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5: Microbial Metabolism - Biology

5: Microbial Metabolism - Biology


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5: Microbial Metabolism

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Assessment of Planetary Protection Requirements for Spacecraft Missions to Icy Solar System Bodies (2012)

The vast repertoire of metabolism and physiology allows different kinds of terrestrial microbes to colonize diverse environments. Because of niche competition, individual taxa have evolved to grow optimally under a limited range of conditions. For example, microbes that grow optimally at &ndash15°C do not survive at 122°C, the known upper temperature limit for terrestrial life. Decisions about planetary protection must consider the interplay between availability of water (Decision Point 1), bioavailability of trace elements and sources of energy (Decision Points 2 and 4), microbial metabolism and physiology (Decision Points 2, 4, and 6), the techniques used to reduce bioloads (Decision Point 7), and the environment of the target bodies (Decision Points 1, 2, 3, 4, and 6). Geophysical considerations (Decision Point 5) are less relevant. All require knowledge about the following:

1. The physical and chemical environment of the target body (Chapter 4)

2. The environmental source of organisms on the spacecraft and their ability to survive and grow at temperatures found on icy moons (e.g., at 0°C or below)

3. The relationship between growth at low temperatures and tolerance to heat-mediated bioload reduction and

4. The survival tactics of microbial life in response to high levels of radiation or extremely low vacuum, which causes desiccation.

In addition to Decision Points 1-7, the location of assembly and launch facilities will influence planetary protection concerns. The cold environments of icy bodies might provide habitats for terrestrial microbes that can grow only at very low temperatures. On Earth, environments capable of supporting microbial growth at 0°C or below typically include temperate and high-latitude marine environments, high-latitude ice, soils, cryopegs, the upper atmosphere, seasonally cold soils, and dairy products, meats, and seafoods that are maintained at low temperature. Because of the location of spacecraft assembly facilities in the United States, soils from temperate environments are the most likely source of spacecraft contamination with an organism capable of growing on an icy planetary body. These organisms would have to grow at 0°C or below on the target bodies and also survive temperatures and other conditions involved with the assembly and launch of the spacecraft. A study of the cultured microorganisms from the spacecraft assembly facility at NASA Kennedy Space Center did not detect psychrophilic or psychrotolerant microorganisms or high-salt-tolerant organisms. 1 The predominant groups of organisms isolated included thermophiles, acidophiles, and ultraviolet-C- and H2O2-resistant bacteria. Molecular studies based on

rRNA sequences and shotgun metagenomic analyses (enabled by anticipated improvements in DNA sequencing efficiencies) of low-biomass samples would provide a cultivation-independent assessment of microbial community composition within spacecraft assembly facilities and within and on a spacecraft.

Decision Point 1&mdashLiquid Water

The absolute and unambiguous requirement of liquid water for the propagation of terrestrial organisms on Earth or on icy bodies in the outer solar system constrains the possibility of forward contamination to a relatively small number of objects in the outer solar system. See Chapter 4 for a detailed discussion of this point.

Decision Point 2&mdashKey Elements

The origin and development of life are intimately linked to the periodic table of elements. The most important elements required by living systems for catalysis, organization of macromolecular structure, or energy transduction include, but are not limited to, carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, potassium, magnesium, calcium, and iron. Sometimes other elements such as boron participate in chemical signaling between bacteria, 2 or elements like selenium can incorporate into specific proteins as selanocysteine, now referred to as the twenty-first essential amino acid. 3

Because of its pervasive role in many biological processes, phosphorus plays an indispensible role in living systems. In some marine organisms, arsenic can incorporate into lipids in place of phosphorus, 4 but this generally toxic compound does not replace phosphorus in nucleic acids, in protein structures, or in catalytic functions. There is no consensus as to the minimum concentration of phosphorus required for growth by microorganisms. The cultivation of different bacterial taxa in phosphate at varying concentrations reveals a complex set of genes that mediate stress-response to phosphate limitation. In general, phosphorus limitation triggers adaption, including the up-regulation of specific genes involved in phosphate response stress that shift cells from utilization of inorganic phosphate to scavenging of organo-phosphate and polyphosphate from the environment, 5,6 substituting sulfur for phosphate in membrane lipids in marine photosynthetic bacteria, 7 changes in cell morphology to increase surface-to-volume ratio of the cell, 8 and shutting down cell metabolism to survive in a dormant stage. 9,10,11 In most cases, these studies were preformed with bacteria that grow in high concentrations of organic nutrients, and the concentrations of phosphorus at which the stress response is stimulated are considerably higher than those measured in oligiotrophic oceans (0.2 to 1 nM inorganic phosphate). Even in studies with the freshwater oligiotrophic bacterium Caulobacter crescentus, 30 &muM of phosphate induced an adaptive response. 12 In contrast, various strains of Rhizobium species, a nitrogen-fixing soil microbe, grew as rapidly at 0.05 &muM phosphate as at 2 mM. 13 The data on the effects of phosphate limitation on spore-forming microorganisms includes studies only with the mesophiles Bacillus subtilis and Clostridium perfringens. In B. subtilis, concentrations of phosphorus below 0.1 mM led to reduced growth rates and entry into stationary growth phase, 14,15 whereas in C. perfringens, sporulation did not occur when phosphorus concentrations were less than 3 mM. 16 There were no studies found that looked at the effects of phosphorus limitations on psychrophilic or psychrotolerant spore-forming bacteria.

The studies on phosphorus limitation using pure cultures of microorganisms have revealed the exquisite complexity of physiological responses and survival mechanisms. However, complex ecosystems exist in oligiotrophic environments where the concentration of phosphate is lower than the lowest concentration that either prevents growth or induces stress responses in most isolated microbes tested. Oligiotrophic oceans such as the Sargasso Sea in the northwestern Atlantic, the North Pacific subtropical gyre, and eastern part of the Mediterranean Sea have extremely low levels of dissolved phosphate. For example, the concentrations of phosphate in surface waters of the subtropical Sargasso Sea are from 0.2 to 1.0 nM. 17,18,19 The canonical &ldquoRedfield ratio&rdquo used in biogeochemical models of the ocean is 106C:16N:1P and does not apply to oligiotrophic oceans where the N:P ratio can be higher than 30. 20 Although these environments show limited phosphate stress, they have active ecosystems anchored by Prochlorococcus spp. as the primary producers. These photosynthetic bacteria are highly adapted to low levels of

nutrients, including phosphate, and can compensate by synthesizing sulfur lipids instead of phospholipids. 21 It was further observed that the synthesis of membrane lipids normally accounted for 18 to 28 percent of the phosphate utilized by phytoplankton. The dominant heterotrophic bacteria in these oligiotrophic oceans, Pelagobacter ubique, can like the Prochlorococcus species grow in situ in phosphate at low concentrations while utilizing carbon compounds in the low levels found in the dissolved organic compound fraction. 22 Both of these organisms are small (<1 &mum) and have the smallest genomes of &ldquofree-living&rdquo organisms and are genetically surprisingly well adapted to grow in the presence of phosphate and other inorganic nutrients at ultralow concentrations. It is apparent that microorganisms have adapted to phosphorus limitations and, in particular, have developed the ability to grow in phosphate at concentrations that are at the edge of researcher&rsquos ability to measure. Consequently, it might not be possible to measure phosphorus in the oceans or ice of icy moons if it is present only at the low levels measured in present day oligiotrophic oceans.

Decision Point 3&mdashPhysical Conditions

Radiation flux and temperature extremes that exceed the documented limits tolerated by life on Earth will constrain the potential growth of terrestrial microbial life forms in target body environments. These same parameters have important implications for Decision Points 6 and 7, which consider the survivability of irradiated microbes in oligotrophic environments and at temperature in ranges in which cold-loving organisms can survive.

Determining the minimal energy requirements for life is far more difficult than constraining the possibilities of contamination according to the presence or absence of water or essential elements. Discoveries each year of novel extremophiles with new types of metabolism continuously change understanding of life&rsquos minimal energy criterion and the chemical dimensions of Earth&rsquos &ldquohabitable zone.&rdquo Two considerations suggest taking an optimistic approach to the presence of energy: (1) work in the fields of electron transport and metabolism in the past 20 years has made it clear that some group of terrestrial organisms has made use of nearly any redox couple that can yield significant energy 23-28 and (2) observational, laboratory, and theoretical studies show that icy bodies contain a vast number of oxidized and reduced compounds, many of which might serve as potential electron donors or acceptors (Table 5.1).

Researchers currently lack conclusive information about the presence of energy and elemental sources necessary to support the growth of potential contaminating organisms on icy bodies. Electron donors (e.g., Fe 2+ , SH &minus , organic carbon) and electron acceptors (e.g., CO2, SO4 2&minus , O2, H2O2) 29-33 might be present on some icy bodies. Given the poorly constrained knowledge of the chemistry of these environments, a supply of energy cannot be ruled out. Here the committee takes the conservative assumption that if an environment contains essential elements and water, then a source of energy might exist.

Radiation-resistant microorganisms might present a special problem when the possibility of forward contamination is considered. &ldquoStowaway&rdquo bacteria and archaea on spacecraft targeting the outer planets and their moons will experience exposure to high-level radiation. 34 Yet the extreme resistance of some bacteria on Earth to acute and chronic forms of ionizing radiation that feasibly mimic conditions during transit argues that some microbes within sealed spacecraft components might survive such a journey, because of their resistance to gamma rays afforded by biochemical properties and/or by microenvironments of biofilms, and ultimately could reach life-supporting environments. 35,36,37 For example, as the level of cell grouping increases, survival characteristics of irradiated organisms typically increase as a result of the effects imposed by the limitation of atmospheric dioxygen, whereby cells within biofilms or within clumps are shielded from oxygen effects. Hence, prokaryotes under oxidative stress tend to adhere to surfaces and to each other during growth. 38 Given the possibility that such organisms might survive irradiation exposure and come into contact with a habitable environment, efforts to prevent forward contamination must consider the ultimate fate of these potentially viable organisms on icy moons.

TABLE 5.1 Examples of Electron Donors or Acceptors for Life in Icy Bodies Both Inferred and Measured in Past Work

Europa Comments Enceladus Comments Titan Comments
Electron Donors (observed)
Organics Detected on surface of Callisto, Ganymede Reference a Expected on the surface. Interior unknown Organic compounds Reference j Size of some known structures not known Methane and other organics detected in the plume. Organics and methane Reference l and m suggested as a source of energy for organisms by references n and o Surface organics from hydrocarbon cycle
Hydrogen n/a n/a n/a n/a Reference o
Electron Donors (suggested in literature as plausible candidates)
Hydrogen Reference b Reference k
Electron Acceptors (observed)
Oxygen Observed on surface Reference c Interior unknown
CO/CO2 CO2 on surface Reference d Reference j Observed in plume CO and N2 peaks cannot be differentiated Trace quantities of CO2 observed Reference o
SO2 Reference e
Electron Acceptors (suggested)
Sulfur Sulfate inferred on surface Reference f and g Elemental sulfur also suggested Reference h Interior unknown
Fe3+, other metals Fe3+, other metals Reference b, i Fe3+, other metals depends on connection with silicate core

NOTE: Comments are provided as caveats and context.

a K.P. Hand, C. Chyba, J.C. Priscu, R.W. Carlson, and K.H. Nealson, Astrobiology and the potential for life on Europa, pp. 589-630 in Europa (R. Pappalardo, W. McKinnon, and K. Khurana, eds.), University of Arizona Press, Tucson, Ariz., 2009.

b D. Schulze-Makuch and L.N. Irwin, Energy cycling and hypothetical organisms in Europa&rsquos ocean, Astrobiology 2:105-121, 2002.

c J.R. Spencer and W.M. Calvin, Condensed O2 on Europa and Callisto. Astronomy Journal 124:3400-3403, 2002.

d K.P. Hand, R. Carlson, and C.F. Chyba, Energy, chemical disequilibrium, and geological constraints on Europa, Astrobiology 7:1006-1022, 2007.

e A.L. Lane, R.M. Nelson, and D.L. Matson, Evidence for sulfur implantation in Europa&rsquos UV absorption band, Nature 292:38-39, 1981.

f T.B. McCord, G.B. Hansen, F.P. Fanale, R.W. Carlson, D.L. Matson, T.V. Johnson, W.D. Smythe, J.K. Crowley, P.D. Martin, A. Ocampo, C.A. Hibbitts, J.C. Granahan, and the NIMS Team, Salts on Europa&rsquos surface detected by Galileo&rsquos Near Infrared Mapping Spectrometer, Science 280:1242-1245, 1998.

g R.W. Carlson, R.E. Johnson, and M.S. Anderson, Sulfuric acid on Europa and the radiolytic sulfur cycle, Science 286:97-99, 1999.

h R.W. Carlson, W.M. Calvin, J.B. Dalton, G.B. Hansen, R.L. Hudson, R.E. Johnson, T.B. McCord, and M.H. Moore, Europa&rsquos surface composition, pp. 283-327 in Europa (R. Pappalardo, W. McKinnon, and K. Khurana, eds.), University of Arizona Press, Tucson, Ariz., 2009.

i E.J. Gaidos, K.H. Nealson, and J.L. Kirschvink, Life in ice-covered oceans, Science 284:1631, 1999.

j J.H. Waite, Jr., M.R. Combi, W.-H. Ip, T.E. Cravens, R.L. McNutt, Jr., W. Kasprzak, R. Yelle, J. Luhmann, H. Niemann, D. Gell, B. Magee, G. Fletcher, J. Lunine, and W.-L. Tseng, Cassini ion and neutral mass spectrometer: Enceladus plume composition and structure, Science 311:1419-1422, 2006.

k C.P. McKay, C.C. Porco, T. Altheide, W.L. Davis, and T.A. Kral, The possible origin and persistence of life on Enceladus and detection of biomarkers in the plume, Astrobiology 8:909-919, 2008.

l C.C. Porco, E. Baker, J. Barbara, K. Beurle, A. Brahic, J.A. Burns, S. Charnoz, N. Cooper, D.D. Dawson, A.D. Del Genio, T. Denk, et al., Imaging of Titan from the Cassini spacecraft, Nature 434:159-168, 2005.

m H.B. Niemann, S.K. Atreya, S.J. Bauer, G.R. Carignan, J.E. Demick, R.L. Frost, D. Gautier, J.A. Haberman, D.N. Harpold, D.M. Hunten, G. Israel, et al., The abundances of constituents of Titan&rsquos atmosphere from the GCMS instrument on the Huygens probe, Nature 438:779-784, 2005.

n A.D. Fortes, Exobiological implications of a possible ammonia-water ocean inside Titan, Icarus 146:444-452, 2000.

o F. Raulin, Astrobiology and habitability of Titan, Space Science Reviews 135:37-48, 2007.

Unlike many terrestrial extremophiles that grow within a singular extreme environment, species of the genus Deinococcus demonstrate a suite of extreme survival advantages similar to that needed to survive multiple challenges encountered on missions to the outer planets. One of these species, Deinococcus radiodurans, can survive exposures to ionizing radiation (x rays and gamma rays), ultraviolet C (254 nm) radiation, and charged particles. 39,40 For example, D. radiodurans can survive exposure to 12,000 Gy of gamma rays in aqueous preparations and notably, when desiccated in vacuo or when deeply frozen, D. radiodurans shows significantly increased resistance to gamma rays and ultraviolet C (Figure 5.1). 41,42,43,44 Thus, the psychrotolerant, desiccation-resistant D. radiodurans could survive the simultaneous assaults of impinging cosmic radiation (e.g., far-ultraviolet light and charged subatomic particles), drying, deep freezing, and, possibly, the exposure to high-level ionizing radiation anticipated during orbits that transect the radiation belts of Jupiter or Saturn. 45,46 There is, however, a prerequisite for recovery of D. radiodurans&rsquos enhanced DNA repair, a capacity that is absolutely dependent on the availability of a rich source of aqueous heterotropic organic growth substrates. Thus, the survival traits of D. radiodurans render it the best currently known model for estimating the outer limits of microbial survival in missions to icy solar system bodies. 47-51 Remarkably, the amount of DNA damage caused by most of the physico-chemical insults to which D. radiodurans is most notably resistant is about the same as that in radiation-sensitive cell-types. 52 For example, the yield of DNA double-strand breaks (DSB) in D. radiodurans caused by gamma rays is about the same as that seen in sensitive bacteria, simple eukaryotes, and animals (0.004 DSB/Gy/Mbp). 53,54,55 Deinococcus and other radiation/desiccation-resistant microbes rely on conventional DNA repair enzymes that function extraordinarily efficiently in those species. 56-59 Resistant bacteria and archaea have evolved potent chemical defenses that specifically protect their proteins from oxidative damage, thereby preventing inactivation of enzymes, including those needed to repair and replicate DNA. 60,61 Under this model, a single system rather than a series of separate repair mechanisms evolved to provide resistance to multiple stressors. 62

The survival of D. radiodurans following genotoxic assault depends on the availability of fresh complex nutrients during recovery. 63,64,65 Under nutrient-poor conditions, metabolic capabilities limit DNA repair in acutely irradiated D. radiodurans, 66,67 and similarly in chronically irradiated D. radiodurans. 68 This nutrient-dependent phenotypic reversal from radiation resistance to radiation sensitivity alters scientists&rsquo view of radiation survival in the context of planetary protection. Figure 5.1 illustrates the effects of nutrient conditions and temperature on the recovery of D. radiodurans exposed to gamma radiation. Under standard laboratory conditions, D. radiodurans exposed to 12,000 Gy (from a 60 Co source) on wet ice (at 0°C) displays 10 percent survival (D10) 69 for radiation inactivation when re-covered in liquid rich medium (TGY, tryptone/glucose/yeast extract) at 32°C 70 the D10 for D. radiodurans irradiated at &minus79°C and recovered in TGY is 50,000 kGy. 71,72 However, if irradiated D. radiodurans cells are transferred to an aqueous solution of 10 mM MgCl2 (without addition of complex carbohydrates, peptides, sugars, or vitamins), the D10 for radiation inactivation falls to 5,000 Gy within a few hours of incubation (Figure 5.1), followed by a progressive loss in viability. 73 It follows that the accumulating radiation doses in frozen, hence non-repairing, cells on spacecraft would eventually destroy them unless they were transferred to a liquid environment that contains a rich source of complex organic compounds. Similar arguments and observations apply to radioresistant Bacillus spores 74,75 and radioresistant archaea, 76,77 which are significantly less resistant than D. radiodurans (Figure 5.1). DNA repair in irradiated Bacillus spores occurs at the onset of germination, which requires heterotrophic organic substrates that would not be present in oceans or liquid water reservoirs of moons of


5: Microbial Metabolism - Biology

Enzymes function is to _____________________________________.

catalyze cheical reactionsby loering the activation energy

Enzymes are generally __________proteins with characterstic ____________ shape.

Enzymes are efficient and can operate at relatively ________ temperatures and are subject to various cellular controls.

Enzyme names usually end in _________.

The 6 classes of enzymes are defined on the basis of the types of ________ they _____________.

Most enzymes are _____________ consisting of a _________ and a _________.

protein portion- (apoenzyme)
non-protein porttion- (co-factor)

The cofactor can be a __________ (iron, cobalt, copper, magnesium, manganese, zinc and calcium) or a complex organic molecule known as ________________ (NAD+, NADP+, FMN, FAD, or coenzyme A).

True or false. When an enzyme and substrate combine the substrate is transformed and the enzyme is recovered.

Enzymes are characterized by ________________ which is characterized by their active sites.

At ____________ temperatures enzymes undergo ____________ and lose their catalytic properties.

At __________ temperatures enzymes _________ rate _______________.

low
reaction rate
decreases

The pHat which enzymatic activity is maximal is known as the __________ pH.

Enzymatic activity increases as substrate concentration ___________ until the enzymes are _______________.

________ inhibitors compete with normal substrate for the ________ site of the enzyme.

_________ inhibitors act on other parts of the apoenzyme or on the cofactor and decrease the enzyme's ability to combine with normal substrate.

__________ ________ occurs when the end product of a metabolic pathway inhibits an enzyme's activity near the start of the pathway.

________ are enzymatic RNA molecules that cut and splice RNA in eukaryotic cells.

_______ it the removal of one or more electrons from a substrate. Protons (H+) are removed with the electrons.

Reduction of a substrate refers to its ______ of one or more ______________.

True or false. Each time a substance is oxidized another is simultaneously reduced.

NAD+ is the reduced or oxidized form

True or false. Glucose is a reduced molecule energy is released during a cell's oxidation of glucose.

Energy released during certain metabolic reactions can be trapped to form _____ from ___________ and (P)-phosphate.

Adding a (P) to a molecule is called _______________.

During substrate-level phosphorylation a ______________ (P) from an intermediate in catabolism is added to ADP.

True or False. During oxidative phosphorylation energy is released as electrons are passed to a series of of electron acceptors (an electron transport chain) and finally to O2 or another inorganic compound,

Photophosphorylation only happens in ___________ organisms.

1.breakdown reactions
2. release energy (exergenic)
3. typically occur via hydrolysis

Synthesis reactions-put together -build
require the input of energy (endergonic)
typically occur via dehydration synthesis

dehydration synthesis (left to right)

a chemical reaction in which a molecule of water is released in the reaction of the monosaccharides glucose and fructose combine to form a molecule of the disaccharide sucrose.

in hydrolysis the sucrose molecule breaks down into the smaller molecules glucose and fructose. For the hydrolysis reaction to proceed, water must be added to the sucrose.

What is the most usable form of energy?

Catabolic ______ and _______ _________.

Anabolic ________ and ______ _______.

There are different types of energy

heat
light-plants
chemical energy

ATP is _____________ energy.

True or false. Heat is a useless energy it can't be reused.

Organic molecules contain energy stored in their bonds. More specifically energy is associated with _______ that form those bonds.

Most of a cell's energy is produced from the __________ of ________________.

oxidation of carbohydrates

What is the most commonly used carbohydrate?

The two major types of glucose catabolism are __________in which glucose is completely broken down and _________ is when it is partially broken down,

What is the most common pathway for the oxidation of glucose?

What is the end product of glycolysis?

Two ATP and two NADH are produced rom one ________ ________.

Cells extract energy and store it in ?

Oxidation reactions involves the oxidation of a molecule. A molecule loses energy-containing electrons. Reduction reactions involves the reduction of a molecule. A molecule gains energy containing electrons. What is a good way to remember this ?

LEO goes GER
Loss of electrons is oxidation gain of electrons is reduction
or
OIL RIG
oxidation is loss and Reduction is gain

Adenosine triphosphate (ATP) does what?

1. stores chemical energy released by catabolic reactions
2. provides energy for anabolic reactions

Adenosine unit (ribose and adenine) + 3 phosphate groups (3 like charges forced together =high energy bonds)

What are the three mechanisms of ATP?

1. substrate level phosphorylation - transfer of a high energy phosphate from a phosphorylated compound to ADP (sharing phosphate with ADP)
2. Oxidative phosphorylation- cellular respiration
-ETC creates proton motive force
-H+ channeled through ATP synthase along the concentration gradient
-energy from proton motive force used to phosphorylate ADP
3. Photophosphorylation-Photosynthetic organisms
-occurs only in photosynthetic organisms
-process similar to phosphorylation

During respiration _______ molecules are ________.

organic molecules
oxidized

During cellular respiration energy is generated from the ________________.


Contact

Principal Investigator
John D. Coates
Department of Plant and Microbial Biology, University of California, Berkeley
Energy & Biosciences Institute, University of California, Berkeley,
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
[email protected]

Program Manager
Boris Wawrik
Department of Energy Office of Science
Office of Biological and Environmental Research
Biological Systems Science Division
[email protected]


Contents

All microbial metabolisms can be arranged according to three principles:

1. How the organism obtains carbon for synthesizing cell mass: [1]

  • autotrophic – carbon is obtained from carbon dioxide ( CO
    2 )
  • heterotrophic – carbon is obtained from organic compounds
  • mixotrophic – carbon is obtained from both organic compounds and by fixing carbon dioxide

2. How the organism obtains reducing equivalents (hydrogen atoms or electrons) used either in energy conservation or in biosynthetic reactions:

  • lithotrophic – reducing equivalents are obtained from inorganic compounds
  • organotrophic – reducing equivalents are obtained from organic compounds

3. How the organism obtains energy for living and growing:

In practice, these terms are almost freely combined. Typical examples are as follows:

  • chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. Examples: Nitrifying bacteria, sulfur-oxidizing bacteria, iron-oxidizing bacteria, Knallgas-bacteria[4]
  • photolithoautotrophs obtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds. Examples: Cyanobacteria (water ( H
    2 O ) as reducing equivalent = hydrogen donor), Chlorobiaceae, Chromatiaceae (hydrogen sulfide ( H
    2 S ) as hydrogen donor), Chloroflexus (hydrogen ( H
    2 ) as reducing equivalent donor)
  • chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide ( CO
    2 ). Examples: some Thiobacilus, some Beggiatoa, some Nitrobacter spp., Wolinella (with H
    2 as reducing equivalent donor), some Knallgas-bacteria, some sulfate-reducing bacteria [citation needed]
  • chemoorganoheterotrophs obtain energy, carbon, and hydrogen for biosynthetic reactions from organic compounds. Examples: most bacteria, e. g. Escherichia coli, Bacillus spp., Actinobacteria
  • photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples: Rhodobacter, Rhodopseudomonas, Rhodospirillum, Rhodomicrobium, Rhodocyclus, Heliobacterium, Chloroflexus (alternatively to photolithoautotrophy with hydrogen)

Some microbes are heterotrophic (more precisely chemoorganoheterotrophic), using organic compounds as both carbon and energy sources. Heterotrophic microbes live off of nutrients that they scavenge from living hosts (as commensals or parasites) or find in dead organic matter of all kind (saprophages). Microbial metabolism is the main contribution for the bodily decay of all organisms after death. Many eukaryotic microorganisms are heterotrophic by predation or parasitism, properties also found in some bacteria such as Bdellovibrio (an intracellular parasite of other bacteria, causing death of its victims) and Myxobacteria such as Myxococcus (predators of other bacteria which are killed and lysed by cooperating swarms of many single cells of Myxobacteria). Most pathogenic bacteria can be viewed as heterotrophic parasites of humans or the other eukaryotic species they affect. Heterotrophic microbes are extremely abundant in nature and are responsible for the breakdown of large organic polymers such as cellulose, chitin or lignin which are generally indigestible to larger animals. Generally, the oxidative breakdown of large polymers to carbon dioxide (mineralization) requires several different organisms, with one breaking down the polymer into its constituent monomers, one able to use the monomers and excreting simpler waste compounds as by-products, and one able to use the excreted wastes. There are many variations on this theme, as different organisms are able to degrade different polymers and secrete different waste products. Some organisms are even able to degrade more recalcitrant compounds such as petroleum compounds or pesticides, making them useful in bioremediation.

Biochemically, prokaryotic heterotrophic metabolism is much more versatile than that of eukaryotic organisms, although many prokaryotes share the most basic metabolic models with eukaryotes, e. g. using glycolysis (also called EMP pathway) for sugar metabolism and the citric acid cycle to degrade acetate, producing energy in the form of ATP and reducing power in the form of NADH or quinols. These basic pathways are well conserved because they are also involved in biosynthesis of many conserved building blocks needed for cell growth (sometimes in reverse direction). However, many bacteria and archaea utilize alternative metabolic pathways other than glycolysis and the citric acid cycle. A well-studied example is sugar metabolism via the keto-deoxy-phosphogluconate pathway (also called ED pathway) in Pseudomonas. Moreover, there is a third alternative sugar-catabolic pathway used by some bacteria, the pentose phosphate pathway. The metabolic diversity and ability of prokaryotes to use a large variety of organic compounds arises from the much deeper evolutionary history and diversity of prokaryotes, as compared to eukaryotes. It is also noteworthy that the mitochondrion, the small membrane-bound intracellular organelle that is the site of eukaryotic oxygen-driven [3] energy metabolism, arose from the endosymbiosis of a bacterium related to obligate intracellular Rickettsia, and also to plant-associated Rhizobium or Agrobacterium. Therefore, it is not surprising that all mitrochondriate eukaryotes share metabolic properties with these Proteobacteria. Most microbes respire (use an electron transport chain), although oxygen is not the only terminal electron acceptor that may be used. As discussed below, the use of terminal electron acceptors other than oxygen has important biogeochemical consequences.

Fermentation is a specific type of heterotrophic metabolism that uses organic carbon instead of oxygen as a terminal electron acceptor. This means that these organisms do not use an electron transport chain to oxidize NADH to NAD +
and therefore must have an alternative method of using this reducing power and maintaining a supply of NAD +
for the proper functioning of normal metabolic pathways (e.g. glycolysis). As oxygen is not required, fermentative organisms are anaerobic. Many organisms can use fermentation under anaerobic conditions and aerobic respiration when oxygen is present. These organisms are facultative anaerobes. To avoid the overproduction of NADH, obligately fermentative organisms usually do not have a complete citric acid cycle. Instead of using an ATP synthase as in respiration, ATP in fermentative organisms is produced by substrate-level phosphorylation where a phosphate group is transferred from a high-energy organic compound to ADP to form ATP. As a result of the need to produce high energy phosphate-containing organic compounds (generally in the form of Coenzyme A-esters) fermentative organisms use NADH and other cofactors to produce many different reduced metabolic by-products, often including hydrogen gas ( H
2 ). These reduced organic compounds are generally small organic acids and alcohols derived from pyruvate, the end product of glycolysis. Examples include ethanol, acetate, lactate, and butyrate. Fermentative organisms are very important industrially and are used to make many different types of food products. The different metabolic end products produced by each specific bacterial species are responsible for the different tastes and properties of each food.

Not all fermentative organisms use substrate-level phosphorylation. Instead, some organisms are able to couple the oxidation of low-energy organic compounds directly to the formation of a proton (or sodium) motive force and therefore ATP synthesis. Examples of these unusual forms of fermentation include succinate fermentation by Propionigenium modestum and oxalate fermentation by Oxalobacter formigenes. These reactions are extremely low-energy yielding. Humans and other higher animals also use fermentation to produce lactate from excess NADH, although this is not the major form of metabolism as it is in fermentative microorganisms.

Methylotrophy Edit

Methylotrophy refers to the ability of an organism to use C1-compounds as energy sources. These compounds include methanol, methyl amines, formaldehyde, and formate. Several other less common substrates may also be used for metabolism, all of which lack carbon-carbon bonds. Examples of methylotrophs include the bacteria Methylomonas and Methylobacter. Methanotrophs are a specific type of methylotroph that are also able to use methane ( CH
4 ) as a carbon source by oxidizing it sequentially to methanol ( CH
3 OH ), formaldehyde ( CH
2 O ), formate ( HCOO −
), and carbon dioxide CO
2 initially using the enzyme methane monooxygenase. As oxygen is required for this process, all (conventional) methanotrophs are obligate aerobes. Reducing power in the form of quinones and NADH is produced during these oxidations to produce a proton motive force and therefore ATP generation. Methylotrophs and methanotrophs are not considered as autotrophic, because they are able to incorporate some of the oxidized methane (or other metabolites) into cellular carbon before it is completely oxidized to CO
2 (at the level of formaldehyde), using either the serine pathway (Methylosinus, Methylocystis) or the ribulose monophosphate pathway (Methylococcus), depending on the species of methylotroph.

In addition to aerobic methylotrophy, methane can also be oxidized anaerobically. This occurs by a consortium of sulfate-reducing bacteria and relatives of methanogenic Archaea working syntrophically (see below). Little is currently known about the biochemistry and ecology of this process.

Methanogenesis is the biological production of methane. It is carried out by methanogens, strictly anaerobic Archaea such as Methanococcus, Methanocaldococcus, Methanobacterium, Methanothermus, Methanosarcina, Methanosaeta and Methanopyrus. The biochemistry of methanogenesis is unique in nature in its use of a number of unusual cofactors to sequentially reduce methanogenic substrates to methane, such as coenzyme M and methanofuran. [5] These cofactors are responsible (among other things) for the establishment of a proton gradient across the outer membrane thereby driving ATP synthesis. Several types of methanogenesis occur, differing in the starting compounds oxidized. Some methanogens reduce carbon dioxide ( CO
2 ) to methane ( CH
4 ) using electrons (most often) from hydrogen gas ( H
2 ) chemolithoautotrophically. These methanogens can often be found in environments containing fermentative organisms. The tight association of methanogens and fermentative bacteria can be considered to be syntrophic (see below) because the methanogens, which rely on the fermentors for hydrogen, relieve feedback inhibition of the fermentors by the build-up of excess hydrogen that would otherwise inhibit their growth. This type of syntrophic relationship is specifically known as interspecies hydrogen transfer. A second group of methanogens use methanol ( CH
3 OH ) as a substrate for methanogenesis. These are chemoorganotrophic, but still autotrophic in using CO
2 as only carbon source. The biochemistry of this process is quite different from that of the carbon dioxide-reducing methanogens. Lastly, a third group of methanogens produce both methane and carbon dioxide from acetate ( CH
3 COO −
) with the acetate being split between the two carbons. These acetate-cleaving organisms are the only chemoorganoheterotrophic methanogens. All autotrophic methanogens use a variation of the reductive acetyl-CoA pathway to fix CO
2 and obtain cellular carbon.

Syntrophy Edit

Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve a chemical reaction that, on its own, would be energetically unfavorable. The best studied example of this process is the oxidation of fermentative end products (such as acetate, ethanol and butyrate) by organisms such as Syntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is energetically unfavorable. However, when a hydrogenotrophic (hydrogen-using) methanogen is present the use of the hydrogen gas will significantly lower the concentration of hydrogen (down to 10 −5 atm) and thereby shift the equilibrium of the butyrate oxidation reaction under standard conditions (ΔGº’) to non-standard conditions (ΔG’). Because the concentration of one product is lowered, the reaction is "pulled" towards the products and shifted towards net energetically favorable conditions (for butyrate oxidation: ΔGº’= +48.2 kJ/mol, but ΔG' = -8.9 kJ/mol at 10 −5 atm hydrogen and even lower if also the initially produced acetate is further metabolized by methanogens). Conversely, the available free energy from methanogenesis is lowered from ΔGº’= -131 kJ/mol under standard conditions to ΔG' = -17 kJ/mol at 10 −5 atm hydrogen. This is an example of intraspecies hydrogen transfer. In this way, low energy-yielding carbon sources can be used by a consortium of organisms to achieve further degradation and eventual mineralization of these compounds. These reactions help prevent the excess sequestration of carbon over geologic time scales, releasing it back to the biosphere in usable forms such as methane and CO
2 .

While aerobic organisms during respiration use oxygen as a terminal electron acceptor, anaerobic organisms use other electron acceptors. These inorganic compounds have a lower reduction potential than oxygen, [3] meaning that respiration is less efficient in these organisms and leads to slower growth rates than aerobes. Many facultative anaerobes can use either oxygen or alternative terminal electron acceptors for respiration depending on the environmental conditions.

Most respiring anaerobes are heterotrophs, although some do live autotrophically. All of the processes described below are dissimilative, meaning that they are used during energy production and not to provide nutrients for the cell (assimilative). Assimilative pathways for many forms of anaerobic respiration are also known.

Denitrification – nitrate as electron acceptor Edit

Denitrification is the utilization of nitrate ( NO −
3 ) as a terminal electron acceptor. It is a widespread process that is used by many members of the Proteobacteria. Many facultative anaerobes use denitrification because nitrate, like oxygen, has a high reduction potential. Many denitrifying bacteria can also use ferric iron ( Fe 3+
) and some organic electron acceptors. Denitrification involves the stepwise reduction of nitrate to nitrite ( NO −
2 ), nitric oxide (NO), nitrous oxide ( N
2 O ), and dinitrogen ( N
2 ) by the enzymes nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase, respectively. Protons are transported across the membrane by the initial NADH reductase, quinones, and nitrous oxide reductase to produce the electrochemical gradient critical for respiration. Some organisms (e.g. E. coli) only produce nitrate reductase and therefore can accomplish only the first reduction leading to the accumulation of nitrite. Others (e.g. Paracoccus denitrificans or Pseudomonas stutzeri) reduce nitrate completely. Complete denitrification is an environmentally significant process because some intermediates of denitrification (nitric oxide and nitrous oxide) are important greenhouse gases that react with sunlight and ozone to produce nitric acid, a component of acid rain. Denitrification is also important in biological wastewater treatment where it is used to reduce the amount of nitrogen released into the environment thereby reducing eutrophication. Denitrification can be determined via a nitrate reductase test.

Sulfate reduction – sulfate as electron acceptor Edit

Dissimilatory sulfate reduction is a relatively energetically poor process used by many Gram-negative bacteria found within the deltaproteobacteria, Gram-positive organisms relating to Desulfotomaculum or the archaeon Archaeoglobus. Hydrogen sulfide ( H
2 S ) is produced as a metabolic end product. For sulfate reduction electron donors and energy are needed.

Electron donors Edit

Many sulfate reducers are organotrophic, using carbon compounds such as lactate and pyruvate (among many others) as electron donors, [6] while others are lithotrophic, using hydrogen gas ( H
2 ) as an electron donor. [7] Some unusual autotrophic sulfate-reducing bacteria (e.g. Desulfotignum phosphitoxidans) can use phosphite ( HPO −
3 ) as an electron donor [8] whereas others (e.g. Desulfovibrio sulfodismutans, Desulfocapsa thiozymogenes, Desulfocapsa sulfoexigens) are capable of sulfur disproportionation (splitting one compound into two different compounds, in this case an electron donor and an electron acceptor) using elemental sulfur (S 0 ), sulfite ( SO 2−
3 ), and thiosulfate ( S
2 O 2−
3 ) to produce both hydrogen sulfide ( H
2 S ) and sulfate ( SO 2−
4 ). [9]

Energy for reduction Edit

All sulfate-reducing organisms are strict anaerobes. Because sulfate is energetically stable, before it can be metabolized it must first be activated by adenylation to form APS (adenosine 5’-phosphosulfate) thereby consuming ATP. The APS is then reduced by the enzyme APS reductase to form sulfite ( SO 2−
3 ) and AMP. In organisms that use carbon compounds as electron donors, the ATP consumed is accounted for by fermentation of the carbon substrate. The hydrogen produced during fermentation is actually what drives respiration during sulfate reduction.

Acetogenesis – carbon dioxide as electron acceptor Edit

Acetogenesis is a type of microbial metabolism that uses hydrogen ( H
2 ) as an electron donor and carbon dioxide ( CO
2 ) as an electron acceptor to produce acetate, the same electron donors and acceptors used in methanogenesis (see above). Bacteria that can autotrophically synthesize acetate are called homoacetogens. Carbon dioxide reduction in all homoacetogens occurs by the acetyl-CoA pathway. This pathway is also used for carbon fixation by autotrophic sulfate-reducing bacteria and hydrogenotrophic methanogens. Often homoacetogens can also be fermentative, using the hydrogen and carbon dioxide produced as a result of fermentation to produce acetate, which is secreted as an end product.

Other inorganic electron acceptors Edit

Ferric iron ( Fe 3+
) is a widespread anaerobic terminal electron acceptor both for autotrophic and heterotrophic organisms. Electron flow in these organisms is similar to those in electron transport, ending in oxygen or nitrate, except that in ferric iron-reducing organisms the final enzyme in this system is a ferric iron reductase. Model organisms include Shewanella putrefaciens and Geobacter metallireducens. Since some ferric iron-reducing bacteria (e.g. G. metallireducens) can use toxic hydrocarbons such as toluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminated aquifers.

Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use other inorganic ions in anaerobic respiration. While these processes may often be less significant ecologically, they are of considerable interest for bioremediation, especially when heavy metals or radionuclides are used as electron acceptors. Examples include:

    ( Mn 4+
    ) reduction to manganous ion ( Mn 2+
    ) ( SeO 2−
    4 ) reduction to selenite ( SeO 2−
    3 ) and selenite reduction to inorganic selenium (Se 0 ) ( AsO 3−
    4 ) reduction to arsenite ( AsO 3−
    3 ) ion ( UO 2+
    2 ) reduction to uranium dioxide ( UO
    2 )

Organic terminal electron acceptors Edit

A number of organisms, instead of using inorganic compounds as terminal electron acceptors, are able to use organic compounds to accept electrons from respiration. Examples include:

TMAO is a chemical commonly produced by fish, and when reduced to TMA produces a strong odor. DMSO is a common marine and freshwater chemical which is also odiferous when reduced to DMS. Reductive dechlorination is the process by which chlorinated organic compounds are reduced to form their non-chlorinated endproducts. As chlorinated organic compounds are often important (and difficult to degrade) environmental pollutants, reductive dechlorination is an important process in bioremediation.

Chemolithotrophy is a type of metabolism where energy is obtained from the oxidation of inorganic compounds. Most chemolithotrophic organisms are also autotrophic. There are two major objectives to chemolithotrophy: the generation of energy (ATP) and the generation of reducing power (NADH).

Hydrogen oxidation Edit

Many organisms are capable of using hydrogen ( H
2 ) as a source of energy. While several mechanisms of anaerobic hydrogen oxidation have been mentioned previously (e.g. sulfate reducing- and acetogenic bacteria), hydrogen can also be used to unlock the chemical energy of O2 [3] in the aerobic Knallgas reaction: [10]

In these organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes. In many organisms, a second cytoplasmic hydrogenase is used to generate reducing power in the form of NADH, which is subsequently used to fix carbon dioxide via the Calvin cycle. Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen. [11]

Sulfur oxidation Edit

Sulfur oxidation involves the oxidation of reduced sulfur compounds (such as sulfide H
2 S ), inorganic sulfur (S), and thiosulfate ( S
2 O 2−
3 ) to form sulfuric acid ( H
2 SO
4 ). A classic example of a sulfur-oxidizing bacterium is Beggiatoa, a microbe originally described by Sergei Winogradsky, one of the founders of environmental microbiology. Another example is Paracoccus. Generally, the oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed. This two step process occurs because energetically sulfide is a better electron donor than inorganic sulfur or thiosulfate, allowing for a greater number of protons to be translocated across the membrane. Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow, an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH. Biochemically, reduced sulfur compounds are converted to sulfite ( SO 2−
3 ) and subsequently converted to sulfate ( SO 2−
4 ) by the enzyme sulfite oxidase. [12] Some organisms, however, accomplish the same oxidation using a reversal of the APS reductase system used by sulfate-reducing bacteria (see above). In all cases the energy liberated is transferred to the electron transport chain for ATP and NADH production. [12] In addition to aerobic sulfur oxidation, some organisms (e.g. Thiobacillus denitrificans) use nitrate ( NO −
3 ) as a terminal electron acceptor and therefore grow anaerobically.

Ferrous iron ( Fe 2+ ) oxidation Edit

Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric ( Fe 3+
) form and is hydrolyzed abiotically to insoluble ferric hydroxide ( Fe(OH)
3 ). There are three distinct types of ferrous iron-oxidizing microbes. The first are acidophiles, such as the bacteria Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, as well as the archaeon Ferroplasma. These microbes oxidize iron in environments that have a very low pH and are important in acid mine drainage. The second type of microbes oxidize ferrous iron at near-neutral pH. These micro-organisms (for example Gallionella ferruginea, Leptothrix ochracea, or Mariprofundus ferrooxydans) live at the oxic-anoxic interfaces and are microaerophiles. The third type of iron-oxidizing microbes are anaerobic photosynthetic bacteria such as Rhodopseudomonas, [13] which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron oxidation is a very energetically poor process which therefore requires large amounts of iron to be oxidized by the enzyme rusticyanin to facilitate the formation of proton motive force. Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.

Nitrification Edit

Nitrification is the process by which ammonia ( NH
3 ) is converted to nitrate ( NO −
3 ). Nitrification is actually the net result of two distinct processes: oxidation of ammonia to nitrite ( NO −
2 ) by nitrosifying bacteria (e.g. Nitrosomonas) and oxidation of nitrite to nitrate by the nitrite-oxidizing bacteria (e.g. Nitrobacter). Both of these processes are extremely energetically poor leading to very slow growth rates for both types of organisms. Biochemically, ammonia oxidation occurs by the stepwise oxidation of ammonia to hydroxylamine ( NH
2 OH ) by the enzyme ammonia monooxygenase in the cytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzyme hydroxylamine oxidoreductase in the periplasm.

Electron and proton cycling are very complex but as a net result only one proton is translocated across the membrane per molecule of ammonia oxidized. Nitrite oxidation is much simpler, with nitrite being oxidized by the enzyme nitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms. Oxygen is required in both ammonia and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.

In 2015, two groups independently showed the microbial genus Nitrospira is capable of complete nitrification (Comammox). [14] [15]

Anammox Edit

Anammox stands for anaerobic ammonia oxidation and the organisms responsible were relatively recently discovered, in the late 1990s. [16] This form of metabolism occurs in members of the Planctomycetes (e.g. Candidatus Brocadia anammoxidans) and involves the coupling of ammonia oxidation to nitrite reduction. As oxygen is not required for this process, these organisms are strict anaerobes. Amazingly, hydrazine ( N
2 H
4 – rocket fuel) is produced as an intermediate during anammox metabolism. To deal with the high toxicity of hydrazine, anammox bacteria contain a hydrazine-containing intracellular organelle called the anammoxasome, surrounded by highly compact (and unusual) ladderane lipid membrane. These lipids are unique in nature, as is the use of hydrazine as a metabolic intermediate. Anammox organisms are autotrophs although the mechanism for carbon dioxide fixation is unclear. Because of this property, these organisms could be used to remove nitrogen in industrial wastewater treatment processes. [17] Anammox has also been shown to have widespread occurrence in anaerobic aquatic systems and has been speculated to account for approximately 50% of nitrogen gas production in the ocean. [18]

Manganese oxidation Edit

In July 2020 researchers report the discovery of chemolithoautotrophic bacterial culture that feeds on the metal manganese after performing unrelated experiments and named its bacterial species Candidatus Manganitrophus noduliformans and Ramlibacter lithotrophicus. [19] [20] [21]

Many microbes (phototrophs) are capable of using light as a source of energy to produce ATP and organic compounds such as carbohydrates, lipids, and proteins. Of these, algae are particularly significant because they are oxygenic, using water as an electron donor for electron transfer during photosynthesis. [22] Phototrophic bacteria are found in the phyla Cyanobacteria, Chlorobi, Proteobacteria, Chloroflexi, and Firmicutes. [23] Along with plants these microbes are responsible for all biological generation of oxygen gas on Earth. Because chloroplasts were derived from a lineage of the Cyanobacteria, the general principles of metabolism in these endosymbionts can also be applied to chloroplasts. [24] In addition to oxygenic photosynthesis, many bacteria can also photosynthesize anaerobically, typically using sulfide ( H
2 S ) as an electron donor to produce sulfate. Inorganic sulfur ( S
0 ), thiosulfate ( S
2 O 2−
3 ) and ferrous iron ( Fe 2+
) can also be used by some organisms. Phylogenetically, all oxygenic photosynthetic bacteria are Cyanobacteria, while anoxygenic photosynthetic bacteria belong to the purple bacteria (Proteobacteria), Green sulfur bacteria (e.g. Chlorobium), Green non-sulfur bacteria (e.g. Chloroflexus), or the heliobacteria (Low %G+C Gram positives). In addition to these organisms, some microbes (e.g. the Archaeon Halobacterium or the bacterium Roseobacter, among others) can utilize light to produce energy using the enzyme bacteriorhodopsin, a light-driven proton pump. However, there are no known Archaea that carry out photosynthesis. [23]

As befits the large diversity of photosynthetic bacteria, there are many different mechanisms by which light is converted into energy for metabolism. All photosynthetic organisms locate their photosynthetic reaction centers within a membrane, which may be invaginations of the cytoplasmic membrane (Proteobacteria), thylakoid membranes (Cyanobacteria), specialized antenna structures called chlorosomes (Green sulfur and non-sulfur bacteria), or the cytoplasmic membrane itself (heliobacteria). Different photosynthetic bacteria also contain different photosynthetic pigments, such as chlorophylls and carotenoids, allowing them to take advantage of different portions of the electromagnetic spectrum and thereby inhabit different niches. Some groups of organisms contain more specialized light-harvesting structures (e.g. phycobilisomes in Cyanobacteria and chlorosomes in Green sulfur and non-sulfur bacteria), allowing for increased efficiency in light utilization.

Biochemically, anoxygenic photosynthesis is very different from oxygenic photosynthesis. Cyanobacteria (and by extension, chloroplasts) use the Z scheme of electron flow in which electrons eventually are used to form NADH. Two different reaction centers (photosystems) are used and proton motive force is generated both by using cyclic electron flow and the quinone pool. In anoxygenic photosynthetic bacteria, electron flow is cyclic, with all electrons used in photosynthesis eventually being transferred back to the single reaction center. A proton motive force is generated using only the quinone pool. In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the protein ferredoxin, an energetically favorable reaction. In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center. In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase.

Most photosynthetic microbes are autotrophic, fixing carbon dioxide via the Calvin cycle. Some photosynthetic bacteria (e.g. Chloroflexus) are photoheterotrophs, meaning that they use organic carbon compounds as a carbon source for growth. Some photosynthetic organisms also fix nitrogen (see below).

Nitrogen is an element required for growth by all biological systems. While extremely common (80% by volume) in the atmosphere, dinitrogen gas ( N
2 ) is generally biologically inaccessible due to its high activation energy. Throughout all of nature, only specialized bacteria and Archaea are capable of nitrogen fixation, converting dinitrogen gas into ammonia ( NH
3 ), which is easily assimilated by all organisms. [25] These prokaryotes, therefore, are very important ecologically and are often essential for the survival of entire ecosystems. This is especially true in the ocean, where nitrogen-fixing cyanobacteria are often the only sources of fixed nitrogen, and in soils, where specialized symbioses exist between legumes and their nitrogen-fixing partners to provide the nitrogen needed by these plants for growth.

Nitrogen fixation can be found distributed throughout nearly all bacterial lineages and physiological classes but is not a universal property. Because the enzyme nitrogenase, responsible for nitrogen fixation, is very sensitive to oxygen which will inhibit it irreversibly, all nitrogen-fixing organisms must possess some mechanism to keep the concentration of oxygen low. Examples include:

  • heterocyst formation (cyanobacteria e.g. Anabaena) where one cell does not photosynthesize but instead fixes nitrogen for its neighbors which in turn provide it with energy
  • root nodule symbioses (e.g. Rhizobium) with plants that supply oxygen to the bacteria bound to molecules of leghaemoglobin
  • anaerobic lifestyle (e.g. Clostridium pasteurianum)
  • very fast metabolism (e.g. Azotobacter vinelandii)

The production and activity of nitrogenases is very highly regulated, both because nitrogen fixation is an extremely energetically expensive process (16–24 ATP are used per N
2 fixed) and due to the extreme sensitivity of the nitrogenase to oxygen.


Summary

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    5: Microbial Metabolism - Biology

    MICROBIOLOGY - AN INTRODUCTION , by Tortora, Funke, and Case, 10th edition

    I recommend you download and print (handout format!) the lecture notes before coming to class.

    Chapter 1: The Microbial World and You
    PowerPoint file
    PDF

    Semmelweis and Lister from the amazing Blood and Guts series.
    Antonie van Leeuwenhoek from MicrobiologyBytes

    Review: 2cefg, 3, 4, 5eijmnp, 6, 7b, 8
    Multiple Choice: 1-4, 6, 7, 10
    Critical Thinking: 2 - 4
    Clinical Application: 1, 2

    Chapter 3: Observing Microorganisms Through a Microscope
    PowerPoint file
    PDF

    Reproduction by budding (Yeast and few bacteria)

    Three interesting DNA Replication animations from YouTube: 1 2 3

    Chapter 14: Principles of Disease and Epidemiology
    (PowerPoint file )
    (PDF)

    Chapter 16: Innate Immunity: Nonspecific Defenses of the Host
    PowerPoint
    PDF

    Chapter 19: Disorders Associated with the Immune System - AIDS
    PowerPoint
    PDF

    Review:
    Multiple Choice:
    Critical Thinking: 2, 3, 4
    Clinical Application:

    Chapter 21: Microbial Diseases of the Skin and Eyes
    Part 1: Bacterial Skin infections (PP) (PDF )

    Part 2: Viral and Eukaryotic Skin infections, and Eye Infections (PP) (PDF )

    Chapter 24: Microbial Diseases of the Respiratory System
    PowerPoint file
    PDF

    Chapter 25: Microbial Diseases of the Digestive System
    PowerPoint
    PDF

    Chapter 26: Microbial Diseases of the Urinary and Reproductive Systems
    PowerPoint
    PDF


    Watch the video: Intro to Microbial Metabolism Ch 5 (June 2022).


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