The document contains slides from a lecture on biodiversity and the tree of life. It discusses the diversity of form and function seen in different domains of life. The slides provide examples of different shapes, structures and modes of living seen in bacteria, archaea and eukaryotes. These include various cell shapes in prokaryotes, colonial and multicellular lifestyles, and specialized cell types in eukaryotes like dinoflagellates, ciliates and parasites. "Tours" are included to highlight some of the morphological diversity within major groups like alveolates, rhizarians and excavates. The slides aim to demonstrate the wide range of forms that organisms can take on and how these relate
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 8.
Introduction to Microbial Diversity, part 2.
Slides for Lectures by Jonathan Eisen
Innovations in Sequencing & Bioinformatics
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The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
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Exposé invité Journées Nationales du GDR GPL 2024
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
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1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 9:
Diversity of Form and Function
Prof. Jonathan Eisen
2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some insects from my yard in Davis Western HoneyBee
3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some insects from my yard in Davis Argentine ant
4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some insects from my yard in Davis Tiger fly?
5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some insects from my yard in Davis Carpenter bee
6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
iNaturalist
• Take pictures
• Upload them
!http://iNaturalist.org
!Inaturalist App
!Seek App (real time identification)
• Use their AI system and also community to
help with identification
• My observations here: https://
www.inaturalist.org/observations/
phylogenomics
7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Learning Goals
• Understand general patterns of diversity of form
seen in Bacteria, “Prokaryotic Archaea” and
Eukarya
• Understand key ways that organisms acquire
carbon and use energy and electrons
• Understand how one can use culturing to study
extremophiles in the lab
• Understand example patterns of the evolution of
extremophily
8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!8: Phylogenetic Diversity
!9: Diversity of Form and Function
!10: Pathogens and Parasites
Lecture 9 Context
9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lab Connections
• Lab 2 Station B: Microbial Metabolic
Diversity
• Lab 2 & 3 Microscopy
• Lab 2 Station F: Winogradsky columns
12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Review Lecture 8
13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus tours
14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #1
• The overall structure of the tree of life has
been determined by analysis of molecular
sequence data
• Molecular data particularly important for
placing most microbes into the tree of life
15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Two Domain Tree of
Life with Some Major
Subbranches Shown
16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #2
• Most microbes were only included in the tree
of life if they could be grown in the lab
17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
http://www.google.com/url?
sa=i&rct=j&q=&esrc=s&source=images&cd
=&docid=rLu5sL207WlE1M&tbnid=CRLQYP
7d9d_TcM:&ved=0CAUQjRw&url=http%3A%
2F%2Fwww.biol.unt.edu%2F~jajohnson%2F
DNA_sequencing_process&ei=hFu7U_TyCtO
qsQSu9YGwBg&psig=AFQjCNG-8EBdEljE7-
yHFG2KPuBZt8kIPw&ust=140487395121142
4
DNA
“Culture Independent
DNA Studies”
19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Environmental Sampling
genome genomegenome
ACUGCACCUAU
CGUUCGACUGCACC
UAUCGUUCGACUGC
ACCUAUCGUUCGAC
UGCACCUAUCGUUC
GACCUAUCGUUCGA
CUGCACCUAUCGUU
CGACCUAUCGUUCG
ACUGCACCUAUCGU
UCG
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
CUAUCGUUCG
20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Also true for the
microbial lineages in
eukaryotes
No way to cover all
this diversity in this
class
21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
Can infer
traits using
character
state
reconstruction
methods
23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
BCA
BCA
Bacterial
Common
Ancestor
24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor
25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Some features
previously
thought to be
“Eukaryotic”
innovations
were likely
present in the
Eukaryote-
Asgard
ancestor
Cytoskeleton
Chromatin
26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Unicellularity & Multicellularity continuum
• Unicellular: one cell does
everything
R
• Colonial: collections of many
attached cells (usually of the
same genotype); no
differentiation or division of
labor or reproduction capabilities
• Multicellular: collection of many
attached cells (usually of same
genotype); differentiation and
division of labor and
reproductive capabilities
30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Bacteria & “Prokaryotic Archaea” : Major Cell Forms
• Among the Bacteria and Archaea, three
shapes are common:
! Sphere or coccus (plural cocci), occur singly
or in plates, blocks, or clusters.
! Rod—bacillus (plural bacilli)
! Helical
• Rods and helical shapes may form chains or
clusters.
Cocci = Spheres Bacilli = Rods Spirilla = Curved
31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Bacteria & “Prokaryotic Archaea” : Major Cell Forms
• Among the Bacteria and Archaea, three
shapes are common:
! Sphere or coccus (plural cocci), occur singly
or in plates, blocks, or clusters.
! Rod—bacillus (plural bacilli)
! Helical
• Rods and helical shapes may form chains or
clusters.
Cocci = Spheres Bacilli = Rods Spirilla = Curved
These are the most common forms seen but
there are all sorts of other forms
What follows is a brief tour of this diversity. You do
not have to know the details unless presented
elsewhere in class
32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR BEGINS
Diversity of Form in Bacteria and “Prokaryotic Archaea”
33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
“Full Tree”
34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Compressed
Tree
Compressed Tree of Life
35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Many are single celled but not all have the
“simple” sphere, rod, or spiral shapes
TOUR
Diversity of Form in Bacteria and “Prokaryotic Archaea”
36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Endospores: Only
Seen in Firmicutes
Phylum
Resistant to
Everything
Diversity of Form in Bacteria and “Prokaryotic Archaea”
37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Heterocysts Unique
to Cyanobacteria
Used for N2 fixation
Diversity of Form in Bacteria and “Prokaryotic Archaea”
38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
“Spiral” shape
comes in many
kinds
Diversity of Form in Bacteria and “Prokaryotic Archaea”
39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Some Chlamydia
species change forms
during life cycle
Diversity of Form in Bacteria and “Prokaryotic Archaea”
40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thiomargarita
Epulopiscium
TOUR
Some Bacteria are
not microbial (can
see with eyes
without aids)
Diversity of Form in Bacteria and “Prokaryotic Archaea”
41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Square Archaea
Diversity of Form in Bacteria and “Prokaryotic Archaea”
42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Some are colonial
Diversity of Form in Bacteria and “Prokaryotic Archaea”
TOUR
43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
Clumps of
Cocci Seen
in Many
Phyla
Diversity of Form in Bacteria and “Prokaryotic Archaea”
44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOURFilaments Seen in Many Phyla
Diversity of Form in Bacteria and “Prokaryotic Archaea”
45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• A few may be truly multicellular
Diversity of Form in Bacteria and “Prokaryotic Archaea”
TOUR
46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR
More Complex
Structure in Some
Taxa
Fruiting body of gliding bacterium
Stigmatella aurantiaca. SEM.
Diversity of Form in Bacteria and “Prokaryotic Archaea”
47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Vibrio
Cyanobacterium
Many are Motile
TOUR
Diversity of Form in Bacteria and “Prokaryotic Archaea”
48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR ENDS
Diversity of Form in Bacteria and “Prokaryotic Archaea”
Need to Know Material not in the “Tours”
49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• More than just cocci, bacilli, and spirals but
these are common
• Most are single celled but some are colonial and
a few may be multicellular
• Many are motile
• Some can be identified from morphology
• In most cases morphology does not match
phylogeny and is more related to ecology or
functions
• Most phylogenetic studies are based on
sequence data
Diversity of Form in Bacteria and “Prokaryotic Archaea”
50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotic Diversity of Form
51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR BEGINS
Eukaryotic Diversity of Form
52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Many are single celled
Eukaryotic Diversity of Form
TOUR
53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Dinoflagellates
TOUR
54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Apicomplexans
Apical complex
TOUR
55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Ciliates
TOUR
56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizarians: Cercozoans
TOUR
57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizarians: Foraminiferans
TOUR
58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizarians: Radiolarians
TOUR
59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans: Loboseans
TOUR
60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Trypanosoma sp.
mixed with blood cells
Excavates: Kinetoplastids
TOUR
61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Euglenids
TOUR
Movement in the euglenoid Eutreptia
TOUR
62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Diplomonads and Parabasalids
TOURTOUR
63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Heteroloboseans
TOUR
64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Many are colonial
Eukaryotic Diversity of Form
TOUR
65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Diatoms
TOUR
66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts: Choanoflagellates
The choanoflagellate Salpingoeca sp. feeding
TOUR
67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Many are multicellular
Eukaryotic Diversity of Form
TOUR
69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest
TOUR
70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans: Plasmodial Slime Molds
TOUR
71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Kary
Amoebozoans: Cellular Slime Molds
TOUR
72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Red Algae
Motile spores from
Purpureofilum
Audouinella pacificaSpyridia
TOUR
73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Chlorophytes
Movement in the green
alga Volvox
Micrasterias
TOUR
74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
TOUR ENDS
Eukaryotic Diversity of Form
75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Range from single celled to colonial to
multicellular
• Incredible diversity in form & motility among
Eukaryotes
• For many, but not all taxa, morphology (aka
form) is a valuable trait for identification and
phylogeny
Eukaryotic Diversity of Form (Need to Know This)
76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lesson: Convergence of Form is Common
77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Fungal Hyphae
78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Oomycetes
Phytophthora
Sudden Oak Death
Potato Late Blight
79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Actinobacterial Branching Filaments
80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
The similarity in appearance of ooymcetes to
fungi is an example of _______
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
• E. Synapomorphy
81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
The similarity in appearance of ooymcetes to
fungi is an example of _______
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
• E. Synapomorphy
82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Trophy
• Organisms exhibit incredible diversity in how
they obtain nutrition (i.e., the processes by
which an they assimilates chemicals and
energy and uses them for growth)
• Generally referred to with the suffix “trophy”
• Origin: Greek -trophiā, from trophē, from
trephein, to nourish.
85. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Trophy
• Three main components to “trophy”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
86. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from
inorganics
Auto
Carbon from
organics
Hetero
• E. coli • Chemo organo hetero trophy
• Chemo hetero trophy
Trophy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
87. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from
inorganics
Auto
Carbon from
organics
Hetero
• Humans? • Chemo organo hetero trophy
• Chemo hetero trophy
Trophy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
88. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from
inorganics
Auto
Carbon from
organics
Hetero
Cyanobacteria
• Photo litho auto trophy
• Photo auto trophy
Trophy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
89. Trophy
• Bacteria and “prokaryotic archaea” are very diverse in
types of trophy
• There are many distinct mechanisms to carry out each
form of “trophy”
• Also a great deal of diversity in some eukaryotes groups
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Clicker Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Clicker Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Clicker Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Clicker Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily
96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Extremophiles
Extremophile:
Organism that survives and thrives extreme
conditions
(as compared to conditions where other forms
of life survive and thrive).
97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Extreme Environments
105°C
CH3
CO, 80°CH2S, pH 0, 95°C High salt
CO2 4°Clow pH
98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Methods for Studying Microbes
Observation
What Next?
Collect Sample
Look in Microscope
See Cells
99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Methods for Studying Microbes
Culturing Observation
What Next?
Collect Sample
Look in Microscope
See Cells
100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Methods for Studying Microbes
<<<<
Culturing Observation
What Next?
The Great Plate Count
Anomaly
Collect Sample
Look in Microscope
See Cells
101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Methods for Studying Microbes
<<<<
Culturing Observation
DNA
What Next?
The Great Plate Count
Anomaly
Culture independent
DNA studies
Collect Sample
Look in Microscope
See Cells
102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Methods for Studying Microbes
<<<<
Culturing Observation
DNA
What Next?
The Great Plate Count
Anomaly
Culturing can work,
and this allows all
sorts of studies
Culture independent
DNA studies
Collect Sample
Look in Microscope
See Cells
103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Culturing Microbes
104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Example 1: Thermophiles
107. Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
108. Set up some
flasks with
growth media
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
109. Set up some
flasks with
growth media
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
110. Set up some
flasks with
growth media
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
111. Set up some
flasks with
growth media
1 2 3 4 Use different
flasks for
different
conditions
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
112. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
113. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
114. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
115. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
116. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
1 2 3 4
60° 70° 80° 90°
3h 3h 3h 3h
Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
117. Growth vs. Time
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
60° 70° 80° 90°
Plot Growth vs. Time for Each Condition
Time Elapsed
DensityofGrowth
118. Growth Rate
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
0.0
12.5
25.0
37.5
50.0
60 °C 70 °C 80 °C 90° C
Calculate and Plot Growth Rate vs. Conditions
Temperature
GrowthRate
119. Optimal growth temperature (OGT) for Different Species
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
120. Optimal growth temperature (OGT) for Different Species
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Extremophile Type Low High
Psychrophile -20 °C 10 °C
Mesophile 11 °C 40 °C
Thermophile 41 °C 80 °C
Hyperthermophile 81 °C 122 °C
121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Two Domain Tree of
Life with Some Major
Subbranches Shown
122. Hug et al 2016
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Hug et al. 2016 Tree of Life
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
Two Domain Tree of
Life with Some Major
Subbranches Shown
Laura Hug
U. Waterloo
Jill Banfield
UC Berkeley
123. Hug et al 2016
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
41 - 80 °C
Thermophiles Across
Tree of Life
124. Hug et al 2016Thermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios that
would account for this
pattern of presence of
thermophily across the Tree
of Life?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
125. Hug et al 2016
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Hyperthermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
Hyperthermophiles
Across Tree of Life
No Eukaryotes
Only a few Bacteria
81 - 122 °C
126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Example 2: Halophiles
127. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
128. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
129. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
130. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
131. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
132. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
133. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
134. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
135. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
136. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
137. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
138. Determining Optimal Salt Concentrations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
1 2 3 4
1M 2M 3M 4M
3h 3h 3h 3h
139. Growth vs. Time
Plot Growth vs. Time for Each Condition
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
1M 2M 3M 4M
Time Elapsed
DensityofGrowth
140. Growth Rate
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
0.0
12.5
25.0
37.5
50.0
1M 2M 3M 4M
Calculate and Plot Growth Rate vs. Conditions
Salinity
GrowthRate
141. Optimal salt concentration for different species
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
142. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigments – very visible
• Have been found at
pH up to 11.5.
• Unusual adaptations
to high salt,
desiccation
• Many have
bacteriorhodopsin
which uses energy of
light to synthesize ATP
(photoheterotrophs)
143. Hug et al 2016
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Extreme Halophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
Most extreme
halophiles are from a
single clade of
“prokaryotic
Archaea”
144. Hug et al 2016Extreme Halophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios that
would account for this
pattern across the Tree of
Life?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
145. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Uses of extremophiles
Type of
environment
Examples Example of
mechanism of
survival
Practical Uses
High temp
(thermophiles)
Deep sea vents,
hotsprings
Amino acid
changes
Heat stable enzymes
Low temp
(psychrophile)
Antarctic ocean,
glaciers
Antifreeze
proteins
Enhancing cold
tolerance of crops
High pressure
(barophile)
Deep sea vents,
hotsprings
Solute changes Industrial processes
High salt
(halophiles)
Evaporating
pools
Incr. internal
osmolarity
Soy sauce production
High pH
(alkaliphiles)
Soda lakes Transporters Detergents
Low pH
(acidophiles)
Mine tailings Transporters Bioremediation
Desiccation
(xerophiles)
Deserts Spore formation Freeze-drying
additives
High radiation
(radiophiles)
Nuclear reactor
waste sites
Absorption, repair
damage
Bioremediation,
space travel
146. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Novozymes in Davis
147. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!8: Phylogenetic Diversity
!9: Diversity of Form and Function
!10: Pathogens and Parasites
Lecture 9 Context