Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Describe the abundance and diversity of microbes, the “unseen majority”, in all natural and manufactured environments. 2. Explain the common measures of microbial diversity, and how diversity is measured. 3. What is the purpose of diversity?

1. Student hours
are for you!
But all lectures
are based on
these textbooks

2. 2
All synchronous meetings are
Optional, BUT…
We have found that students
who participate more, learn
more in this course

3. These are the
assessment
questions!

4. Quizzes and
exams will cover
what we talk
about in class

5. Only your top 7
quizzes count.
The 8th, if you
take it, is
extra credit

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moodle.umass.edu
If you are struggling so much that
you are considering compromising your
integrity, PLEASE COME TALK TO US!

7. 7
Let one of us know
if you are
struggling!

8. What to expect
• How to meet the course learning goals
q Listen to lecture recordings on moodle BEFORE class
q Come to synchronous meetings to review material
q Be ready to ask and answer questions, in our classroom and in your
breakout rooms !
• How we spend our synchronous time (will be recorded)
– 5-10 mins: logistics, questions, social bookmarking
– 3 parts: 15 m lecture, 5 m activity
– During or after class: edit shared jamboard
• How you should spend your time
– Spend 6-9 hours per week on studying and interacting in this class
– Log in 2-3 times per week to Moodle & look at the Upcoming Events,
Announcements
– Check your email 2-3 times per week (minimum)
• Student help
– Student hours are to answer questions and discuss material
– I will schedule zoom & chat hours ahead of assessments
8

9. 9

10. Assessments Schedule
Assessment Topic Opens Closes
Quiz 1 Lecs 1-3 Tues 2/9 @ 11:15 am 2/14 @ 10:00 am
Quiz 2 Lecs 4-5 Tues 2/16 @ 11:15 am 2/21 @ 10:00 am
Exam 1 Lecs 1-5 Tues 2/23 @ 11:15 am Wed 2/24 @ 11:15 am
Quiz 3 Lecs 6-8 Tues 3/2 @ 11:15 am 3/7 @ 10:00 am
Quiz 4 Lecs 9-11 Thurs 3/11 @ 11:15 am 3/16 @ 10:00 am
Exam 2 Lecs 6-11 Thurs 3/18 @ 11:15 am Fri 3/19 @ 11:15 am
Quiz 5 Lecs 12-14 Tues 3/30 @ 11:15 am 4/4 @ 10:00 am
Quiz 6 Lecs 15-17 Thurs 4/8 @ 11:15 am 4/13 @ 10:00 am
Exam 3 Lecs 12-17 Tues 4/13 @ 11:15 am Wed 4/14 @ 11:15 am
Quiz 7 Lecs 18-20 Thurs 4/22 @ 11:15 am 4/27 @ 10:00 am
Quiz 8 Lecs 21-22 Tues 5/4 @ 11:15 am 5/9 @ 10:00 am
Exam 4 Lecs 18-22 During finals week TBD Finals are 5/6 – 5/12
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11. Class Jamboard
• Jamboard link shared on Moodle
• Everyone in our class can edit (link on Moodle) & there is
version control
• These will serve as the review sheets for the exams
• I will be available to chat online through this document the
day before the exams.
11

12. Engagement strategies
• I want this class to be a place where we
can build a community around talking
about microbial diversity and physiology!
So please…
q add a profile picture to your Zoom & Moodle
q unmute yourself and say ”Hello” in the
morning!
q turn your video on, even for a short while,
during our synchronous meetings
q participate in the breakout room
conversations, challenges & jamboards
12

13. Bacteroidetes
Green sulfur bacteria
Chlamydia
Planctomycetes
Proteobacteria
Cyanobacteria
Spirochaetes
Firmicutes
Actinobacteria
Deinococcus/Thermus
Thermotoga
Aquifex
Green nonsulfur bacteria
Euryarchaea
Nanoarchaea
Crenarchaea
Korarchaeum
Chromalveolates
Plantae
Unikonts
Rhizaria
Excavata
Unit 6. Diversity of Microbial Mats
Unit 7. Diversity of Soils and Sediments
Unit 8. Diversity of Rare and Uncultivable Species
Unit 9. Diversity of the Human Microbiome
Unit 10. Diversity of Permafrost
Unit 11. Diversity of Acellular Life: Viruses & Prions
Part 2. Exploring Microbial Diversity
Bacteria
Archaea
Eukarya
Units in this section will apply concepts from Part 1 to example ecosystems as a way to explore
microbial groups; groups covered in each unit are shown in the tree by open circles ( ).
Unit 1. Microbial Diversity Introduction
... what is diversity?
Why does it matter?
How do you measure it?
Unit 3. Phylogenetic Diversity, or
Taxonomy and Trees
Unit 2. Origins of Diversity, or
Microbiology of Early Earth
Unit 5. Morphological Diversity,
or Biofilms and Motility
Unit 4. Funcitonal Diversity, or
the Baas Becking hypothesis,
“Everything is everywhere,
but the environment selects.”
Part 1. Measuring
Microbial Diversity
Units in this section will explore origins of
diversity and how diversity is understood
and applied.
Graphical Syllabus
13

14. HOW TO MEASURE DIVERSITY
Unit 01, 2.2.2021
Reading for today: Brown Ch. 1 & 2
Reading for next class: Brown Ch. 4, 5 & 6
Dr. Kristen DeAngelis
Office Hours by appointment
deangelis@microbio.umass.edu
14

15. Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and
diversity of microbes, the “unseen
majority”, in all natural and
manufactured environments.
2. Explain the common measures of
microbial diversity, and how diversity is
measured.
3. What is the purpose of diversity?
15

16. Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and
diversity of microbes, the “unseen
majority”, in all natural and
manufactured environments.
2. For common measures of microbial
diversity, explain how diversity is
measured.
3. Identify the important historical
founders of modern microbiology and
describe their contributions to our 16

17. What are microbes?
l Any living thing you need a microscope to see...
17

18. The microbial world is vast
• Are there more microbes on Earth or
stars in the known universe?
http://www.skyandtelescope.com/astronomy-resources/how-many-stars-are-there/
18

19. http://www.skyandtelescope.com/astronomy-resources/how-many-stars-are-there/
19

20. 106 per mL
109 per g
101-3 per m3
How many microbes are there?
106 per mL
109 per g
101-3 per m3
20

21. How many microbes are there?
1013 bacteria
vs
1013 human
cells
1-3% body
mass
21
1013 bacteria
vs
1013 human
cells
1-3% body
mass

22. How many species are there?
…but what is a
species?
HMS Beagle being hailed by native Fuegians during the survey of Tierra del Fuego, by Conrad Martens.
22

23. Species definition
1. New species are defined based on similar genotypes
a. genome sequences, as average nucleotide identity (ANI)
b. Organisms within a species have DNA-DNA re-
association values are more than 70%
c. The 16S rRNA gene sequences of organisms in the same
species are > 97% identical
2. All strains within a species must show similar
phenotypes
a. Gram stain is an example of a phenotype, which indicates
the presence of a cell wall
b. Catalase activity or other enzyme activity is another
example
23

24. How can we expand known diversity?
• Cultivation and
enrichment
• Molecular
techniques
24

25. How can there be so much diversity?
25

26. How can there be so much
diversity?
• Ecological Niche - The place or function of a
given organism within its ecosystem.
• Niche space is defined by all of the
environmental factors that permit or constrain
the growth of a certain organism
• This includes but is not limited to: pH,
temperature, carbon source availability,
terminal electron acceptor availability, redox
potential, micronutrient status, water
availability, predation and many others
26

27. Activity for Review of
Unit 01.1 Extent of Diversity
For each set of pairs, which environment has the most
microbes? Which has the most diversity? Why?
Discuss in groups, then we will review answers together
1. Open ocean (top)
or salt marsh (bottom)?
2. Top, surface soil (top)
or deep soil (bottom)?
3. Skin (top)
or gut (bottom)?
27

28. Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and
diversity of microbes, the “unseen
majority”, in all natural and
manufactured environments.
2. Explain the common measures of
microbial diversity, and how diversity is
measured.
3. What is the purpose of diversity?
28

29. Early (wrong) Trees of Life #1
Carl Linnaeus
Woesian ToL: Pace NR, Science 1997
29

30. Carl Linnaeus (1707–1778)
• Introduced the rank-based system of
nomenclature into biology
• Wrong because organisms are related by degrees
(= phylogeny)
• promoted scientific racism in his classification of
Homo subspecies
– https://www.linnean.org/learning/who-was-linnaeus/linnaeus-and-race
• D – K – P – C – O – F – G – S
– Domain – Kingdom – Phylum – Class – Order – Family –
Genus – Species
– “Dear King Phillip Came Over From Great Spain”
– “Determined, Kind People Can Often Follow Ghastly
Screams”
– “Didn’t Know Popeyes Chicken Offers Free Gizzard Strips”
30

31. Early (wrong)
Trees of Life
#2
Ernst Haeckl
31

32. Ernst Haeckel (1834-1919)
• proposed the kingdom “Protista,” which
later housed the Bacteria and Archaea
• Though he supported the theory of
evolution, he believed in Lamarckism
(which is mostly wrong)
– “Acquired inheritance”: the idea that an
organism can pass on characteristics that it
acquired during its lifetime to its offspring
(aka heritability of acquired characteristics,
or soft inheritance)
– modern epigenetics is a form of “Neo-
Lamarckism
32

33. Early (wrong) Trees of Life #3
Robert Whittaker
33

34. Robert Whittaker (1920-1980)
• Introduced the importance of fungi
• proposed the 5 kingdom tree, which
was wrong because it was based
roughly on differences in nutrition
34

35. Modern Tree of Life
• Woesian tree was based on sequencing
SSU ribosomal RNA genes
Bacteria Archaea Eukaryotes
35

36. Carl Woese
Discovered that the sequence of the small subunit
ribosomal RNA gene is a phylogenetic marker.
Woese, Candler & Wheelis. 1990. Towards a natural
system of organisms: Proposal for the domains
Archaea, Bacteria, and Eucarya. PNAS
36

37. Carl Woese
• Discovered that the 16S ribosomal RNA gene
is a good phylogenetic marker
• Phylogenetic markers are
– a way of quantifying the relatedness of
organisms to one another
– based on shared evolutionary history
– Indicative of many traits (behaviors, forms,
functions), which are phylogenetically conserved
• Dr. Woese’s sequencing also revealed the
existence of the Archaea, which were
previously thought to be bacteria
37

38. l Small subunit (16S) ribosomal
RNA from Thermus thermophilus
l Proteins in blue
l Single strand rRNA in orange
Small subunit ribosomal RNA
38

39. Small subunit ribosomal RNA as a
phylogenetic marker for all of life
1. Structural RNA so information dense
2. Highly conserved and highly variable regions
3. Essential, so low horizontal gene transfer rate
4. Short ~1500 bp, so perfect for Sanger
sequencing
5. Cultivation independent
6. RNA copy number proportional to life strategy
39

40. What are some different kinds of
diversity?
• Taxonomic diversity
• Phylogenetic
diversity
• Genetic diversity
• Functional diversity
• Morphological
• Structural
• Metabolic
• Ecological
• Behavioral
THERE ARE MANY DIFFERENT WAYS
OF MEASURING DIVERSITY.
40

41. What are the different kinds of
diversity?
l Taxonomic diversity – based on a marker gene
usually, some way of splitting organisms into
groups
l Phylogenetic diversity – considers the degrees of
relatedness, usually by a gene or family of genes
l Genetic diversity – the complement of genes that
mark an organism or community's potential
function
l Functional diversity – the range of actual
functions of an organism or community
41

42. What is diversity?
l Diversity = Richness + evenness
42

43. What is diversity?
l Alpha diversity – within a sample
l Richness = how many different things
l Observed richness is always an
underestimate
l Estimated richness can be calculated using
the number of singletons & doubletons
l Estimated richness can also be calculated
by rarefaction analysis
l Evenness = how frequently each thing occurs
l Beta Diversity – between samples
43

44. Diversity Activity
• When estimating diversity, we
always fall short, but some
methods are better than others.
Why?
• Use the handout and a blank
piece of paper to calculate
diversity three ways.
44

45. Rarefaction analysis
a way to estimate total richness
Also sometimes called a “collector’s curve”
l Most organisms exist at very low relative abundance
l A potentially bottomless well of diversity: rare biosphere
45

46. Activity for Review of
Unit 01.2 Measures of Diversity
Which of the following should be the lowest
number?
a. Observed richness
b. Actual richness
c. Estimated richness using rarefaction analysis
46

47. Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and
diversity of microbes, the “unseen
majority”, in all natural and
manufactured environments.
2. Explain the common measures of
microbial diversity, and how diversity is
measured.
3. What is the purpose of diversity?
47

48. Microbial diversity is associated with health &
loss of diversity is associated with disease
48
Mosca et al., 2016

49. Why is diversity important?
l Direct link between plant and microbial diversity and
l stress resistance
l Net N mineralization
l Microbial biomass
l Microbial activity
Zak et al., 2003;
49

50. Why is diversity important?
l Microbes are everywhere: what are they doing?
l Making and spoiling our food
l Causing disease
l More diverse communities are more resistant
to stress & perturbations
l Differences in fecal microbial community diversity,
composition and function have also been correlated
with Crohn's disease, ulcerative colitis, irritable
bowel syndrome (IBS), Clostridium difficile-
associated disease (CDAD) and acute diarrhea
l Plant communities are more tolerant of stress when
they live in more complex communities
Lozupone et al., Science 2012 50

51. Activity for Review of
Unit 01.3 Importance of Diversity
Describe one example of how your
standard of living is improved because of
microbial diversity.
51

52. Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and diversity of
organisms microbes, the “unseen majority”,
in all natural and manufactured
environments.
2. Explain the common measures of microbial
diversity, and how diversity is measured.
3. What is the purpose of diversity?
Next class is Unit 2: Phylogeny
Reading for next class: Brown Ch. 4, 5 & 6
52