Bacteria Archaea Eucarya

Thermotogales

FlavobacteriaCyanobacteria

Purplebacteria

Grampositives

Greennon-sulfurbacteria

Pyrodictium

ThermoproteusT.celerMethanococcusMethanobacterium

Methanosarcina

Halophiles

EntamoebaeSlimemoldsAnimals

Fungi

PlantsCiliates

Flagellates

Trichomona

MicrosporidDiplomonads

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

Pyrodictium

ThermoproteusT.celerMethanococcusMethanobacterium

Methanosarcina

Halophiles

EntamoebaeSlime 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

ugeuge 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 g

Whitman et al. PNAS 1998

Biomass of Microbes in the Biosphere

DD

OO

MMPOCPOC

Microbes as a keyeterotrophic 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+ � H2

NH4+ � N2 N2 � NH4

+

CH4 � CO2 CO2 � CH4

H2S � 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

Pyrodictium

ThermoproteusT.celerMethanococcusMethanobacterium

Methanosarcina

Halophiles

EntamoebaeSlime molds

Animals

Fungi

PlantsCiliates

Flagellates

Trichomonad

MicrosporidiDiplomonads

Woese et al. PNAS 1990

Microbial Ecology, a young discipline

�� MicroorganismsMicroorganisms playplay 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

WeWe cannot

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 ofHigh 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!!

A Microbiologist Toolkit