
squares indicate mixed environments.
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10. Compatible solutes are produced by
microbes to combat osmotic stress
Organic
compatible
solutes
Inorganic
compatible
solutes
K+
Na+
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11. Compatible solutes are produced by
microbes to combat osmotic stress
• Some reasons why a microbe would
use inorganic or organic compatible
solutes:
– C source availability
– enzymes adapted to high salt
– energetics may explain why
methanogens and ammonia oxidizers
have not been isolated from high salt
environments
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12. pH
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13. pH
• pH effect depends on the group.
• Acidobacteria prefer low pH
– Acidobacteria are found in all environments
though are dominant in soils.
• Actinobacteria and Bacteroidetes prefer
higher pH
– Actinobacteria are high-GC Gram-positive, tend to
live filamentously, and are also known for antibiotic
production.
– Bacteroidetes are Gram-negative, non-spore
forming, rod-shaped bacteria that are widely
distributed in the environment, including in soil, sea
water, and animal guts and skin.
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14. Temperature
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15. Temperature
• Microbes often live below their optimum
growth temperature.
• Adaptations to temperature extremes include
– Heat shock or cold shock proteins
– Membrane lipid composition that may include
modification of lipids, production of lipid bilayer
proteins that make the membrane more fluid (in
cold) or more rigid (in heat)
– In heat, production of thermophilic membrane
lipids may include membrane-spanning tetra-
ether lipids (archaeal-based lipids)
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16. Activity for Review of
Unit 05.1
This is an aerial photo of
the Don Juan Pond in
Antarctica has >40% salinity;
this is the saltiest known
body of water on Earth.
1. This is a C-limiting
environment. What kind
of compatible solutes do
microbes make here?
2. Would you expect this
environment to have high
or low diversity? Why?
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17. Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and
describe the environmental traits are the
strongest drivers of microbial community.
2. Explain how to measure community
dissimilarity. Explain why the Baas
Becking hypothesis continues to be
tested today.
3. Describe methods to link community to
function.
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18. Baas Becking Hypothesis
"Everything is everywhere,
but the environment selects”
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19. What microbial traits drive
community dissimilarity?
• Gene content
– Gene content describes the potential for an
organism to live in an environment.
– Phylogeny is a proxy for gene content
• Life strategy
– the schedule and duration of key events in an
organism's lifetime are shaped by natural
selection to produce the largest possible number
of surviving offspring
– Changes to this schedule can affect evolution
• Surveying these traits is a measure of
community dissimilarity
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20. Gene content
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Phylogeny is a proxy for gene content

21. 21

22. 22

23. Comparative metagenomics of
microbial communities
• Figure 1: rarefaction curve based on 16S
rRNA amplicon gene community analysis,
whale fall is much less diverse than soils
• Figure 2: rarefaction curve based on
functional gene analysis of orthologous
groups, whale fall is similarly diverse when
compared to soils
• Taken together, this is functional
redundancy
– Many species
– Fewer overlapping functions 23

24. Activity for Review of
Unit 05.2
Some marine bacteria display bipolar
distributions in the Earth's oceans, occurring
exclusively at the north and south poles and
nowhere else. Is this evidence for or against
the Baas-Becking Hypothesis? Explain, and
be sure to restate the Baas-Becking
Hypothesis.
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25. Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. Quote the Baas Becking hypothesis, and
describe the environmental traits are the
strongest drivers of microbial community.
2. Explain how to measure community
dissimilarity. Explain why the Baas
Becking hypothesis continues to be
tested today.
3. Describe methods to link taxonomic or
community structure to function.
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26. How to link phenotype to genotype?
• Comparative
metagenomics
– e.g., the Sargasso
sea microbiome
• Comparative
genomics
• Phylogenetic
inference
• Stable isotope
probing
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27. How to link phenotype to genotype?
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• Comparative
metagenomics
– e.g., the Sargasso
sea microbiome
• Comparative
genomics
• Phylogenetic
inference
• Stable isotope
probing

28. 28

29. The evolutionary history of
Chlamydia
• Chlamydiae is a bacterial phylum and class whose
members are obligate intracellular pathogens.
• One of the most common STDs, caused by
Chlamydia trachomatis. The C. trachomatis
genome improves our ability of understand,
diagnose, and combat the pathogen.
• This study compares pathogenic chlamydiae (4
human pathogenic isolates) to environmental
chlamidiae), the Acanthamoeba sp. endosymbiont
UWE25.
• UWE25 is NOT an ancestor of pathogenic
chlamydiae but a “primitive” cousin
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30. Horn et al., 2004
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31. Horn et al., 2004
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32. Horn et al., 2004
The evolutionary history of
Chlamydia
• UWE25 and the pathogenic chlamydiae both have
type three secretion systems (TTSS).
• This tree of TTSS has the same topology as the 16S
rRNA gene tree. This shows that these TTSS are not
horizontally acquired, suggesting that this system
would have been used as a pre-adaptation to the
pathogenic lifestyle in the common ancestor. The
TTSS is an ancestral trait for these Clostridia
• TTSS are strict virulence factors in pathogens, though
their role in UWE25 is not clear, maybe they involve
secreting some kind of protease-like activity factor
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33. How to link phenotype to genotype?
• Comparative
metagenomics
– e.g., the Sargasso
sea microbiome
• Comparative
genomics
– e.g., chlamydia
• Phylogenetic
inference
• Stable isotope
probing (SIP)
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Nutrient concentration
Growth
rate
oligotrophs
copiotrophs
Life strategy or
trophic strategy

34. Life strategy
Morrissey et al., ISME J 2016
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Maximum
growth rate is
phylogenetically
conserved
- Copiotrophs
are fast but
inefficient
- Oligotrophs
are slow but
efficient

35. Life strategy, a.k.a. trophic strategy
• Growth rate and efficiency exist as a tradeoff…
• Copiotrophs are capable of fast maximum growth
rate, and have feast or famine growth strategy;
• Oligotrophs have relatively slow maximum growth
rates, and do not change growth rate when rich
substrates are available.
• Copiotrophs grow fast but inefficiently, meaning
that the produce more CO2 per C assimilated;
• Oligotrophs grow slowly but efficienty, meaning that
most C assimilated ends up in biomass not CO2.
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36. How to link phenotype to genotype?
• Comparative
metagenomics
– e.g., the Sargasso sea
microbiome
• Comparative
genomics
– e.g., chlamydia
• Phylogenetic inference
– e.g., life strategy
• Stable isotope probing
(SIP)
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37. Stable-isotope
probing
”SIP”
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38. Stable-isotope probing
• Feed a community isotopically-heavy
substrate
• The organisms that eat the heavy substrate
become enriched
• The “heavy” DNA can be separated from
the light DNA
• Sequences enriched in the heavy fraction
compared to the light indicate organisms
that took up the substrate
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39. NanoSIMS =
SIP + microscopy
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40. Activity for Review of
Unit 05.3
If you wanted to know what bacteria were
capable of nitrogen fixation in a sediment
sample, which method of sequencing would
be appropriate? Circle all that apply.
a. Comparative genomics
b. Metagenomics
c. metatranscriptomics
d. phylogenetics
e. Stable isotope probing
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41. Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and
describe the environmental traits are the
strongest drivers of microbial community.
2. Explain how to measure community
dissimilarity. Explain why the Baas Becking
hypothesis continues to be tested today.
3. Describe methods to link taxonomic or
community structure to function.
Next class is Unit 6: Diversity of Microbial Mats
Reading for next class: Brown Ch. 8 & 9
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