1. EXTINCTION
OF MICROBES...
SHOULD WE CARE?
Marilen M. Parungao-Balolong, MSc, SMic
Associate Professor
Bioweek 2012 BIOSeminar
Wednesday, August 15, 2012
2. WE ALWAYS CARED ABOUT
PLANT EXTINCTION
Wednesday, August 15, 2012
3. WE ALWAYS CARED ABOUT
ANIMAL EXTINCTION
Wednesday, August 15, 2012
4. WE ALWAYS CARED ABOUT
HUMAN EXTINCTION
Wednesday, August 15, 2012
5. BUT...MICROBES?
ALWAYS TAGGED AS
THE REASON FOR
EXTINCTION...
Wednesday, August 15, 2012
6. MICROBES: THREAT TO
PLANTS
Phytophthora infestans = Hemileia vastatrix or coffee rust Cratocyctis ulmi = Dutch Elm
Europe and Ireland, (1840) Ceylon (1860s) Disease (1900s)
Wednesday, August 15, 2012
7. MICROBES: THREAT TO
HUMANS
BLACK DEATH & SPANISH FLU
Wednesday, August 15, 2012
10. “Extinction is a
Principle of
Evolution”
Wednesday, August 15, 2012
11. EXTINCTION
• Over 99% of the species that have
ever lived have become extinct
• Guesstimate: we lose about 1
species per day
• CURRENTLY: they say that we are
living in a period of mass extinction
(6th) = brought about by human
activity as driving force
Wednesday, August 15, 2012
12. “Microbes are
Everywhere”
Wednesday, August 15, 2012
15. ca. 4 to 5 × 1030 prokaryotic cells on Earth, with
the open ocean, soil, and oceanic and terrestrial
subsurface showing the highest abundances
Wednesday, August 15, 2012
16. A typical coastal water sample
contains 10 7 viruses, 106 bacteria and
10 3 protists /ml
Wednesday, August 15, 2012
17. Microbes come in diverse forms; however, it
is not known how many different species of
microbes inhabit the planet....WHY?
Wednesday, August 15, 2012
18. Microbes come in diverse forms; however, it
is not known how many different species of
microbes inhabit the planet....WHY?
• problems involved in defining a microbial
species
Wednesday, August 15, 2012
19. Microbes come in diverse forms; however, it
is not known how many different species of
microbes inhabit the planet....WHY?
• problems involved in defining a microbial
species
• majority of prokaryotic cells cannot be
easily grown in culture, which is a
prerequisite for species identification of
microbes
Wednesday, August 15, 2012
20. Microbes come in diverse forms; however, it
is not known how many different species of
microbes inhabit the planet....WHY?
• problems involved in defining a microbial
species
• majority of prokaryotic cells cannot be
easily grown in culture, which is a
prerequisite for species identification of
microbes
• NOTE: Only about 5000 to 6000 prokaryotic
species have been formally described
Wednesday, August 15, 2012
21. With the birth of NON-CULTURE
METHODOLOGIES....
Wednesday, August 15, 2012
22. With the birth of NON-CULTURE
METHODOLOGIES....
• At least 1800 species and 1.2 million new genes were
found using a shotgun sequencing approach of
microorganisms from a single sample in the Sargasso Sea
(Venter et al. 2004)
Wednesday, August 15, 2012
23. With the birth of NON-CULTURE
METHODOLOGIES....
• At least 1800 species and 1.2 million new genes were
found using a shotgun sequencing approach of
microorganisms from a single sample in the Sargasso Sea
(Venter et al. 2004)
• About 643 new species were identified using a 99%
similarity as delineation between prokaryotic phylotypes
or species based on 16S rRNA gene sequences (Venter
et al. 2004)
Wednesday, August 15, 2012
24. With the birth of NON-CULTURE
METHODOLOGIES....
• At least 1800 species and 1.2 million new genes were
found using a shotgun sequencing approach of
microorganisms from a single sample in the Sargasso Sea
(Venter et al. 2004)
• About 643 new species were identified using a 99%
similarity as delineation between prokaryotic phylotypes
or species based on 16S rRNA gene sequences (Venter
et al. 2004)
• Up to 7000 viral types have been detected using a
metagenomics (community genomics) approach and it is
believed that viruses represent the largest unknown
sequence space (Breitbart et al. 2002)
Wednesday, August 15, 2012
26. PROKARYOTIC MICROBES AS
SHAKERS & MOVERS OF THE
BIOSPHERE
• They invented photosynthesis long before eukaryotes
evolved
Wednesday, August 15, 2012
27. PROKARYOTIC MICROBES AS
SHAKERS & MOVERS OF THE
BIOSPHERE
• They invented photosynthesis long before eukaryotes
evolved
• Their oxygen production changed the atmosphere to the
oxygenic status we are currently experiencing
Wednesday, August 15, 2012
28. PROKARYOTIC MICROBES AS
SHAKERS & MOVERS OF THE
BIOSPHERE
• They invented photosynthesis long before eukaryotes
evolved
• Their oxygen production changed the atmosphere to the
oxygenic status we are currently experiencing
• Microorganisms degrade and remineralize organic material,
others produce methane, reduce sulfate to sulfide, integrate
molecular nitrogen or change the forms of inorganic
nitrogen
Wednesday, August 15, 2012
29. PROKARYOTIC MICROBES AS
SHAKERS & MOVERS OF THE
BIOSPHERE
• They invented photosynthesis long before eukaryotes
evolved
• Their oxygen production changed the atmosphere to the
oxygenic status we are currently experiencing
• Microorganisms degrade and remineralize organic material,
others produce methane, reduce sulfate to sulfide, integrate
molecular nitrogen or change the forms of inorganic
nitrogen
• Microorganisms drive the global cycles of carbon, nitrogen,
phosphorus and sulfur
Wednesday, August 15, 2012
30. “WITHOUT
MICROORGANISMS
ALL OTHER LIFE
FORMS WILL NOT
SURVIVE”
Wednesday, August 15, 2012
31. SO HOW DO
THEY ADAPT...
• Symbiosis
• between multicellular
organisms with microorganisms
showed great evolutionary
success (e.g. Lichens = 1500
species)
Wednesday, August 15, 2012
32. SO HOW DO
THEY ADAPT...
• Symbiosis
• between plant roots and
fungi (mycorrhiza) = reason
for spread of plants in the
continents
Wednesday, August 15, 2012
33. SO HOW DO
THEY ADAPT...
• Symbiosis
• between coral host and photosynthetic
dinoflagellate
• coral host obtains sugars from the algae and
the interference of algae with carbon
cycling enhances calcification
• reason why coral reefs one of most diverse
ecosystem
Wednesday, August 15, 2012
34. SO HOW DO
THEY ADAPT...
• Exchange of Genes (Horizontal Gene Transfer or
Microbial Sex)
Wednesday, August 15, 2012
35. SO HOW DO
THEY ADAPT...
• Exchange of Genes (Horizontal Gene Transfer or
Microbial Sex)
Wednesday, August 15, 2012
36. CONSEQUENCES OF
GENE TRANSFERS
• Cohan (2001)
• gene transfer among species increases
diversity
• gene exchange can help to sustain co-
existence of genetically different ecotypes
• gene exchange would help protect ecotypes
from extinction if the adaptive mutation can
be transferred
Wednesday, August 15, 2012
37. BIOGEOGRAPHY
OF MICROBES
Wednesday, August 15, 2012
38. ON DISTRIBUTION
• Finlay & Fenchel 1999
• “there are no distributional barriers for small free-living
organisms such as microbes”
• Finlay et al. 1996
• “global species diversity is inversely related to body
size”
• suggests that the shear number of protists makes
global dispersal very likely by mechanisms such as
hurricanes, ocean circulations, groundwater
connections, damp fur, etc
Wednesday, August 15, 2012
39. ON EXTINCTION
• Cohan, 2001
• “the large number of microbial cells per
species makes extinction unlikely,
extinction is not a threat”
• works only for “free-living microbes”
Wednesday, August 15, 2012
40. ON ENDEMICITY
• More evidence of endemicity and
biogeography is available for
microorganisms associated with plants or
animals
• Hosts can be considered as islands, which
permit the development of endemism in
prokaryotes
Wednesday, August 15, 2012
41. EVIDENCE OF
EXTINCTION
Wednesday, August 15, 2012
42. EVIDENCES
• Local extinctions (or strong reductions in the
abundance of microbial species) probably occur
quite frequently, e.g. due to clearing of forests,
agricultural activity or erupting volcanoes
• a multicellular organism is best regarded as an
association of species — a
mini-ecosystem — and
many of
these species exist only in this
association (e.g. coral reefs destruction, microbes
in Dodo or mammoth etc)
Wednesday, August 15, 2012
44. ARE THERE FOSSILS TO
GUIDE US?
• Listgarten & Loomer 2003
• Detection of microbial fossils is difficult compared to
detection of plant and animal fossils
• one of the reasons for our lack of knowledge on
extinction rates of microbes.
• Stromatolites (microbial reefs) were globally distributed in
the Proterozoic but the abundance decreased markedly and
at present there are only a few sites left
• suggests at least local extinctions in the geological past
Wednesday, August 15, 2012
45. ENDANGERED
• Most free-living microbes are likely not
endangered, although their local distribution
might vary considerably and local extinctions
• However, associated species may be ‘threatened’
in the same way as the multicellular hosts
organisms
Wednesday, August 15, 2012
46. THE INFECTIOUS
PARTICLE...
• Emiliani 1982, 1993
• Microbes may also become extinct when
one partner in a predator – prey
or
parasite – host
system loses the
adaptation race
• Example: As long as the virus cannot find
an alternative host, this means self-
extinction
Wednesday, August 15, 2012
47. SO...SHOULD WE
CARE ABOUT THE
POTENTIAL LOSES
OF MICROBIAL
SPECIES???
Wednesday, August 15, 2012
48. RECALL...the prokaryotic
DNA world constitutes a
‘global superorganism’ that
shares the gene pool by
horizontal gene transfer, the
microbial ‘kamasutra’
(Doolittle 1999)
Wednesday, August 15, 2012
53. OUR CONTRIBUTIONS TO
POSSIBLE EXTINCTION
• antimicrobials
• habitat fragmentation
• pollution and contamination of aquatic
systems
• The BIGGER THREAT: Climate Change
Wednesday, August 15, 2012
54. EXTINCTION
OF MICROBES...
WE SHOULD CARE!!!
Wednesday, August 15, 2012
55. THANK YOU
VERY MUCH!!!
Wednesday, August 15, 2012