Roles of Microbes in
Environmental
Control
Microbial Communities
and Global Change
Milton Saier
The 3-Domain
System
Based on ribosomal RNA gene
sequences
Almost all life is microbial!
The diversity of
microorganisms is vast
The “crown group”
of Eukaryotes
includes animals,
plants, fungi and
multicellular algae
Microbial Communities
Fantastically diverse:
Thousands of bacterial species are present in a gram of soil.
Most have never been isolated in a laboratory.
They are not well understood.
Control global (and local) biogeochemistry:
Most steps in the C, N, S cycles are performed exclusively by
prokaryotes (including trace gas production).
Decomposition is dominated by microorganisms (bacteria and fungi).
Photosynthesis: ~half of Earth’s primary production of carbon is by
cyanobacteria and algae. Plants and algae use cyanobacterial
photosynthesis because chloroplasts evolved from cyanobacteria.
Species-specific interactions with plants, animals and fungi:
Mutualisms (mycorrhizae, nitrogen fixers); Parasitisms (diseases).
Possible Microbial feedbacks in global change
Plant community
change
?
Plant growth
_
Nutrient
mineralization
_
+
+
Warming
+
CO2
increase
Microbial
Respiration
Red = positive feedback (destabilizing)
Green = negative feedback (stabilizing)
Purple = uncertain
Microbial
trace gas
production
Nitrous oxide (N2O)
About 300 ppb in the atmosphere.
Strong greenhouse gas: 200X worse than CO2.
Lifetime = 150 years.
Contributes to stratospheric ozone depletion (after conversion to
NO, nitric oxide).
Methane (CH4)
About 1.7 ppm in atmosphere.
Strong greenhouse gas. About 25 times worse than CO2.
Important in ozone chemistry.
Elevated atmospheric CO2
NOx in fossil fuel emissions
Clean air act
However, N2O concentrations now increase ~0.3%/year.
Atmospheric methane is increasing in the industrial age…
But why?
(aerobic)
(anaerobic)
CO2
respiration
C fixation*
Organic C
Methanogenesis
(methane synthesis)
Methanotrophy
(methane oxidation)
CH4 (methane)
*- primary production, i.e. photosynthesis,
chemoautotrophy, nonphotosynthetic CO2 fixation.
Methanogens
(Archaea)
Methanopyrus sp.
Methanococcus jannaschii
Trichonympha, a symbiotic protist
(a flagelated protozoan) in the
termite gut. It possesses its own
symbiotic methanogens (archaea)
which break down cellulose and
produce nutrients + methane.
It also has spirochetes embedded
in the outer leaflet of its
membrane which confers
coordinated motility to the host. It
is not known if Trichonympha
directs the motility of the
spirochete, or if the spirochetes
coordinate their motility
themselves to move the
Trichonympha (“teardrops with
wigs”).
More symbiotic termite gut
protists are present in termites:
the flagellated protozoans
Dynenympha and Microjoenia.
They contain their own symbiotic
methanogens.
Termite gut epithelium with
symbiotic methanogens (E)
Global N cycle
(Units are 1012g/year)
Simplified Nitrogen cycle
anaerobic
N2
Nitrogen fixation
NH4+
(by-products of
nitrification)
N2O
(N2O,
NO)
Organic N
denitrification
ammonium oxidation
(nitrification)
NO3-
NO2nitrite oxidation
(nitrification)
aerobic
Nitrosococcus
nitrifiers
Nitrosolobus
Nitrospina
Nitrosospira
Nitrosomonas
Methane production in rice paddies
Rice paddies:
Projected to increase by 70% in the next 25 years.
Anaerobic: rich in organic C – leads to methane production.
Some oxidation occurs due to the presence of O2 conducted
by the rice plants into the rhizosphere.
Effects of N fertilizers:
They STIMULATE plant and methanogen growth. This
STIMULATES methane production.
They also INHIBIT methane oxidation (in most studies of upland
rice and other ecosystems…). This also STIMULATES methane
production.
Agriculture and Nitrous oxide
N2O
NH3
NO3-
“leaky pipe” model
More N fertilization leads to more NOx emissions
N2O
Eutrophication
Nitrogen and phosphorous nutrients lead to blooms; the oxygen is
used up; algae decompose, and fish suffocate.
Effects of fertilizer runoff on denitrification
in coastal areas
Off the coast of India during monsoon season:
N in runoff causes eutrophication of coastal waters.
Lower oxygen leads to fish kills and increased biological
pollution.
Lower oxygen also leads to increased rates of denitrification.
This may eventually lead to nitrogen deficiency.
Insufficient N may result in stunted aquatic plant growth.
Unavailability of nutrients can then prevent fish reproduction.
(Naqvi et al. 2000)
Hypothesized denitrification effects on
global climate after the last glacial
maximum (~22,000 ya)
High denitrification rates in ocean
Lower NO3- in marine environments
Lower plant production rates in the oceans
Slower CO2 removal by ocean
Climate warms
Beneficial Bacterial Bioprocessing
1, Photosynthesis
2, N2 Fixation
3, Symbioses
4, Gut nutrition
5, Probiotics; prebiotics
6, C, N, S, P cycles
7, Mineralization/demineralization
8, Denitrification
9, Waste decomposition
10, Methane oxidation
11, Food production
12, Biofuel production
13, Diverse, interesting and entertaining
14, Human population control?
Quiz
1, Please name and describe four distinct processes that
bacteria catalyze that affect our biosphere in a beneficial
way.
2, Termites have endosymbionts with endosymbionts within
them. Please explain in general terms what these three (or
four) types of organisms are, what they do for the termite,
and how they affect the biosphere.
3, Please show or describe how denitrification is believed to
affect global warming.
4, Please describe what “living in a McDonald’s society”
means, and what the consequences to people and the
environment are.