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Metabolic Diversity and Microbial Ecology

A microbial cell must be able to adapt to new environments, turn genes on and off, and obtain energy from its surroundings to convert the energy into necessary molecules etc.

Catabolism is the breaking down of complex molecules. Anabolism is the synthesising of complex molecules. Microbial cells must be able to establish electrochemical gradients across a membrane to retain nutrients, cell constituents and generate energy as well as carry out transport of molecules. Different microbes require different enzymes depending on their environmental niches. These enzymes may be used for regulation transcription, post-transcription, translation or post-translation.

For microbial growth, sufficient energy sources are needed as well as anabolic raw materials: mainly C, N, S and P. They also require some trace elements such as some elements like Se, metal ions eg manganese (II) ions and vitamins for use as enzyme co-factors. Iron (II) and (III) ions are extremely important, especially for pathogenic bacteria. Fe is limiting in blood and tissues due to being bound so bacteria use siderophores to capture iron.

Chemolithotroph - obtains energy from inorganic compounds eg elemental S.

Phototrophs obtain energy from light eg plant or algal photosynthesis.

Chemoorganotrophs are most common and obtain their energy from organic compounds (reduced carbon compounds).

Autotrophs are organisms that can produce organic molecules from inorganic nutrients. They assimilate C1 compounds, typically CO2.

Heterotrophs use pre-formed organic molecules acquired from outside to generate energy and precursors for cell material. They cannot produce organic molecules from inorganic nutrients.

Most of the biosphere has low available nutrients, or at least one limiting nutrients so oligotrophy occurs, the ability to grow at low nutrient concentrations. Soil has between 5 and 20 mg/l dissolved organic C whereas broth media in the lab contains 800 mg/l dissolved organic C allowing rapid growth.

Microbes often exhibit syntrophy (‘cross-feeding’), where 2+ microbial species work together to degrade a single substance. These interdependent metabolic fluxes are an example of mutualism. They may or may not involve direct cell-cell contact and can be obligate or facultative.

Lichens consist of cyanobacteria and ascomycete fungus. The cyanobacteria provide organic compounds via photosynthesis, and can fix nitrogen. The ascomycete fungus provides protection, water retention, and extracts substrate minerals and nutrients. This interaction may involve a 3rd partner, basidiomycete fungus.

Microbes are capable of using many different carbon sources, from carbon dioxide to carbon compounds which are toxic to humans. To use a specific C source, genes for transport and catabolism are required. The ability/inability to utilise a certain C source could act as a selective pressure.

Xyloglucans are polysaccharide fibres found in lettuce and tomatoes. Bacteroidetes which make up a small number of our gut microbes are able to digest these due to a PUL locus acquired by horizontal gene transfer. Enzymes break the fibres down into short oligosaccharides then monosaccharides which can be transported into the cell. Organisms sense the nutrients present and express genes for catabolism of the most favourable.

The majority of complex carbohydrates are broken down into glucose. Glucose can be broken down anaerobically by fermentation or aerobically by respiration.

Central metabolism = glycolysis and the TCA cycle - ‘housekeeping’ pathways present in most organisms. Most glycolysis steps are reversible, and gluconeogenesis can generate more glucose if needed.

Fermentation = electrons → organic products. Fermentation is used to make a variety of foods and drinks such as wine, beer, bread and cocoa. Industrial fermentation is used to produce vitamins, amino acids and fine chemicals. Fermentation may also be used diagnostically in clinical microbiology eg fermentation of lactose by certain Enterobacteriaceae.

Respiration: electrons → inorganic electron acceptor eg oxygen/nitrate

The production of energy carriers eg ATP and NADH, as well as intermediates, is key for biosynthesis reactions.

The electron transport system is a set of redox reactions which generate an electrochemical gradient across the membrane. ATP synthases use the electrochemical gradient to synthesise ATP. The final electron acceptor in microbes may be oxygen, nitrate, nitrite, carbon dioxide, sulphate etc etc. Depends on the conditions and the microbe’s genome.

Secondary metabolism involves metabolites not directly involved in growth, development, or reproduction - not required for survival. Involved in ecological interactions, niche adaptation and signalling, as well as antibiotic resistance.

Some examples are photoautotrophs are green sulphur bacteria, purple sulphur bacteria and cyanobacteria.

Cyanobacteria use hydrogen from water to reduce CO2 to carbohydrates and produce oxygen. They make up a significant proportion of marine plankton, and are a major part of the marine microbial food web.

Some examples of chemoautotrophs are the organisms involved in nitrification eg Nitrosomonas, Nitrosospira, Nitrospina and Nitrococcus.

Nitrification in natural environments plays a central role in the global nitrogen cycle, nitrate pollution, loss of ammonia-based fertilisers, N removal in wastewater treatment, competes with primary producers for ammonia. Also involved in building corrosion, production of greenhouse gases and biodegradation of organic pollutants.

An example of a photoheterotroph is Halobacteria. Halobacteria have a protein called Bacteriorhodopsin. They use light energy to transfer protons across the membrane out of the cell to create a proton gradient for ATP generation. The protein gives Halobacteria their distinctive pink colour. These bacteria can’t fix CO2 so use organic carbon.

Example chemoheterotrophs are E.coli, Pseudomonads and Bacillus species, alongside most other pathogenic bacteria. They use organic compounds for both carbon requirement and energy generation.

Archaea and bacteria have far greater metabolic diversity than eukaryotes. Eukaryotes solely aerobically respire using glucose whereas microbes may carry out methanogenesis, autotrophic ammonia oxidation, or sulphate reduction with acetate.

Methanogenesis: 4H2 + CO2 → CH4 + 2H2O

Autotrophic ammonia oxidation: NH3 + O2 → NO2^- + H2O, where oxygen is added from conversion of Co2 to inorganic C

Sulphate reduction with acetate: CH3COO + SO4²- → 2CO2 + HS + 2H2O

Baas Becking hypothesis = ‘everything is everywhere, but the environment selects’.

Van Niel hypotheses =

  • every molecule existing in nature can be used as a source of carbon or energy by a microbe somewhere

  • microbes are found in every environment on Earth

Each population of organisms in a community fills a specific niche.

Niche construction is the shaping of the biochemical dimensions of a habitat by organisms. Cooperation is necessary and competition occurs when there’s too much overlap between two species’ niches. Different microbes have different physical growth requirements, often mainly shaped by genomic factors.

Microbes are able to inhabit almost anywhere with liquid water. Temperatures microbes survive at range between -10 and 121 degrees Celsius. There is a range of 20 to 40 degrees in size which a particular species will be able to survive in.

pH of a microbial environment could be between 0 and 11. A microbial species can survive a range of 3 to 5 pH units.

Microbes have been found from NaCl concentrations of between 0 and 6M.

Some microbes may have very narrow ranges of conditions they can survive but others are able to adapt to many different environments.

Extremophiles live in extreme conditions whereas mesophiles live in non extreme conditions.

Psychrophiles live in cold conditions. Thermophiles live in hot conditions. Hyperthermophiles live in very hot conditions.

Acidophiles live in acidic conditions. Alkaliphiles live in alkaline conditions.

Halophiles and halotolerant microbes live in/can survive high NaCl concentrations.

Barophiles/piezophiles live in high pressure conditions eg may be found subsurface or on a deep submarine.

Xerophiles are able to survive environments with little water.

An environment can be either oxic or anoxic. Microbes can be classified based on oxygen requirements. Anaerobes may use alternative electron acceptors or fermentation whereas aerobes require oxygen. Microbial blooms can create oxygen minimum zones because microbial respiration depletes available oxygen.

Microaerophiles require a specific amount of oxygen.

Microbes are available to adapt to grow at different temperatures by altering their proteins or membranes, or they may synthesised compatible solutes or antifreeze proteins. Minimum, optimum and maximum temperatures at which a microbe can survive are different for each species.

Bacteria live in complex communities with inter and intra-species interactions eg cell-cell signalling, community behaviour and division of labour. Bacteria often work together due to their small size in order to have an effect on their environment eg quorum sensing.

Mutualism = both the host and microbes benefit from the association eg Aliivibrio fischeri (bioluminescence) or Actinobacteria (antibiotic production).

Pathogenesis is where microbes cause harm to the host eg Staphylococcus aureus and Yersinia pestis (black death).

Microbes are key constituents of the food web and their production of oxygen and other compounds contributes to global biogeochemical cycles. They both contribute to and help precent plant and animal disease. Their use has benefitted humans in many industries eg food production and industrial fermentation.

Metabolic Diversity and Microbial Ecology

A microbial cell must be able to adapt to new environments, turn genes on and off, and obtain energy from its surroundings to convert the energy into necessary molecules etc.

Catabolism is the breaking down of complex molecules. Anabolism is the synthesising of complex molecules. Microbial cells must be able to establish electrochemical gradients across a membrane to retain nutrients, cell constituents and generate energy as well as carry out transport of molecules. Different microbes require different enzymes depending on their environmental niches. These enzymes may be used for regulation transcription, post-transcription, translation or post-translation.

For microbial growth, sufficient energy sources are needed as well as anabolic raw materials: mainly C, N, S and P. They also require some trace elements such as some elements like Se, metal ions eg manganese (II) ions and vitamins for use as enzyme co-factors. Iron (II) and (III) ions are extremely important, especially for pathogenic bacteria. Fe is limiting in blood and tissues due to being bound so bacteria use siderophores to capture iron.

Chemolithotroph - obtains energy from inorganic compounds eg elemental S.

Phototrophs obtain energy from light eg plant or algal photosynthesis.

Chemoorganotrophs are most common and obtain their energy from organic compounds (reduced carbon compounds).

Autotrophs are organisms that can produce organic molecules from inorganic nutrients. They assimilate C1 compounds, typically CO2.

Heterotrophs use pre-formed organic molecules acquired from outside to generate energy and precursors for cell material. They cannot produce organic molecules from inorganic nutrients.

Most of the biosphere has low available nutrients, or at least one limiting nutrients so oligotrophy occurs, the ability to grow at low nutrient concentrations. Soil has between 5 and 20 mg/l dissolved organic C whereas broth media in the lab contains 800 mg/l dissolved organic C allowing rapid growth.

Microbes often exhibit syntrophy (‘cross-feeding’), where 2+ microbial species work together to degrade a single substance. These interdependent metabolic fluxes are an example of mutualism. They may or may not involve direct cell-cell contact and can be obligate or facultative.

Lichens consist of cyanobacteria and ascomycete fungus. The cyanobacteria provide organic compounds via photosynthesis, and can fix nitrogen. The ascomycete fungus provides protection, water retention, and extracts substrate minerals and nutrients. This interaction may involve a 3rd partner, basidiomycete fungus.

Microbes are capable of using many different carbon sources, from carbon dioxide to carbon compounds which are toxic to humans. To use a specific C source, genes for transport and catabolism are required. The ability/inability to utilise a certain C source could act as a selective pressure.

Xyloglucans are polysaccharide fibres found in lettuce and tomatoes. Bacteroidetes which make up a small number of our gut microbes are able to digest these due to a PUL locus acquired by horizontal gene transfer. Enzymes break the fibres down into short oligosaccharides then monosaccharides which can be transported into the cell. Organisms sense the nutrients present and express genes for catabolism of the most favourable.

The majority of complex carbohydrates are broken down into glucose. Glucose can be broken down anaerobically by fermentation or aerobically by respiration.

Central metabolism = glycolysis and the TCA cycle - ‘housekeeping’ pathways present in most organisms. Most glycolysis steps are reversible, and gluconeogenesis can generate more glucose if needed.

Fermentation = electrons → organic products. Fermentation is used to make a variety of foods and drinks such as wine, beer, bread and cocoa. Industrial fermentation is used to produce vitamins, amino acids and fine chemicals. Fermentation may also be used diagnostically in clinical microbiology eg fermentation of lactose by certain Enterobacteriaceae.

Respiration: electrons → inorganic electron acceptor eg oxygen/nitrate

The production of energy carriers eg ATP and NADH, as well as intermediates, is key for biosynthesis reactions.

The electron transport system is a set of redox reactions which generate an electrochemical gradient across the membrane. ATP synthases use the electrochemical gradient to synthesise ATP. The final electron acceptor in microbes may be oxygen, nitrate, nitrite, carbon dioxide, sulphate etc etc. Depends on the conditions and the microbe’s genome.

Secondary metabolism involves metabolites not directly involved in growth, development, or reproduction - not required for survival. Involved in ecological interactions, niche adaptation and signalling, as well as antibiotic resistance.

Some examples are photoautotrophs are green sulphur bacteria, purple sulphur bacteria and cyanobacteria.

Cyanobacteria use hydrogen from water to reduce CO2 to carbohydrates and produce oxygen. They make up a significant proportion of marine plankton, and are a major part of the marine microbial food web.

Some examples of chemoautotrophs are the organisms involved in nitrification eg Nitrosomonas, Nitrosospira, Nitrospina and Nitrococcus.

Nitrification in natural environments plays a central role in the global nitrogen cycle, nitrate pollution, loss of ammonia-based fertilisers, N removal in wastewater treatment, competes with primary producers for ammonia. Also involved in building corrosion, production of greenhouse gases and biodegradation of organic pollutants.

An example of a photoheterotroph is Halobacteria. Halobacteria have a protein called Bacteriorhodopsin. They use light energy to transfer protons across the membrane out of the cell to create a proton gradient for ATP generation. The protein gives Halobacteria their distinctive pink colour. These bacteria can’t fix CO2 so use organic carbon.

Example chemoheterotrophs are E.coli, Pseudomonads and Bacillus species, alongside most other pathogenic bacteria. They use organic compounds for both carbon requirement and energy generation.

Archaea and bacteria have far greater metabolic diversity than eukaryotes. Eukaryotes solely aerobically respire using glucose whereas microbes may carry out methanogenesis, autotrophic ammonia oxidation, or sulphate reduction with acetate.

Methanogenesis: 4H2 + CO2 → CH4 + 2H2O

Autotrophic ammonia oxidation: NH3 + O2 → NO2^- + H2O, where oxygen is added from conversion of Co2 to inorganic C

Sulphate reduction with acetate: CH3COO + SO4²- → 2CO2 + HS + 2H2O

Baas Becking hypothesis = ‘everything is everywhere, but the environment selects’.

Van Niel hypotheses =

  • every molecule existing in nature can be used as a source of carbon or energy by a microbe somewhere

  • microbes are found in every environment on Earth

Each population of organisms in a community fills a specific niche.

Niche construction is the shaping of the biochemical dimensions of a habitat by organisms. Cooperation is necessary and competition occurs when there’s too much overlap between two species’ niches. Different microbes have different physical growth requirements, often mainly shaped by genomic factors.

Microbes are able to inhabit almost anywhere with liquid water. Temperatures microbes survive at range between -10 and 121 degrees Celsius. There is a range of 20 to 40 degrees in size which a particular species will be able to survive in.

pH of a microbial environment could be between 0 and 11. A microbial species can survive a range of 3 to 5 pH units.

Microbes have been found from NaCl concentrations of between 0 and 6M.

Some microbes may have very narrow ranges of conditions they can survive but others are able to adapt to many different environments.

Extremophiles live in extreme conditions whereas mesophiles live in non extreme conditions.

Psychrophiles live in cold conditions. Thermophiles live in hot conditions. Hyperthermophiles live in very hot conditions.

Acidophiles live in acidic conditions. Alkaliphiles live in alkaline conditions.

Halophiles and halotolerant microbes live in/can survive high NaCl concentrations.

Barophiles/piezophiles live in high pressure conditions eg may be found subsurface or on a deep submarine.

Xerophiles are able to survive environments with little water.

An environment can be either oxic or anoxic. Microbes can be classified based on oxygen requirements. Anaerobes may use alternative electron acceptors or fermentation whereas aerobes require oxygen. Microbial blooms can create oxygen minimum zones because microbial respiration depletes available oxygen.

Microaerophiles require a specific amount of oxygen.

Microbes are available to adapt to grow at different temperatures by altering their proteins or membranes, or they may synthesised compatible solutes or antifreeze proteins. Minimum, optimum and maximum temperatures at which a microbe can survive are different for each species.

Bacteria live in complex communities with inter and intra-species interactions eg cell-cell signalling, community behaviour and division of labour. Bacteria often work together due to their small size in order to have an effect on their environment eg quorum sensing.

Mutualism = both the host and microbes benefit from the association eg Aliivibrio fischeri (bioluminescence) or Actinobacteria (antibiotic production).

Pathogenesis is where microbes cause harm to the host eg Staphylococcus aureus and Yersinia pestis (black death).

Microbes are key constituents of the food web and their production of oxygen and other compounds contributes to global biogeochemical cycles. They both contribute to and help precent plant and animal disease. Their use has benefitted humans in many industries eg food production and industrial fermentation.

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