Microbial ecology (chpt 23 12th ed; chpt 19 11th ed) study of interrelationships between microorganisms and their environments ecosystem: a community of organisms and their natural environment population guild microbial communities + communities of macroorganisms ? energy flow and materials cycling ME1 (Fig 23.2, 12th ed; 19.1, 11th ed) Energy and carbon flow in microbial metabolism ME2 (e.g., NH4+, S, H2S, Fe2+) heterotroph autotroph (Fig 5.23a) (Fig 5.23b) (Fig 5.23c) objectives in microbial ecology: to explore & understand the biodiversity of microorganisms in nature, and interactions in communities (2) to measure of microbial activities in nature, and monitor effects of microbes on ecosystems ME3 activities commonly measured when studying microorganisms within an ecosystem: primary production of organic matter (phototrophic, chemolithotrophic activity) CO2 + H2O + energy ? new biomass decomposition of organic matter (chemoorganotrophic/heterotrophic activity) dead biomass ? CO2 + H2O + energy biogeochemical cycling of elements C, N, P, S, Fe Microorganisms in nature live in ?common? habitats suited to higher organisms, also in ?extreme? environments extremes in temperature, pH, pressure, salinity; anoxic habitats inanimate (soil, sediment, water, food) & animate habitats (on/in animals, plants, insects) necessities for growth include available resources (nutrients), suitable physiochemical conditions ME4 (Table 19.1, 11th ed) psychrophiles, thermophiles, hyperthermophiles: ?extremophiles? that live in habitats of extreme temperature, incl. cold (e.g., deep sea, Antarctica, the Arctic), or hot habitats (e.g., compost piles, deep sea hydrothermal vents) ME5 seawater evaporating ponds near San Francisco Bay, for harvesting ?solar? salt. The red colour is due to pigments of the extreme halophile Halobacterium, an archaeal genus that inhabits the ponds. (Fig 6.19 12th ed; 6.17 11th) (Fig 17.2, 12th ed; 13.2, 11th) niche: the functional role of an organism within an ecosystem; combined description of the physical habitat, functional role, and interactions of the microorganism occurring at a given location microenvironment: where a microorganism lives, metabolizes within its habitat physicochemical gradients spatial, temporal variability O2 contours (as %O2) within a soil particle, measured by microelectrode (air is 21% O2) each zone in the soil particle could be considered a different microenvironment ME6 (Fig 23.3 12th; 19.2 11th) Nutrient levels and growth rates: microbial life in nature often differs from microbial life in lab culture (i) entry of nutrients into an ecosystem is often intermittent ?feast-or-famine? existence adaptations: accumulate reserves in times of plenty (e.g., inclusions of poly-?-hydroxybutyrate (PHB), polyphosphate); high growth rates when growth is possible, quiescence when growth is not possible extended periods of exponential growth probably rare in nature E. coli in intestinal tract: tgen ~12 h; E. coli in lab culture: tgen ~20 min growth of some soil bacteria in nature is less than 1% of maximal growth rate possible under laboratory conditions (ii) distribution of resources in nature is often non-uniform e.g., soil underlying a dead animal versus soil nearby (iii) competition for resources is likely microbial monocultures are rare in nature ME7 Surfaces and biofilms: biofilm: a community of microorganisms embedded in a matrix of organic polymer (extracellular polymeric substances, EPS), adhering to a surface physicochemical gradients within mature biofilm result in a number of potential microenvironments within a small area advantages to biofilm mode: protection from toxicants, predators, immune system cells; ability to remain within a favourable niche; cooperative interactions possible; nutrient trapping disadvantages: highly competitive; localized biomass can be efficiently preyed upon, infected by viruses ME8 Time (Fig 23.6a) Fig 23.7: Biofilms of Pseudomonas aeruginosa ?early? ?mature? ME9 120 ?m bacterial microcolonies developing on a microscope slide immersed in a river (phase contrast microscopy) ME9a natural biofilm on a leaf surface cell colour indicates depth in biofilm: red (surface) ? blue (18 ?m deep) (confocal laser scanning microscopy) (Fig 23.4a; 19.3 11th) (Fig 23.5b; 19.4 11th) biofilm developed on a stainless steel pipe stained with DAPI (fluorescent; interacts with nucleic acids) note water channels through biofilm ME9b (Fig 23.6b) evidence of a dental biofilm: left front tooth exposed to sucrose solution for 5 min; right tooth served as a control both then stained with iodine solution brown colouration results from reaction of iodine with extracellular dextran (EPS) produced by the sucrose-supplied biofilm ME9c biofilm of iron-oxidizing prokaryotes on rocks; Rio Tinto Spain (Fig 23.5c) problems resulting from biofilm formation: pipe clogging accelerated corrosion of pipelines and structural steelwork high microbial numbers in potable water distribution systems increased drag on ship?s hull periodontal disease exploitation of biofilms: slow sand filtration (water purification) microbial leaching of low-grade ores vinegar production ME10 Streptococcus mutans: contributes to tooth decay (Fig 28.7 12th; 21.7 11th) microbial mats: specialized microbial communities often composed mainly of photosynthetic prokaryotes macroscopic, often layered a distinction between these and other biofilms is dependence on photosynthetic primary productivity as source of energy hot springs & other extreme environments, marine intertidal zones ME11 green: cyanobacterial layers (aerobic phototrophs) orange: layers of anoxygenic phototrophic bacteria core taken through a microbial mat from a hot spring ~3 cm thick (Fig 22.20a 12th; 18.19 11th) (Fig 15.5 12th; 12.5 11th) ME12 Interactions between microbial populations: (i) negative effect for (one or both) interacting populations: competition ? outcome depends on innate capabilities of nutrient uptake, metabolic rates ?competitive exclusion? is one possible outcome antagonism ? specific inhibitor or metabolic product may impede growth/metabolism of others antibiotic or bacteriocin release, lactic acid production (ii) positive effect for (one or both) interacting populations: cooperative interactions - interacting microbes must share same/nearby microenvironment syntrophy ? microorganisms together carry out transformation neither can conduct alone microbes can carry out complementary metabolic interactions nitrification: NH3 ? NO2- (ammonifiers); NO2- ? NO3- (nitrifiers) symbioses: relationships between two or more organisms that share a particular ecosystem e.g., mutualism - both species benefit
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