3728bbs introduction to environmental microbiology...
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3728BBS 3728BBS IntroductionIntroduction toto EnvironmentalEnvironmentalMicrobiologyMicrobiology (& (& MicrobialMicrobial EcologyEcology))
Bacteria Archaea Eucarya
Thermotogales
FlavobacteriaCyanobacteria
Purple bacteria
Gram positives
Green non-sulfur bacteria
PyrodictiumThermoproteusT.celer
MethanococcusMethanobacterium
MethanosarcinaHalophiles
Entamoebae Slime molds
Animals
Fungi
PlantsCiliates
Flagellates
Trichomonad
MicrosporidiDiplomonads
Who, where, what & how
Microbial Ecology & Environmental Microbiology-the study of microbes & their processes in vivo:
What is an ecosystem? Are all ecosystems colonised by microbes?What do we know about numbers & diversity of microbes in nature?Do they live in isolation and or do they interact?How many microbial species are there & can we culture them all in the laboratory
Why Study ecosystems?
To date, much of what we know about the origin, maintenance and distributionof biological diversity stems from research on terrestrial macroorganisms suchas birds, plants and insects.
Bacteria Archaea Eucarya
Thermotogales
FlavobacteriaCyanobacteria
Purple bacteria
Gram positives
Green non-sulfur bacteria
PyrodictiumThermoproteusT.celer
MethanococcusMethanobacterium
MethanosarcinaHalophiles
Entamoebae Slime molds
Animals
Fungi
PlantsCiliates
Flagellates
Trichomonad
MicrosporidiDiplomonads
??
AbundanceAbundance ofof aquaticaquatic microbesmicrobes
• Extremely abundant • High and constant abundances in very different environments• Bacterial biomass equivalent to phytoplankton and zooplankton • Key global heterotrophic process at ecosystem level: DOM--->POM• Key role as primary producers
Groundwater 1 x 104 - 4 x 105 cells/mlCentral Atlantic Ocean 2 x 105 - 8 x 105 cells/mlMediterranean Sea 2 x 105 - 7 x 105 cells/mlAntartic coastal areas 2 x 105 - 7 x 105 cells/mlCoastal lagoons 7 x 105 - 2 x 106 cells/mlContinental lakes 1 x 106 - 3 x 106 cells/mlEutrophic lakes 6 x 106 - 3 x 107 cells/mlHyperhaline ponds up to 108 cells/ml
Microbes
UnderstandingUnderstanding thethe distributiondistribution andand basicbasic ecologyecology ofof oneone ofof thethemostmost abundantabundant andand diversediverse groupsgroups ofof organismsorganisms onon EarthEarth isisstillstill a a unsolvedunsolved crucial crucial issueissue in in environmentalenvironmental researchresearch
Microbes are small
but…
…… sometimes they have conspicuous colors in pure culturessometimes they have conspicuous colors in pure cultures……
and we can see them and we can see them easilyeasily ……
PHOTOSYNTHETIC SULFUR BACTERIA
……making visible the invisiblemaking visible the invisible!!LAKE CISO, SPAIN
PURPLE SULFUR BACTERIA
A B
C D
E F
G H
HugeHuge biogeochemicalbiogeochemical activityactivity……
IRON BACTERIA
……making visible the invisible!making visible the invisible!RIO TINTO, SPAIN
huge cells accumulationshuge cells accumulations……
Up Up toto 101088 cellscells/ml!/ml!
ST POLA SOLAR SALTERNS, SPAIN
Hyperhaline Haloquadratum and Salinibacter
MakingMaking visible visible thethe invisibleinvisible……
ST POLA SOLAR SALTERNS, SPAIN
…… eveneven fromfrom 800 800 kmkm distancedistance!!
A “milk sea” of luminescent Vibrio detected by satelliteCOASTAL WATERS, SOMALIA
Biomass of Microbes in the Biosfere_______________________________________________________________Habitat Population size
(cells)_____________________________________________________Oceans 1.2 x 1029
Soil 2.6 x 1029
*Subsurface 4.9 x 1030
Global 5 x 1030
_____________________________________________________Whitman et al. PNAS 1998
*terrestrial habitats below 8 m (grounwater included) and marine sediments below 10 cm
Sometimes we cannot see them, but we can count them
_______________________________________________________________
Habitat Population size Biomass Plant Biomass
(cells) (Pg of C) (Pg of C)
_______________________________________________________________
Oceans 1.2 x 1029 4 0
Soil 2.6 x 1029 26 560
Subsurface 4.9 x 1030 325-520 0
Global 5 x 1030 350-545 562
_______________________________________________________________
1 Pg = 1015 gWhitman et al. PNAS 1998
Biomass of Microbes in the Biosphere
DD
OO
MMPOCPOC
Microbes as a keyheterotrophic component…
DOM POM
Microbes as the most versatile primary producers…
Huge metabolic diversity
P870* P870+ (hŋ)
P680* P680+ (hŋ)
CH2O CO2 - CO2 CH2OH2 H+ H+ H2NH4
+ N2 N2 NH4+
CH4 CO2 CO2 CH4H2S So So H2SH2S SO4
2– SO42– H2S
Fe2+ Fe(OH)3 0 Fe(OH)3 Fe2+
NH4+ NO3
– NO3– NH4
+
P870+ P870*
Mn2+ MnO4 MnO4 Mn2+
CO CO2 CO2 CO
N2 NO3– + NO3
– N2
H2O O2 (hŋ) O2 H2O
P680+ P680*
(Reductants) pE (Oxidants)
RRED --- ROX OOX ---- ORED
Huge genetic diversity
Bacteria Archaea Eucarya
Thermotogales
FlavobacteriaCyanobacteria
Purple bacteria
Gram positives
Green non-sulfur bacteria
PyrodictiumThermoproteusT.celer
MethanococcusMethanobacterium
MethanosarcinaHalophiles
Entamoebae Slime molds
Animals
Fungi
PlantsCiliates
Flagellates
Trichomonad
MicrosporidiDiplomonads
Woese et al. PNAS 1990
Microbial Ecology, a young discipline
•• MicroorganismsMicroorganisms play play farfarmore more importantimportant ecologicalecologicalroles in natural roles in natural environmentsenvironmentsthanthan theirtheir smallsmall sizessizes wouldwouldsuggestsuggest ((BrockBrock et al. et al. 19881988))
We realized about that only a few years ago!
DespiteDespite theirtheir central central ecologicalecological importanceimportance andand numericalnumericaldominancedominance, , thethe truetrue extentextent ofof microbialmicrobial diversitydiversity stillstill remainsremainspoorlypoorly resolved resolved duedue toto significantsignificant theoreticaltheoretical andand practicalpracticalproblemsproblems thatthat havehave hinderedhindered thethe quantificationquantification ofof bacterial bacterial diversitydiversity in in thethe pastpast andand thethe disciplinarydisciplinary boundariesboundaries thatthat tendtend totoseparateseparate microbiologistsmicrobiologists fromfrom ecologistsecologists
““We have catalogued and named all the celestial bodies we can We have catalogued and named all the celestial bodies we can detect in the universe but still we do not know how many detect in the universe but still we do not know how many biological species are living in our planetbiological species are living in our planet””
RobertRobert May, 1992May, 1992
MicrobialMicrobial ““black boxblack box””
practicalpractical problemsproblems……
TheThe goldengolden dreamdream ofof a a microbialmicrobialecologistecologist wouldwould bebe……
How DAPI stained bacteria looks like through a microscope…
…celestial bodies?
I am a lion
We are zebras
We are trees
WeWecannot
cannottell
tell themthemapart
apart
CulturabilityCulturability
Environment Culturability (%) Oceans and seas 0.001-0.1Continental waters 0.25Mesotrophic lake 0.1 - 1Estuary 0.1 - 3Activated sludges 1 - 15Sediments 0.25Soil 0.3
““the great plate count anomaly"the great plate count anomaly"
andand mostmost ofof thethe times times theythey are are weedsweeds!!
TheThe numbernumber ofof microbialmicrobial speciesspecies: : highhigh oror lowlow??
HIGH NUMBER OF SPECIESHIGH NUMBER OF SPECIES•• The oldest organisms on EarthThe oldest organisms on Earth•• 3.500 millions years of evolution and diversification3.500 millions years of evolution and diversification•• High number of High number of micronichesmicroniches at their size levelat their size level
LOW NUMBER OF SPECIESLOW NUMBER OF SPECIES•• High dispersion rates (cosmopolites)High dispersion rates (cosmopolites)
•• Low extinction ratesLow extinction rates•• Low speciation ratesLow speciation rates••Lateral gene transferLateral gene transfer
Some of the aims of the microbial ecologists are…• to determine how many different microbial species are out there,
• to find out what they can do, • and to provide the know-how to identify environments of high and low microbial diversity
VeryVery simple simple questionsquestions forfor macroorganismsmacroorganisms
……butbut a a veryvery hardhard tasktask forfor microbialmicrobialecologistsecologists!!
The tools: a key issue
The Tools will be discussed in more details in Module 2