Bioweek talk 2012

EXTINCTION
OF MICROBES...
SHOULD WE CARE?

Marilen M. Parungao-Balolong, MSc, SMic
Associate Professor
Bioweek 2012 BIOSeminar

Wednesday, August 15, 2012

WE ALWAYS CARED ABOUT
PLANT EXTINCTION


ANIMAL EXTINCTION


HUMAN EXTINCTION


BUT...MICROBES?
ALWAYS TAGGED AS
THE REASON FOR
EXTINCTION...


MICROBES: THREAT TO
PLANTS

Phytophthora infestans = Hemileia vastatrix or coffee rust Cratocyctis ulmi = Dutch Elm
Europe and Ireland, (1840) Ceylon (1860s) Disease (1900s)

MICROBES: THREAT TO
HUMANS

BLACK DEATH & SPANISH FLU

MICROBES: THREAT TO
ANIMALS


CAN MICROBES FACE
EXTINCTION?


“Extinction is a
Principle of
Evolution”


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

“Microbes are
Everywhere”


ca. 4 to 5 × 1030 prokaryotic cells on Earth, with
the open ocean, soil, and oceanic and terrestrial
subsurface showing the highest abundances


A typical coastal water sample
contains 10 7 viruses, 106 bacteria and

10 3 protists /ml


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



species
• majority of prokaryotic cells cannot be
easily grown in culture, which is a
prerequisite for species identiﬁcation of
microbes



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

With the birth of NON-CULTURE
METHODOLOGIES....


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)


METHODOLOGIES....


• 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)


METHODOLOGIES....


• 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)

PROKARYOTIC MICROBES AS
SHAKERS & MOVERS OF THE
BIOSPHERE


BIOSPHERE
• They invented photosynthesis long before eukaryotes
evolved


BIOSPHERE
evolved

• Their oxygen production changed the atmosphere to the
oxygenic status we are currently experiencing


BIOSPHERE
evolved


• Microorganisms degrade and remineralize organic material,
others produce methane, reduce sulfate to sulﬁde, integrate
molecular nitrogen or change the forms of inorganic
nitrogen


BIOSPHERE
evolved


• 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

“WITHOUT
MICROORGANISMS
ALL OTHER LIFE
FORMS WILL NOT
SURVIVE”


SO HOW DO
THEY ADAPT...

• Symbiosis
• between multicellular
organisms with microorganisms
showed great evolutionary
success (e.g. Lichens = 1500
species)


SO HOW DO
THEY ADAPT...

• Symbiosis
• between plant roots and
fungi (mycorrhiza) = reason
for spread of plants in the
continents


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

SO HOW DO
THEY ADAPT...
• Exchange of Genes (Horizontal Gene Transfer or
Microbial Sex)


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

BIOGEOGRAPHY
OF MICROBES


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


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”


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


EVIDENCE OF
EXTINCTION


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)


MICROBIAL
FOSSILS?


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

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


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

SO...SHOULD WE
CARE ABOUT THE
POTENTIAL LOSES
OF MICROBIAL
SPECIES???

RECALL...the prokaryotic
DNA world constitutes a
‘global superorganism’ that
shares the gene pool by
horizontal gene transfer, the
microbial ‘kamasutra’

(Doolittle 1999)


WITHOUT THEM...CHANGES
IN BIOGEOCHEMICAL
CYCLING


WITHOUT THEM...CORAL
BLEACHING


YOUR
CONTRIBUTION
TO THEIR
EXTINCTION


OUR CONTRIBUTIONS TO
POSSIBLE EXTINCTION

• antimicrobials
• habitat fragmentation
• pollution and contamination of aquatic
systems

• The BIGGER THREAT: Climate Change

EXTINCTION
OF MICROBES...

WE SHOULD CARE!!!

THANK YOU
VERY MUCH!!!

Bioweek talk 2012

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