Organic compounds are catabolized by fermentation when sulfate, nitrate, or iron is absent from an anoxic environment. In Clostridial fermentation, the Clostridium species either ferments sugars or amino acids. In sugar fermentation, butyric acid, acetone, and butanol are produced. If butyrate is synthesized, extra ATP is produced and the organism with continue to prefer butyrate unless the environment becomes unfavorable. When acetone is produced, butanol can also result from the process. For every acetone molecule, two NADH produced in glycolysis are not reoxidized.

Proteolytic Clostridia can also ferment amino acids released from proteins of dead organisms. The amino acid is catabolized to yield fatty acid-CoAs which is used to produce ATP by substrate level phosphorylation. Additionally, amino acid fermentation can be coupled in a process called the Strickland reaction.

In syntrophy, two different organisms cooperate to degrade a substance that one organism could not do alone. Most syntrophic reactions involve secondary fermentation of the fermented products of other organisms. For example, the H2 produced by Pelotomaculum is used as an electron donor by a methanogen to produce methane in an exergonic reaction. Syntrophic bacteria are often key links in anoxic steps of the carbon cycle. Synthrophs use reduced fermentation products to release H2 which is important for anaerobic respiration. This circumvents the problem of running out of electron acceptors other than CO2.

In mixed-acid fermentation, a glucose molecule is converted into a variety of acids. It is an anaerobic process used by bacteria such as E. coli. The products of mixed-acid fermentation includes lactate, acetate, succinate, formate, ethanol, H2, and CO2. The product form depends on the bacteria and what enzymes they contain. This biological process is often valued by biotechnological industries for applications in biofuel.

Chemolithotrophic organisms conserve energy from oxidation of inorganic compounds. In hydrogen oxidation, organisms couple the oxidation of H2 with the reduction of O2 to form water. ATP is produced in this process when H2 is oxidized by O2 and electron transport reactions generate a proton motive force. An important catalyase in these reactions include the hydrogenase. Some hydrogen bacteria uses a cytoplasmic and a membrane-integrated hydrogenase.

In oxidation of sulfur compounds, sulfur bacteria utilize H2S, S0, S2O3, and SO3 as electron donors. The most common oxidation product is SO4. Some bacteria such as Beggiatoa stores sulfur to create a potential for additional electron processes. One important product of the oxidation of reduced sulfur compounds is protons. Due to proton production, the environment often becomes acidic.

In iron oxidation, ferrous iron is oxidized to ferric iron. At low pHs, very small amounts of energy is available from this reaction so organisms often couple the oxidation of large amounts of iron. Ferric iron produced from ferrous iron is converted to iron precipitates and often lowers pH in aquatic environments. This is also coincident with the acidophilic nature of these organisms.

In nitrification, reduced NH3 and NO2 are oxidized aerobically while ammonia is oxidized anaerobically in anammox. The complete oxidation of NH3 to NO3 involves both the ammonia oxidizers and nitrite oxidizers. Energy from nitrification can be explained by electrons gained from reduction of inorganic materials that enter an electron transport chain to create a proton motive force that in turn, synthesizes ATP. Anammox is carried out by aerobic Bacteria and Archaea that thrive in ammonia rich habitats such as sewers and wastewater. Anammox is considered to be useful in the treatment of sewage.

Phototrophy is the use of light energy by various organisms with CO2 as the focus of carbon energy source. Oxygenic photosynthesis with the help of chlorophylls is one of the most important phototrophic processes. In oxygenic phototrophy, electrons flow through photosystem I and photosystem II. The process is often represented by the Z-scheme where the reduction potential of P680 in PS II is strongly electropositive that allows for the splitting of water into oxygen and electrons. The organism harvests light energy and uses it to convert P680 into a strong reductant to reduce pheophytin alpha. An electron from water is donated to the oxidized P680 to return it to a ground-state potential. The electron continues to increase positive potential and is eventually accepted by P700 to generate a proton motive force. Later on, the process is terminated with the reduction of NADP+ to NADPH. Of note, ATP can be produced in cyclic or noncyclic photophosphorylation.

In anoxygenic photosynthesis, PS I is utilized to use cyclic photophosphorylation and CO2 reduction from sources other than water. Cyanobacteria can use H2S as an electron donor and green algae can use H2. Of note, these processes are often less efficient than that of their oxygenic counterparts. However, they are useful for environments with limited or specific resources.

Phycobolins are light harvesting bilins often found in cyanobacteria, red algae, and glaucophytes. They are marked by colors and are bonded to certain water-soluble proteins. These bilins then pass the harvested light energy to chlorophylls for photosynthesis. The phycobilin is known for efficient absorption of the colors red, yellow, orange, and green which allows for supplementation of the chlorophyll’s weaknesses.

Microbes live in all parts of the biosphere. Microbial activities are important in maintaining the stability of the ecosystem. The habitat of a microorganism is governed by the conditions, both physical and chemical, of its location. A habitat can sustain more than one type of microbe due to numerous microenvironments in it!

For every organism there is one niche, called the realized niche, where it is most successful ecologically. Organisms can occupy more than it realized niche but will not be as successful. an important factor in microbial microenvironments is diffusion. If certain nutrients, like oxygen, cannot diffuse into a microbial environment, the deeper layers will contain anaerobic microbes while the outer layers will contain aerobic microbes, making the environment suitable for many types of microorganisms.

Growth rates of microbes are dependant of available nutrients in the environment. Resources are not always available in the environment causing microorganisms in a community to live a “feast-or-famine” existence. This creates competition in a habitat. survival is dependent upon the rate of nutrient uptake, metabolic rate, and growth rate. Some microorganisms can work together to carry out transformation neither can do on its own, called syntrophy.

Phyla of Bacteria is known from 16S rRNA. Though over 80 phyla have been distinguished, most bacteria come from four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. 

There are rules that should be followed in order to make sure that science does not harm anyone or anything. The number one rule is to register new projects so the science community as a whole is aware of what you are doing. It is also important to make sure that everyone in the lab has proper safety training. PPE must be followed. Gloves should only be used once and then disposed of. This is to ensure the safety of people working in the lab. Work surfaces should be decontaminated. Biological waste should be disposed of properly. All sharp items must be placed in the sharps container. There should be a biological spill kit in case of a biological spill taking place. Fabric chairs should be covered in the lab because fabric is not easy to clean. There are regulations and rules that have to followed. It should be checked that each lab is up to date regularly.

Planctomycetes are gram negative bacteria. This phylum contains two orders, Planctomycetales and Brocadiales.  They have stalks, and their cells are arranged in rosettes. Planctomycetes lack peptidoglycan in their cell wall. Since they lack peptidoglycan in their cell wall, they are resistant to antibiotics like penicillin and cephalosporin, antibiotics that interfere with peptidoglycan synthesis.  Planctomycetes also have cellular compartments that resemble organelles in eukaryotes.

Planctomyces, the best-characterized genus in Planctomycetes, is a stalked bacterium. The stalk has no cell wall or cytoplasm and is used for attachment. Planctomyces habitat is primarily aquatic and is facultatively aerobic chemoorganotrophs that grow by fermentation or respiration of sugars.

Chlamydiae is a phylum of gram-negative bacteria that cause dangerous animal and human diseases. This phylum consists of only one order: the Chlamydiales.  This species of bacteria is obligate intracellular parasites and interacts with a wide variety of eukaryotic host cells and display a distinctive life cycle. The Chlamydiales have two life forms: the elementary body and the reticulate body. Elementary bodies are responsible for transmission of infection and are resistant to drying. The reticulate bodies are noninfectious, and their role is to multiply inside the host cell to form a large inoculum for transmission. Chlamydiales can infect a wide variety of eukaryotes including amoebae. In humans, Chlamydia and Chlamydophila, are the genera of several species. Some of these species cause trachoma and psittacosis amongst other diseases.  Chlamydial infections are one of the leading STDs in the world. The Chlamydiales are some of the most biochemically limited of all known bacteria.

Bacteroidetes contains four orders: Bacteroidales, Cytophagales, Flavobacteriales, and Shingobacteriales. There are more than 700 hundred characterized species across the Bacteroidetes orders. The species in the Bacteroidetes phylum are gram negative nonsporulating rods and be both fermentative and aerobic. The most important order of the Bacteroidetes is the Bacteriodales relative to humans. This order contains a genus, Bacteroides, that is well studied because it is a major component of the human gut.

Bacteroides are the dominant bacteria in the human large intestine and other animals. This genus of Bacteroidales are usually commensals but can occasionally become pathogenic, an example being bacteremia. One of the most important bacteria in the human gut is the Bacteroides thetaiotaomicron. A large portion of B. thetaiotaomicron genome specializes in breaking down complex polysaccharides. This Bacteroides species is responsible for our ability to break down certain plant polymers that we would, otherwise, be unable to do on our own. The human genome does not produce the enzymes that can do this, neither does the human genome encode for these enzymes either.

A major group of gram-positive bacteria includes Actinobacteria. This phylum is commonly found in soil and plant materials and contains primarily aerobic bacteria that are rod shaped to filamentous. The Actinobacteria is mostly made of harmless commensals except for Mycobacterium tuberculosis. Therre are nine orders in Actinobacteria, but most belong to Actinomycetales. Coryneform bacteria belongs to the Actinomycetales. These bacteria are gram-positive, aerobic, and nonmotile. They from irregularly shaped cells, club-shaped or V-shaped cells that are a result of snapping division.

An important branch of the Actinobacteria is the Mycobacterium. This genus contains several important human pathogens, including tuberculosis. This species is rod-shaped and possess a distinctive property called acid-fastness. Mycolic acids, unique to Mycobacterium is responsible for a waxy surface around the cell. This waxy surface causes the cell not to stain well with the gram stain.

Mycobacteria may undergo branching or filamentous growth, but the filaments do not form a true mycelium. Mycobacteria are separated into the slow growing species and the fast growing species with tuberculosis belonging to the slow growing species. Most mycobacteria grow aerobically in mineral salts and use ammonium as its nitrogen source and glycerol or acetate as their sole carbon source and electron donor. Tuberculosis is different and requires fatty acids and lipids.

Another important species of Actinobacteria is the Streptomyces. The Streptomyces are a filamentous species.  Filaments form branching hyphae that then form into mycelium. Streptomyces also form spores called conidia that are distinct from endospores made by Bacillus and Clostridium. Streptomyces is primarily found in the soil. Another important fact is that Streptomyces produce antibiotics.