Bacteria: Gram-negatives and Gram-positives

• Learning Outcome 1: Part 2 focuses on the domain of bacteria in the year 2025.

Contents Overview

• Introduction to general bacteria characteristics
• Study of Aquificae and Thermotogae
• Examination of Deinococcus-Thermus
• Details of Non-Proteobacteria Gram-negatives
• Details of Proteobacteria Gram-negatives

General Introduction

• Bacteria are broadly divided into two groups: Gram-negatives and Gram-positives.
• Gram-negative bacteria include Aquificae & Thermotogae, Deinococci, Non-Proteobacteria, and Proteobacteria.
• Gram-positive bacteria are categorized into low GC and high GC Gram positives.

Aquificae and Thermotogae

• They are thermophilic bacteria examples
• The Aquificae phylum represents the deepest, oldest branch of bacteria.
• Two well-studied genera are Aquifex and Hydrogenobacter.
• Aquifex pyrophilus is a Gram-negative, microaerophilic rod
• Aquifex pyrophilus has an optimum temperature of 85°C and a maximum of 95°C.
• Aquifex is a chemolithoautotroph which captures energy by oxidizing hydrogen, thiosulfate, and sulfur with oxygen as the terminal electron acceptor.
• The original bacterial ancestor was probably thermophilic and chemolithoautotrophic.
• The genome of Aquifex is about a third of E. coli's size and contains genes for chemilithoautotrophy.
• Thermotogae are characterized by an outer sheathlike garment
• Thermotogae grow in active geothermal areas of marine hydrothermal systems and terrestrial solfataric springs.
• The optimum growth temperature of Thermotogae is 80°C, with a maximum of 90°C.
• Thermotoga is a chemoheterotroph with a functional glycolytic pathway
• Thermotoga can grow anaerobically on carbohydrates and protein digests.
• Approximately 24% of Thermotoga genes are similar to those of archaea.

Deinococcus-Thermus

• Most species are mesophilic
• Deinococcus geothermalis and D. murrayi are thermophiles
• Thermophiles grow between 45°C and 55°C
• These bacteria are spherical, rod-shaped, and non-motile, often found in pairs or tetrads.
• The bacteria are aerobic and catalase positive.
• Despite staining Gram-positive, their cell wall includes an outer membrane like Gram-negative bacteria.
• Almost all strains resist desiccation and radiation (3 to 5 million rad of radiation), due to their high DNA repair ability.
• The bacteria's natural habitat is unknown
• The bacteria can be isolated from ground meat, feces, air, and freshwater.

Phylum of cyanobacteria

• Cyanobacteria, also known as blue-green algae, are microscopic organisms naturally found in all types of water.
• They are single-celled organisms that live in fresh, brackish, and marine water.
• Cyanobacteria use sunlight to make their food.
• Cyanobacteria are the largest, most diverse group of photosynthetic bacteria with 56 genera.
• Their diversity is reflected by a wide range of GC content (35 to 75%).
• The photosynthetic apparatus of cyanobacteria closely resembles that of eukaryotes, including chlorophyll a as well as photosystems I and II.
• They are capable of oxygenic photosynthesis, using water as an electron donor.
• Endosymbiotic cyanobacteria are believed to have evolved into chloroplasts.
• Cyanobacteria store glycogen as the reserve carbohydrate
• Many other substances are stored as inclusions
• Most cyanobacteria are obligate photolithoautotrophs, though a few can grow in the dark as chemoheterotrophs.
• Many genera produce geosmins.
• High concentrations of cyanobacteria can be a nuisance in waters, even changing the taste of drinking water.
• Their shape and appearance vary.
• Unicellular colonies of various shapes may form filaments called trichomes
• Filaments are a row of bacterial cells that are in close contact over a large area.
• Although many appear blue-green because of phycocyanin pigment; some isolates appear red or brown because of phycoerythrin pigment.
• They can sense light and use gas vacuoles to position themselves in optimum illumination.
• Reproduction can occur by binary fission, budding, fragmentation, and multiple fission.

Phyla of Chlorobi and Chloroflexi

• Chlorobi and Chloroflexi are two other photosynthetic Gram-negative bacteria.
• They perform anoxygenic photosynthesis employing reduced molecules such as H2S, S, and H2 as electron donors.
• Chlorobi are known as Green sulfur bacteria
• Chloroflexi are known as green non-sulfur bacteria.
• Ecologically, cyanobacteria inhabit the aerated upper layers of freshwater, while the anoxygenic photosynthetic bacteria live in the deep anoxic zones rich in hydrogen sulfate and other reduced molecules.

Phylum Spirochaetes

• The phylum Spirochaetes is characterized by their structure and motility.
• They can be anaerobic, facultative aerobic, or anaerobic.
• Spirochaetes use carbohydrates, amino acids, long-chain fatty acids, and long-chain alcohols as energy sources
• Morphologically unique: slender and long 0.1 to 3 µm by 5 to 250 µm) with a flexible, helical shape.
• Spirochaetes have diverse habitats from mud to the human mouth.
• They lack external rotating flagella but have an axial filament or movement by creeping/crawling
• The role of the outer sheath in Spirochaetes is unknown, but it's essential for survival. Spirocheates die once the sheath is damaged or removed.
• Motility is especially adapted for movement in viscous solutions, and they move in a cockscrew-like fashion.
• Spirochaeta are free-living; living in anoxic and sulfide-rich freshwater and marine environments.
• Leptospira grow in oxic water and moist soil.
• Cristispira live symbiotically in the hindguts of termites and wood-eating roaches and the digestive tracts of molluscs and mammals.
• Treponema denticola and T. oralis live in the oral cavities of animals.
• Spirochaetes from termites' hindguts and freshwater sediments are capable of fixing nitrogen.
• Diseases caused by Spirochaetes are called Spirochitoses
• Treponema pallidum causes syphilis
• Borrelia burgdorferi causes Lyme disease.

Proteobacteria Gram-negatives

• Proteobacteria are diverse, with 500 known genera. The name “proteo” emphasizes the vastness of this group).
• Since Proteobacteria comprise various genera, no particular morphology or metabolic pattern characterizes this group.
• Comparison of the 16S rRNA sequences revealed five lineages:
  • Alphaproteobacteria
  • Betaproteobacteria
  • Gammaproteobacteria
  • Deltaproteobacteria
  • Epsilonproteobacteria
• Members of purple photosynthetic bacteria belong to α, β and y proteobacteria.

Alphaproteobacteria

• The unifying characteristic of this class is that they are oligotrophs
• Oligotrophs are organisms capable of living in low-nutrient environments (deep oceanic sediments, glacial ice, or deep under surface soil).
• Except for Rhodocyclus, all members of purple non-sulfur bacteria are Proteobacteria.
• The bacteria use anoxygenic photosynthesis and possess bacteriochlorophylls a and b.
• Some live within animal and plant cells. Those in animal cells tend to have a genome reduction.
• By contrast, those living in plants have expanded genomes due to gene duplication or horizontal gene transfer.
• The bacterium Wolbachia pipientis is capable of changing the male-to-female ratio in insect progeny or feminize male insects in some cases.
• Alphaproteobacteria are known to be methylotrophic
• Methylotrophic bacteria can grow and use methane as a carbon source.
• Rhizobium grow symbiotically within root nodules cells of legumes as nitrogen-fixing bacteroids.
• Two taxa, Chlamydia and Rickettsia, are obligate intracellular pathogens
• Obligate intracellular pathogens must occur inside other cells "host cells".
• When not growing inside a host cell, Chlamydia and Rickettsia are metabolically inactive outside of the host cell. They cannot synthesize their own adenosine triphosphate (ATP) and rely on cells for their energy needs.

Rickettsia

• Rickettsia are rod-shaped, coccoid, or pleomorphic with a typical Gram-negative cell wall and no flagella, generally small (0.3 to 0.5 in diameter and 0.8 to 2 um long.
• All Rickettsia species are parasitic or mutualistic.
• Parasitic forms grow in vertebrate erythrocytes, macrophages, and vascular endothelial cells.
• Some live in blood-sucking arthropods such as fleas, ticks, mites, or lice, which serve as vectors or primary hosts.
• Rickettsia lacks a glycolytic pathway and does not use glucose as an energy source
• Instead Rickettsia oxidizes glutamate and succinate.
• They enter the host cell by inducing phagocytosis but immediately escape the phagocytic vacuoles and reproduce by binary fission in the cytoplasm.
• Eventually, the host cells burst, releasing new organisms.
  • R. prowazekii causes epidemic typhus.
  • R. typhi causes causes endemic murine typhus.
  • R. rickettsia causes spotted fever.
  • Ehrlichia transmitted by ticks causes ehrilichiosis.
• The order Rhizobiales Contains:
  • Rhizobium symbionts to legumes
  • Agrobacterium pathogens to plants
  • Brucellaeae animal and human pathogen

Betaproteobacteria

• Mainly composed of chemoheterotrophs, photolithotrophs, and chemolithotrophs.
• They mostly use substances that diffuse from organic decomposition in anoxic habitats.
• Some bacteria use hydrogen, ammonia, methane, and volatile fatty acids.
• Betaproteobacteria often grow between aerobic and anaerobic areas (e.g., in mammalian intestines).
• Some genera include species that are human pathogens and are able to cause severe, sometimes life-threatening disease.
• The genus Neisseria includes the bacteria N. gonorrhoeae and N. meningitis which are the causative agents of the STI gonorrhea and meningitidis, respectively.
• Neisseria are non-motile, aerobic, Gram-negative cocci
• They are chemoorganotrophic.
• They often occur in pairs with adjacent sides that are flattened.
• Capsules and fimbriae may be present.
• Oxidase and catalase positive.
• The bacteria inhabit the mucous membranes of mammals.
• Nitrosomonas is a genus comprising rod-shaped chemoautotrophic bacteria.
• These bacteria can oxidize ammonia into nitrite as a metabolic process.
• Nitosomonas is useful in the treatment of industrial sewage or in bioremediation.
• Nitosomonas play an important role in the nitrogen cycle by increasing the availability of nitrogen to plants while limiting carbon dioxide fixation.

Gammaproteobacteria

• Gammaproteobacteria constitute the largest group of proteobacteria.
• They have a diverse physiology from chemoorganotrophic and facultative anaerobes, chemoorganotrophs, photolithotrophs, chemolithotrophs, and methylotrophs.
• According to DNA-RNA hybridization, the y-proteobacteria consists of two deeply branched groups:
  • Purple sulfur bacteria
  • Intracellular parasites.
• Intracellular parasites are legionella and coxiella.
• The two largest groups contain a large variety of non-photosynthetic bacteria classified as RNA superfamily I and RNA superfamily II.
  • RNA superfamily I: Vibrionacaea, Enterobacteriacaea, Pasteurellacaea
  • Rana superfamily II; Pseudomonads, Azotobacter, Acinetobacter
• Purple sulfur bacteria are strict anaerobes and usually photolithoautotrophs
• They are found in anoxic, sulfide-rich zones of lakes, marches, and lagoons
• They oxidize hydrogen sulfite to sulfur and deposit it internally as sulfur granules; the sulfur is often oxidized further to sulfate.
• Hydrogen may also serve as an electron donor.
• Typical examples: Thiospirillum, Thiocapsa and Chromatium.
• Order Methylococcales: order contains one family of methylococcaceae.
• The order is rods, vibrio, and cocci that use methane, methanol, and other one-carbon compounds as the sole carbon and energy source, under aerobic and microaerobic conditions (low oxygen).
• A metabolic pathway involves the conversion of methane (CH4) or other single-carbon (C1) compounds into formaldehyde (HCHO), which can then be utilized for two main processes.
• Note the difference between methylotrophs and methanotrophs
• Examples include Methylococcus (spherical non-motile cells) and Methylomonas (straight, curved, and branched rods with a single polar flagellum.
• They are almost all capable of forming cysts.
• These microorganisms grow above habitats of methanogen archaea all over the world
• Methane cycle in wetlands focuses on methanogenic archaea in anoxic soil layers that produce methane (CH4) from organic matter and methanotrophs in oxygenated areas that convert CH4 into carbon dioxide (CO2).
• Methane is released into the atmosphere through diffusion, ebullition, and plant transport
• The balance between methanogenesis and methanotrophy regulates methane emissions in these ecosystems
• Order Legionellales
• The order has two families: Legionellacaea (with a single genus legionella) and Coxiellacaea. The latter has two genera: Coxiella and Ricketsiella (alpha-Proteobacteria
• All these organisms are intracellular pathogens that display dimorphic lifestyle within the host.
• Legionella pneumophila causes legionnaire's disease.
• It is an intracellular parasite that lives in most soil and aquatic environments, including cooling towers, air conditioning units, and hot tubs.
• In its protozoan host and some human cell culture, L. pneumophila replicates by binary fission to give slender, rod-shaped cells.
• In its infectious form, it forms non-replicative cysts called mature intracellular forms, which are heat-tolerant and resist a variety of antibiotics.
• Coxiella also displays two cell types within the host.
• However, it presents a wide range of hosts, including insects, fish, birds, rodents, sheep, goats, and humans.
• Example: C. brunetti causes Q fever, a flu-like illness.
• The ability of L. pneumonale and C. brunetti to form cysts makes them distinct from Chlamydia and Rickettsia, which cannot survive outside their host.
• Order Pseudomonadales
• Pseudomonads are the most important genus in this order.
• They are straight or curved rods that possess one or several flagella
• They are chemoheterotrophs and usually carry out aerobic respiration.
• In anaerobic strains, nitrite is used as the terminal electron acceptor.
• All Pseudomonads have a functional Tricarboxylic Acid Cycle and oxidize substrate completely
• Most hexoses degrade via the Entner-Doudoroff pathway rather than the Embden Meyerhof pathway.
• Pseudomonads are characterized according to the following:
• Presence of poly-ẞ hydroxyburate
• The production of fluorescent pigment
• Pathogenicity
• The presence of arginine dihydrolase
• Practical Impacts of pseudomonads include:
  • many can degrade a wide variety of organic molecules e.g: fluorescent Pseudomonads can use 80 compounds as carbon source used in sewage treatment
  • P. aeruginosa has served as a model organism in many experimental studies.
  • Some Pseudomonads are major animal and plant pathogens:
  • P. aeruginosa infects people with low resistance.
  • P.syringae is an important plant pathogen.
  • P. fluorescens are involved in spoilage of refrigerated milk, eggs, and seafood; they can grow at 4°C and degrade lipids and proteins.
  • The genus Azotobacter contains organisms that can fix nitrogen for nonsymbiotically.

Order Vibrionales

• This order contains one family: Vibrionacaea
• Members of this family are straight or curved flagellated rods
• Most are oxidase-positive and use D-glucose as a sole or primary carbon and energy source
• The majority are aquatic organisms that live in fresh water and sea
• Several vibrios are pathogens:
  • V. cholera causes cholera
  • V. parahaemlyticus can cause gastroenteritis after consumption of contaminated seafood -V. anguillarum and others are responsible for fish diseases.
• Order Enterobacteriales
  • The largest family is Enterobacteriacaea which includes 44 genera
  • Contains peritrichously flagellated or non-motile, facultatively anaerobic, straight rods with simple nutritional requirements -Often called enterobacteria or enteric bacteria pertaining to the intestine
  • They degrade sugar by means of the Embden-Meyerhof pathway
  • Examples include:
  • E. coli used as a model organism and can cause food poisoning.
  • Salmonella typhi causes typhoid fever.
  • Shigella causes bacillary dysentery.
  • The family can be divided into two groups based on their fermentation products
• Pasteurallales
  • Notably small Bacteria
  • Non-motile and oxidase-positive, with complex nutritional requirements
  • Parasitic to Vertebrates
  • Examples include:
    • P. multocida (fowl cholera caused in chickens, turkeys, ducks, etc.,)
    • P. haemolytica pneumonia from cattle, sheep, and goats
    • P.influenza-causes meningitis

Deltaproteobacteria

• Bacteria are a small class of gram-negative bacteria that includes sulfatereducing bacteria (SRBs) and genera such as Bdellovibrios and Myxobacteria. These bacteria are predators.
• Examples include orders Desulforibrionales, Desulfobacteriales and Desulfomonadales
• Bdellovibrios have a distinctive lifestyle:
  • preying on other Gram-negative bacteria
  • alternates between non-growing predatory phase
  • reproduces itracellularly (takes 1 to 3 hours).
• These bacteria often live in aquatic and terrestrial habitats and play a role in cycling sulfur within the ecosystem
• Often the byproducts of sulfur and sulfate reduction smell like hydrogen sulfide
• The compound H2Sunderside-can kill animals, plants, and microorganisms.
  • Order Bdellovibrionales- -The aerobic, Gram-negative curved rods (polar flagella) -Attach and start at a rate of about 100 revolutions per second -Creating a hole through their host by producing hydrolytic enzyme
  • Order Myxococcales- -Are gram-negative aerobic soil bacteria characterized by gliding motility
  • use amino acids as their major source of carbon, energy and nitrogen

Epsilonproteobacteria

• The bacteria are the smallest and are all slender Gram-negative rods which can be straight, curved, or helical.