Microbial

interactions in
aquatic
environments
BL7042 - 15 credits
 Sarahi L. Garcia
About me
2008: B.S. Biochemical engineer, Universidad Autonoma de Coahuila, Mexico

Mıınt
2008-2010: MSc Bioengineering, University of Georgia, USA
2010-2013: PhD Microbiology, Friedrich Schiller Jena University, Germany
2013: Postdoc at University of Wisconsin Madison, USA
2014: Postdoc at Uppsala University, Sweden
2019: Join DEEP as SciLifeLab fellow & Assistant Professor
Research Interests
microbial interactions, carbon cycling, biotechnology
My Research group now
M.S. student Michelle Verstraaten
PhD student Alejandro Rodriguez-Gijon
PhD student Armando Pacheco
Postdoc Justyna Hampel
Maybe YOU?
Photo summer 2022
Recommended literature

13th Edition, 2012

Mandatory literature
• A foraging mandala for aquatic microorganisms.
Vicente Fernandez, Y. Yawata and R. Stocker. The ISME J.
2019
 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

 Quiz about microbial
ecology

Go to www.menti.com and use

code 4893 7699
 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

Microbial diversity and its habitats
 Requirements of life
• Source of energy
• Source of electrons
• Source of carbon (+ other elements)
• Electron acceptor
en.wikipedia.org/wiki/Primary_nutritional_groups
 Diversity of
respiration
reactions

Brock biology of microorganisms 16th ed

 Atmosphere
So n
lar io
Abiotic CH4 oxidation iat
ra
d rad
iat N2 + O2 2NOx; combustion CO2 r
ion
Sola

Fe3+, SO42–/S0 + [CH2O] O2 + [CH2O] Photosynthesis

A biosphere Anoxygenic
photosynthesis
Oxygenic
photosynthesis
H2O is oxidized
model showing HS–/S0
NH4+
CO2 + H2O
(loses electrons)
inputs and
CO2
CO2 N2 fixation
SO42–

CO2 is reduced
SO42–/S0 Fe3+
Mn2+
SO42–/S0 Fe2+ NO3–/NO 2–

outputs of
2+
respiration CO2 Fe N4 Mn4+
H2 O
SO42–/S+
Mn+ respiration
CO2
SO42–
O2 respiration
(gains electrons)
energy and
[CH2O]
H2 + CO2 H2
CH4 Fe3+ respiration [CH2O] NO3–/NO2– [CH2O]
H2 respiration H2
Fermentation

materials
HS–/S0 CH4
Methanogenesis [CH2O] Fe2+ HS–/S0
[CH2O] [CH2O]
H2 H2 Fe2+

Falkowski et al. 2008

HS–/S0 HS–/S0 Mn2+
H2 + CO2 NH4+
NH4+

–0.5 0 0.5 1
E0 (V)
CH4 [CH2O] Metals
Metals H2, CH4 CO2 PO43–
FeS2 CO32–
HS-, SO3 CO2 NH4+
PO43– Ca3 (PO4)2 SiO3 SO42–

Geothermal Tectonics, erosion

Diagenesis
processes Mountain building

Earth’s mantle and crust Sediments

Tree of life

Brock Biology of Microorganisms 13th ed

How did we arrive to the tree of life?

Brock Biology of Microorganisms 13th ed

 Bacteria
A “new” view
of the tree of
life

Eukaryotes

Archaea
Hug et al. 2016 Nat Microb
 Biomass distribution on Earth

A B

Bar-On et al. 2018 PNAS

Biomass vs number of individuals
Grains of sand

Stars in Universe

Bar-On et al 2018
Microbial diversity and its habitats
Microbial ecology of the oceans
 Biomass distribution on Earth
A B
Taxon in marine Biomass Gt C
environment
Bacteria 1.3

Protists 2.0

Arthropods 1.0

C D Fish 0.7

Fungi 0.3

Bar-On et al. 2018

Archaea 0.3

E Molluscs 0.2
Marine food web including the microbial loop and viral
shunt
CO 2 P hot
e s is os y
ynth nth
tos es i
P ho s

Microbial loop Tr aditional food we b

Eukaryotic
E x c re t
ion phytoplankton
tion
A bs orp
tion E x c re
Bacterial C ons
ump
autotrophs tion tion
DOM mp
su

Inf
ec

n
Co
n

tio
ptio

n
sis
C ons um

Ly

A bs orption
E x c retion
Viral shunt
Zooplankton Multicellular

Breitbar et al. 2018, Nat Microb

C on s u
mption eukaryoti c
on
cti
Inf
grazer s
nfe
P hys ic a l mix ing

ec
I
tio
n

io n
Unicellular
eukaryotic

Consumpt
grazers
n
C on ptio
s umpti s um
on Bacteria l C on
heterotrophs

Excretion/death/
aggregation
PO M

Biological pump
 Taxonomy of
Ocean
prokaryotic
diversity
Alphaproteobacteria dominate
the data set (43.1% of 16S
rRNA gene sequences), and
the majority of these are
SAR11-like bacteria (30.9%,
e.g. Pelagibacter ubique)

Cyanobacteria (5.3%, e.g.

Prochlorococcus sp)
Biers et al. 2009 Appl Env Microbiol
 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

 Term
symbiosis
• Derived from the Greek
– “syn” meaning together and
– “bios” meaning life
 Symbiotic relationship continuum

Effect on host or other microbe

Tipton et al. 2019 Frontiers in Micro

 Genome size survey – 64 500 genomes
26 101 “species”

Rodríguez-Gijón et al. 2022 Frontiers in Microbiology

 Genome size across life *
~1.70 m

* ~8 850 m

V * ssDNA Circoviridae ~1 000 bp

Campillo-Balderas et al., 2015 (Frontiers in Ecology and Evolution)

A Pyrococcus furiosus ~1 900 000 bp * ~1 400 000 km

Introduction

Poole et al., 2005 (Journal of Bacteriology)

B * Escherichia coli ~5 000 000 bp

Bergthorsson and Ochman, 1995 (Journal of Bacteriology)

E Homo sapiens ~6 300 000 000 bp

Piovesan et al., 2019 (BMC Research Notes)

E * Polychaos dubium ~670 000 000 000 bp

Parfrey et al., 2008 (Molecular Ecology and Evolution)

Courtesy of Rodríguez-Gijón
Microorganisms with smaller genomes experience tradeoffs

Metabolic potential
Tradeoff
Metabolic versatility

Streamlining

Rodríguez-Gijón, Nuy … Garcia et al. 2022

 Genome size as a dynamic equilibrium
Small genome size Large genome size

Lower energy Gene gains Greater

Introduction

required to metabolic
maintain genome versatility
Gene losses

Courtesy of Rodríguez-Gijón
Black Queen
Hypothesis
• Evolution of dependencies through adaptive
gene loss
• Genomic and metabolic streamlining
reduces required carbon and other limiting
nutrients
Black Queen
Hypothesis
 Group activity
• Make a list of all the functions/molecules that are necessary
for a microorganism to exist.
Amino acid biosynthesis in 6120 sequenced bacterial genomes

Mee et al. 2014 PNAS

 Symbiotic relationship continuum

Effect on host or other microbe

Tipton et al. 2019 Frontiers in Micro

 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

 Microorganisms move the
biogeochemical cycles

Cycles are necessary for the

continuation of life
H, C, N, O, S, and P are the
major building blocks for all
biological macromolecules
 Microorganisms move the
biogeochemical cycles

• Carbon cycle
• Nitrogen cycle
• Sulfur cycle
• Iron cycle
• Phosphorus cycle
• Calcium cycle
• Silica cycle
• Mercury transformations
Biogeochemical cycles are interconnected

Falkowski et al. 2008

 Earth's Carbon Cycle and how it has changed over
time
By Robert Rohde
Research example on frozen lake microbial ecology

Under ice lake experiment

 Increased light availability

A 0 B 0 C 0

1 1 1
Depth (m)

Treatment
snow-covered
snow-free
2 2 2

3 3 3
0 1 2 3 4 5 20 40 60 1 2 3 4
Light (kilolux) Methane (micromolar) Temperature (Celsius)

Garcia et al. 2019 mSphere

 Effects on chlorophyll

A 0 B 0 C 0 D 0

Treatment
snow-covered
1 1 1 1 snow-free
depth (m)

Day
1
2 2 2 2 5
7
12
3 3 3 3
0.2 0.4 0.6 0.8 0.05 0.10 0.15 0.0 2.5 5.0 7.5 10.0 12.5 0 2 4 6
chlorophyll a (μg/l) chlorophyll b (μg/l) bacteriochlorophyll d (μg/l) bacteriochlorophyll e (μg/l)

Garcia et al. 2019 mSphere

Stimulation of primary producers impairs methanotophy

Garcia et al. 2019 mSphere, modified

 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

 A foraging
mandala for
aquatic
microorganisms.
Fernandez,
Yawata and
Stocker. The
ISME J. 2019
 Quiz about microbial ecology

Microbial diversity and its habitats. The microbial

ecology of oceans. The microbial loop

Microbial symbiosis. The Black Queen Hypothesis

Outline Nutrient cycles – biogeochemistry. Research example:

Microbial ecology on frozen lake

Foraging mandala discussion

Quiz about microbial interactions

 Quiz about microbial
ecology

Go to www.menti.com and use

code 7317 5330