Anaerobic degradation-metabolism. Microbes and their habitats the Biofilm

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1 Microbes live where they find energy or food this defines the groups of microbes In the sediment depending on the chemical characteristics Microbes and their habitats the Biofilm Margarete Kalin Boojum Research LTD In the water swimming forms and sessile forms of microbes particles in water sessile conditions change MICROBES - take off - go dormant - encapsulate - form ultra-microforms - spores but essentially they do not cease to exist They are just not active - same as pathogens they kill their host but then Presented in IMWA, 2010 CONCLUSION: there are no sterile rock surfaces!! Nutritional classification of microorganisms All living organisms need sources of carbon, energy and electrons to carry out their metabolic activities. Bacteria have also been classified based on their method(s) used to obtain these three components - carbon, energy and electrons: AUTOTROPHS obtain their carbon from carbon dioxide HETEROTROPHS need pre-made organic compounds as carbon source PHOTOTROPHS are organisms that utilize light as a source of energy CHEMOTROPHS obtain energy by oxidation of inorganic or organic compounds. ORGANOTROPHS obtain their electrons from organic compounds LITHOTROPHS (literally rock eaters) obtain electrons from inorganic compounds Nutritional classification of microorganisms Major nutritional types of prokaryotes Nutritional Type Carbon Source Electron Source Examples Photoautotrophic lithotrophs Light CO2 Inorganic (H2O or H2S) Cyanobacteria (e.g. Oscillatoria), some purple and green bacteria Photoheterotrophic organotrophs Chemoautotrophic lithotrophs Chemoheterotrophic organotrophs Light Rocks or minerals Organic compounds CO2 Organic Organic compounds compounds Organic compounds Some purple (e.g. Rhodobacter) and green bacteria Inorganic compounds Bacteria (e.g. Nitrosomonas) and many archaea Organic compounds Most bacteria (e.g. Escherichia coli) some archaea Anaerobic degradation-metabolism Organic matter in coastal sediments Energy Sun Metabolism (Varnam and Evans, 2000) Without Microbes No compost recalcitrant materials slower 1

2 Electron acceptors and bacteria Electron Acceptors (O 2, NO 3-, SO 4 ) and Mg 2+, K +, Cl - WATER Electron Donors (NH 4, H 2 S, CH 4, Fe 2+ ) and HCO 3-, CO 2, Ca 2+, H 2 SiO 4, HPO 4 An open pit lake with a surface area of 24 ha a maximum depth of 57 m and volume of ca 5 x 10 6 m 3 was formed in the B-Zone Pit after flooding with lake water from Wollaston Lake in early SEDIMENT / SOIL (Varnam and Evan, 2000) 2001 Post Flooding Sedimentation traps from 32, 22, 12 and 2 m Dictyosphaerium sp from B-Zone Pit Lake Cells c 4 µm in diameter Table 1: Chemistry and concentration changes Parameter M ean Concentration (mg/l) Decrease (-) / Increase (+) HCO % C onductivity (µs/cm) % Na % Al % A s % Cl % Fe % Ni % Ra 226 -total ( B q/l) % U (total) % 2

3 The structure of a soil particle Rocks are the parent material of soils Ideal soil 25 % air, 25 % water 45% minerals and silica and 5 % organic matter Fungi and bacteria hold the particle together Soil formation is part of the geologic cycle and soil characteristics are influenced by parent material, climate, topography, weathering, and the amount of time a particular soil has had to develop. Biofilm formation The basic structure of a biofilm Attachment to and detachment of cells and other particles from the biofilm SURFACE Biofilms and Corrosion Micro-Environments or Microbial habitats From: Borenstein, S.B., Microbiologically Influenced Corrosion Handbook, Industrial Press Inc., New York (1994). 3

4 Mineral Surfaces Biofilm additons of NPR High pyrite NPR throughout drum 990 days of weathering BIOFILMS MICROBIAL COLONIES ENCASED IN AN ADHESIVE, USUALLY POLYSACCHARIDE MATERIAL, AND ATTACHED TO A SURFACE. Geomicrobiology pre-biofilms 1838 EHRENBERG Gallionella ferruginea with ochreous deposits of bog iron WINOGRADSKY Beggiatoa oxidation H 2 S to elemental sulfur; Leptothrix ochracea oxidation of FeCO 3 to ferric oxid HARDER microbial iron oxidation and precipitation in iron sedimentary deposits. STUTZER (1911); VERNADSKY ( ) 3 Geomicrobiology ob o ogy Microbial Ecology Microbial Biogeochemistry Where does bio-mineralization take place? Answer: in sediments The major problem is the natural weathering processes which releases minerals to the biosphere both aquatic and terrestrial Weathering /hydro-chemical cycles Chemical Weathering is the major process controlling the global hydro-chemical cycle of elements. Mining increases the surface area available for weathering therefore introduces imbalances in the biosphere Water is the reactant and the transporting agent of dissolved and particulate components from land to sea. 4

5 Geochemical Cycles CLASSICAL GEOCHEMICAL MATERIAL BALANCE (GOLDSCHMIDT, 1933) -H + balance interaction between of igneous rocks with volatile substances. IGNEOUS ROCKS SILICATES CARBONATES OXIDES VOLATILE SUBSTANCES CO 2 H 2 0 SO 2 HCl SEAWATER ATMOSPHERE SEDIMENTS ph 8 pε 12 po 2 = 0.2 pco 2 = CARBONATES SILICATES Weathering Climate is the main driver of the weathering process the production of metals from the rocks - either as: ECONOMIC RESOURCE? OR CONTAMINATION Year 2000 MICROBIAL WEATHERING Pyrite A. ferrooxidans ARD/AMD 2 FeS H 2 O 2 Fe SO H + 4 Fe 2+ + O H + 4 Fe H 2 O 4 Fe H 2 O 4 Fe(OH) H + FeS Fe H 2 O 15 Fe SO H Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing Biologically-induced bio-mineralization Ferromanganese nodules Minerals are formed as byproduct of the cell s metabolic activity or through its interactions with the surrounding aqueous environment. Microbial nucleation and growth Silicates Carbonates Phosphates Sulfates Sulfide minerals Manganese Oxides a) Hydrothermal manganese deposits b) Ferromanganese deposits c) Desert varnish Iron Hydroxides a) Passive iron mineralization b) Chemo-heterotrophic iron mineralization c) Photoautotrophic iron mineralization e) Hydrothermal ferric hydroxide deposits d) Formation of iron oxides Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing 5

6 Biologically -controlled bio-mineralization Fossilization - Pyritization model Completely regulated by the organism, allowing the organism to precipitate minerals that serve some physiological purpose. Magnetite Greigite Calcite Amorphous Silica Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing Biologically-induced bio-mineralization Amorphous Silica Bio-mineralization in Diatoms (Bio-silica) \ Bio-mineralization of Pyrite (Ammonite Fossil) Alden,Erie Co., NY m Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing BIOLOGICALLY-CONTROLLED BIO-MINERALIZATION Scanning electron image of a Gold flake panned from soil Overlaying the Tomakin Park Gold mine Scanning electron image of a gold-encrusted Biofilm on a gold flake panned from soil Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing 6

7 DEFINING LIMITS Eh/pH diagram Baas Becking Total measurements: 6200 Organisms: 2100 Environments: 4100 ph / Eh Range THIOBACTERIA / +855 to -190 IRON BACTERIA / +850 to +60 DENITRIFIERS /+665 to -220 BLUE-GREEN ALGAE /+7 to-293 SULPHATE REDUCERS /+115 to -450 Baas Becking, Kaplan and Moore (1960). Limits of the natural environment in terms of ph and Oxidation-reduction potentials. The journal of Geology, Vol.68, Nº3, pp E H /[mv] H 2 O/H cyan: thiobacteria O 2 /H 2 O red: iron bacteria green: denitrifying and blue-green algae blue: sulphate-reducing bacteria ph Environmental Limits of Eh and ph for aquatic Bacteria A, iron bacteria ; B, thiobacteria; C, denitrifying bacteria; D, facultative and anaerobic heterotrophic bacteria and methanogens; E, sulfatereducing bacteria Iron Bacteria Gallionella ferruginea PROMOTES IRON CORROSION BUT ALSO REMOVES FERROUS IRON FROM SHALLOW AQUIFERS aerobic Micro-aerophilic. Chemo-litho-autotrophic. HABITAT: oligotrophic ferrous iron-bearing waters ( optimally Eh +200 to +300 mv.) Photograph by Eleanor Robbins, U.S. Geological Survey ( IMPORTANT: forms large masses of ferri-hydrite in water bodies and water supply systems. This is probably one of the major culprits for the dirty water samples. REFERENCES Bergey s Manual of Determinative Bacteriology Ninth Edition. Holt, J.G., N.R. Krieg, P.H.A. Sneath, J.T. Staley, and S.T. Williams. (eds.). Williams and Wilkins publishers. Environmental Microbiology,2000, ASM, Varnam A.H. and Evans M.G Acidithiobacillus ferrooxidans - metabolizes iron and sulfur - sulfuric acid generation (AMD) - bioleaching Fe 2+ oxidation to Fe 3+ Chemo-lithoautotrophicp HABITAT: pyrite deposits (ph: ) AMD - generation REFERENCES Environmental Microbiology,2000, ASM, Varnam A.H. and Evans M.G Bergey s Manual of Determinative Bacteriology Ninth Edition. Holt, J.G., N.R. Krieg, P.H.A. Sneath, J.T. Staley, and S.T. Williams. (eds.). Williams and Wilkins publishers. Sulphate reducingbacteria - assimilate oxygen from sulfate compounds and reduce them to sulfides anaerobic /photoautotrophic Rotten egg odor (H 2 S) BACTERIAL CONSORTIA IN ACID MINE GROUNDWATER SEEPAGE Purple and green sulphur bacteria Corrosion HABITAT:oligotrophic/aquatic environments with high organic matter content. REFERENCES Environmental Microbiology,2000, ASM, Varnam A.H. and Evans M.G Source: Konhauser, K. (2007). Introduction to geomicrobiology. Blackwell Publishing 7

8 Commom Bacteria Water Samples (N=5) ABUNDANT BACTERIA Zoogloea Cytophaga Flexibacter Flavobacterium free-living in strictly aerobe or CHEMO- aerobic but organically polluted facultative anaerobe. ORGANOTROPHIC nonmotile. fresh water /waste Some use nitrite strictly aerobic or CHEMO- water at all stages (NO;) as terminal facultatively ORGANOTROPHIC of treatment. - acceptor.- anaerobic. actively motile. CHEMO-ORGANOTROPHS soil and water, Aerobic/anaerobic (nitrate respiration). Denitrification Common in soils, decomposing organic matter, freshwater and marine habitats. Soil and freshwater. Also in raw meats, milk and otherfood. Flavobacterium Cytophaga Electron acceptors and bacteria Electron Acceptors (O 2, NO 3-, SO 4 ) and Mg 2+, K +, Cl - WATER Electron Donors (NH 4, H 2 S, CH 4, Fe 2+ ) and HCO 3-, CO 2, Ca 2+, H 2 SiO 4, HPO 4 SEDIMENT / SOIL (Varnam and Evan, 2000) Year 1985 Carbon addition One year after The microbial community Alkalinity increase Sulphate Reduction SO CH 2 O + H + = 2CO 2 + HS - + H 2 O Iron Reduction 4 Fe(OH) 3 + CH 2 O + 8 H + = CO Fe H 2 O Number of Bacteria 1.E+09 1.E+06 1.E+03 1.E+00 Nitrate Reduction (Denitrification) 4 NO CH 2 O + 4 H + = 5 CO N H 2 O CaCO 3 Dissolution CaCO 3 + CO 2 + H 2 O = Ca HCO 3 - Manganese Reduction 2 MnO 2 + CH 2 O + 4 H + = CO Mn H 2 O BACTERIAL GROWTH RATES OPTIMAL GROWTH CONDITIONS Bacillus subtillus Thiobacillus ferrooxidans Time (Hours) 8

9 CARBON ADDITION Surface ph 2.3 Bottom ph 5.2 Conductivity 11,000 μs/cm August 1993 March 1991 June 1991 July 1992 SEDIMENTS : BIOMINERALIZATION Conversion of Metals into Stable Forms above sediment in sediment above in sediment sediment Al(OH)3 - + pyrite - + Al 4(OH) Cu-metal - + boehmite - + cuprite - + calcite - / + + chalcosite - + dolomite - + djurleite - + gibbsite - + anilite - + magnesite - + blaublei - + siderite - + covellite - + hodochrosite - + chalcopyrite sphalerite - + otavite - + greenockite - + galena - + Ecological engineering effects of NPR and carbon additions Floating cover removes oxygen below Cut brush, acid tolerant moss, phosphate to sediment Scale of thinking about wetlands is essential - MIT Technology Review