3728BBS Introduction to Environmental Microbiology (& Microbial Ecology)

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1 3728BBS Introduction to Environmental Microbiology (& Microbial Ecology) Cyanobacteria Flavobacteria Thermotogales Bacteria Archaea Eucarya Gram positives Purple bacteria Green non-sulfur bacteria Methanobacterium Methanococcus ThermoproteusT.celer Pyrodictium Entamoebae Slime Animals molds Fungi Methanosarcina Halophiles Plants Ciliates Flagellate Trichomona Microspori Diplomonads

2 Microbial Ecology & Environmental Microbiologythe 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 Who, where, what & how

3 Why Study ecosystems? To date, much of what we know about the origin, maintenance and distribution of biological diversity stems from research on terrestrial macroorganisms such as birds, plants and insects. Cyanobacteria Flavobacteria Thermotogales Bacteria Archaea Eucarya Green non-sulfur bacteria? Gram Methanosarcina positives Methanobacterium Halophiles Purple bacteria Methanococcus ThermoproteusT.celer Pyrodictium Entamoebae Slime Animals molds Fungi Plants Ciliates Flagellates Trichomonad Microsporidi Diplomonads

4 Abundance of aquatic microbes Groundwater Central Atlantic Ocean Mediterranean Sea Antartic coastal areas Coastal lagoons Continental lakes Eutrophic lakes Hyperhaline ponds 1 x x 10 5 cells/ml 2 x x 10 5 cells/ml 2 x x 10 5 cells/ml 2 x x 10 5 cells/ml 7 x x 10 6 cells/ml 1 x x 10 6 cells/ml 6 x x 10 7 cells/ml up to 10 8 cells/ml 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

5 Microbes Understanding the distribution and basic ecology of one of the most abundant and diverse groups of organisms on Earth is still a unsolved crucial issue in environmental research

6 Microbes are small but

7 sometimes they have conspicuous colors in pure cultures and we can see them easily PHOTOSYNTHETIC SULFUR BACTERI

8 PURPLE SULFUR BACTERIA making visible the invisible! LAKE CISO, SPAIN

9 ge biogeochemical activity A B C D E F G H IRON BACTERIA

10 making visible the invisible! RIO TINTO, SPAIN

11 huge cells accumulations Hyperhaline Haloquadratum and Salinibacter T POLA SOLAR SALTERNS, SPAIN Up to 10 8 cells/ml!

12 Making visible the invisible ST POLA SOLAR SALTERNS, SPAIN

13 even from 800 km distance! COASTAL WATERS, SOMALIA A milk sea of luminescent Vibrio detected by satellit

14 Sometimes we cannot see them, but we can count them BiomassofMicrobesin thebiosfere Habitat Population size (cells) Oceans 1.2 x Soil 2.6 x *Subsurface 4.9 x Global 5 x *terrestrial habitats below 8 m (grounwater included) and marine sediments below 10 cm Whitman et al. PNAS 1998

15 BiomassofMicrobesin thebiosphere Habitat Population size Biomass Plant Biomass (cells) (Pg of C) (Pg of C) Oceans 1.2 x Soil 2.6 x Subsurface 4.9 x Global 5 x Pg = g Whitman et al. PNAS 1998

16 D O Microbes as a key terotrophic component DOM POM POC M

17 Microbes as the most versatile primary producers

18 Huge metabolic diversity

19 (Reductants) pe (Oxidants) P870 * P870 + (hŋ) P680 * P680 + (hŋ) CH 2 O CO 2 - CO 2 CH 2 O H 2 H + H + H 2 NH + 4 N 2 + N 2 NH 4 CH 4 CO 2 CO 2 CH 4 H 2 S S o S o H 2 S 2 H 2 S SO 4 SO 2 4 H 2 S Fe 2+ Fe(OH) 3 0 Fe(OH) 3 Fe 2+ NH + 4 NO 3 NO + 3 NH 4 P870 + P870 * Mn 2+ MnO 4 MnO 4 Mn 2+ CO CO 2 CO 2 CO N 2 NO 3 + NO 3 N 2 H 2 O O 2 (hŋ) O 2 H 2 O P680 + P680 * R RED --- R OX O OX ---- O RED

20 Cyanobacteria Flavobacteria Thermotogales Huge genetic diversity Bacteria Archaea Eucarya Gram positives Purple bacteria Green non-sulfur bacteria Methanobacterium Methanococcus ThermoproteusT.celer Pyrodictium Entamoebae Slime Animals molds Fungi Methanosarcina Halophiles Plants Ciliates Flagellates Trichomonad Microsporidi Diplomonads Woese et al. PNAS 1990

21 e realized about that only a few years ago! Microorganisms play far more important ecological roles in natural environments than their small sizes would suggest (Brock et al. 1988) Microbial Ecology, a young discipline

22 Despite their central ecological importance and numerical dominance, the true extent of microbial diversity still remains poorly resolved due to significant theoretical and practical problems that have hindered the quantification of bacterial diversity in the past and the disciplinary boundaries that tend to separate microbiologists from ecologists

23 We have catalogued and named all the celestial bodies we can detect in the universe but still we do not know how many biological species are living in our planet Robert May, 1992 Microbial black box

24 practical problems ow DAPI stained bacteria oks like through a microscope elestial bodies? The golden dream of a microbial

25 We are trees I am a lion We are zebras We We cannot cannot tell tell them them apart apart

26 Culturability the great plate count anomaly" Environment Culturability (%) Oceans and seas Continental waters 0.25 Mesotrophic lake Estuary Activated sludges 1-15 Sediments 0.25 Soil 0.3 and most of the times they are weeds!

27 The number of microbial species: high or low? HIGH NUMBER OF SPECIES The oldest organisms on Earth millions years of evolution and diversification High number of microniches at their size level LOW NUMBER OF SPECIES High dispersion rates (cosmopolites) Low extinction rates Low speciation rates Lateral gene transfer

28 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

29 Very simple questions for macroorganisms but a very hard task for microbial ecologists!

30 The tools: a key issue The Tools will be discussed in more details in Module 2