1. Microbes and the Environment
Microbial Communities
and Global Change
Milton Saier

2. 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

3. 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).

4. Possible Microbial feedbacks in global change
Plant community change ?
Plant growth
Nutrient mineralization _ _ +
Warming
Microbial trace gas production + +
CO2 increase
Microbial Respiration
Red = positive feedback (destabilizing)
Green = negative feedback (stabilizing)
Purple = uncertain

5. 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).

6. Methane (CH4) About 1.7 ppm in atmosphere.
Strong greenhouse gas. About 25 times worse than CO2.
Important in ozone chemistry.

7. Elevated atmospheric CO2

8. NOx in fossil fuel emissions
Clean air act
However, N2O concentrations now increase ~0.3%/year.

9. Atmospheric methane is increasing in the industrial age…

10. But why?

11. Methanotrophy (methane oxidation)
(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.

12. Methanogens (Archaea)
Methanopyrus sp.
Methanococcus jannaschii

13. 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”).

14. 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)

15. Global N cycle
(Units are 1012g/year)

16. Simplified Nitrogen cycle
anaerobic
Nitrogen fixation N2
NH4+
(by-products of nitrification)
N2O
(N2O, NO)
Organic N
denitrification
ammonium oxidation
(nitrification)
NO2-
NO3-
nitrite oxidation
(nitrification)
aerobic

17. nitrifiers Nitrosococcus Nitrosolobus Nitrospina Nitrosospira
Nitrosomonas

18. Methane production in 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.

19. Agriculture and Nitrous oxide
N2O
NH3
NO3-
N2O
“leaky pipe” model
More N fertilization leads to more NOx emissions

20. Eutrophication
Nitrogen and phosphorous nutrients lead to blooms; the oxygen is used up; algae decompose, and fish suffocate.

21. 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)

22. Hypothesized denitrification effects on global climate after the last glacial maximum (~22,000 ya)
High denitrification rates in the oceans
Lower NO3- in marine environments
Lower plant production rates in the oceans
Slower CO2 removal by the oceans
Climate warms

23. 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?