Table of contents :

• sizes : from 0.15-0.25 mm (Mycoplasma) up to 1.5 mm (10 mm length in Bacilli and Clostridia, 20 mm length in Spirochaetales; up to 80 mm in swarming forms of Proteus).
• cytoplasmic or plasma membrane or plasmalemma (a.k.a. inner membrane in Gram -ve Bacteria):

Lipids are unbranched fatty acids linked to glycerol by ester bonds (only Aquifex pyrophilus has ether linked lipids).  The fatty acids of Escherichia coliare mostly palmitic (16:0), palmitoleic (16:1), and cis-vaccenic (18:1). These all contain an even number of C atoms : traces of longer and shorter fatty acids also occur. Eukarya and Cyanobacteria have fatty acids with 2 or more double bonds, whereas most Bacteria contain only mono-unsaturates : only Mycobacteria have polyunsaturated fatty acids (PUFAs). Insertion of double bond may occur by 2 mechanisms.
• anaerobes and facultative anaerobes simply omit a reductive step during synthesis. When precursor reaches C₁₀, they produce a cis double bond which cannot be further reduced (they can only reduce trans double bonds). Further elongation gives palmitoleic and cis-vaccenic acids. Another enzyme can isomerize cis => trans at the double bond, thus producing a mixture of cis and trans C₁₀ precursors. The trans precursors go on to become saturated FA, while the cis ones become unsaturated. Note that the previous reaction has two enzymes: a "short" isoenzyme for C₈ and below and a "long" isoenzyme for C₁₂ and above.Similar O₂ dependent hydroxylation is required for steroid synthesis, but only the cell wall-less Bacteria has sterols in the plasma membrane.
• obligate aerobes introduce the double bond after full elongation of the FA chain. Hydroxylation using molecular O₂ is followed by removal of H₂O to leave C=C. May be repeated to give polyunsaturates.
Most represented lipids are PE (65%), PG (18%) and DPG (a.k.a. cardiolipin) (17%) : PC (lecithin), PS and PI are rare, on the contrary of Eukarya. Bacteria can be identified on peculiar phospholipid composition if growing under standard conditions. Cocci present abundant aminoacyl- (Lys-, Ala-, Orn- and/or Gly-) PG and -DPG. . In stationary phase E. coli converts its UFAs to cyclopropane FAs (the methylene group comes from the one carbon pool via S-adenosyl Met) : this is thought to be a protective mechanism but this theory is unproven. In E. coli the change is due to increase in synthesis of only cis-vaccenic acid but not palmitoleic one. E. coli contains 2 fatty acid condensing enzymes, which catalyze the elongation reaction. Enzyme I works well up to the C₁₄ precursor for C₁₆ products. It cannot elongate C₁₆ to C₁₈. Enzyme II can elongate C₁₆ to C₁₈, but only if C₁₆ precursor is unsaturated. Hence, all the cis-vaccenic acid produced in E. coli is due to operation of condensing enzyme II. Enzyme II is inherently sensitive to temperature. At low temperatures, a lot of cis-vaccenate is made; at high temperatures, much less. In Bacillus, where double bonds are made by the O₂ insertion pathway the desaturation enzymes are induced by a drop in temperature and inactivated by an upshift. Plasma membrane also contains :
• transport systems : membrane transport proteins are crucial for maintaining a selective internal cellular environment
• glycerol is the only known substrate that undergoes facilitated diffusion in some Bacteria
• active transports may occur
• in the classical (non-modifying) pathway
• (in anaerobes and facultative anaerobes) through group translocation [e.g. Glc entry within the cell with the phosphoenolpyruvate:phosphotransferase (PEP:PTS) system : PEP =(enzyme I)=> HPr => enzyme III-P => enzyme II-P => Glc/GlcN/2-dGlc/Fru/Man-P. For Man transport no enzyme III is necessary. Only enzymes II and III are substrate specific]
• the largest subset of membrane transport proteins is the major facilitator superfamily (MFS), which convert electrochemical gradients into substrate concentration gradients, and transport ions, sugars, sugar-phosphates, drugs, amino acids and other hydrophilic solutes. In bacteria, MFS proteins are primarily responsible for nutrient uptake, although some act as drug-efflux pumps and are involved in the development of antibiotic resistance. Protonation and binding of substrates induce several conformational changes resulting in switching of the opening of the hydrophilic cavity from the periplasm (outward-facing) to the cytoplasm (inward-facing), thereby allowing transport of substrates across the membrane.
• while simple membrane bilayers are inherently moderately permeable to ammonia, the transport protein AmtB (11 membrane-spanning helices), present in the bacterial inner membrane between the cytoplasmic and periplasmic spaces, may serve to accelerate uptake at sites where ammonia diffusion is too slow for physiological needs. AmtB has the same trimeric structure when crystallized in both the absence and presence of ammonia : it is a channel rather than a transporter that should have flexible elements involved in translocation of the substrate. At either ends of the pore, broader vestibules contain ammonia in equilibrium with ammonium. In AmtB's center midway through the membrane is a hydrophobic pore element roughly 20 angstroms long that allow ammonia to pass but not ammonium or other ions. The trimeric structure of AmtB uncovered now suggests how the 3 Rh polypeptides (to which AmtB is genetically related) of RBCs form the Rh antigen complex in the erythrocyte plasma membrane. They add that these findings could help predict how Rh-related proteins in the mammalian kidney collecting duct and liver mediate ammonia transport.
• lactose permease (LacY) catalyses the symport of b-galactosidase with H⁺
• glycerol-3-phosphate transporter (GlpT) catalyses the exchange of glycerol-3-phosphate with inorganic phosphate.
• enzymes for the late stages in biosynthesis of phospholipids, lipopolysaccharide, peptidoglycan and other envelope components.
• enzymes for energy transduction (including both energy generation by respiratory chain and energy consumption) :
• aerobic dehydrogenases & oxidases (NADH dehydrogenase, succinate dehydrogenase, glycerol3P dehydrogenase, lactate oxidases ("dehydrogenases"), pyruvate oxidase, Pro oxidase)
• anaerobic dehydrogenases (formate dehydrogenase, glycerol3P dehydrogenase, hydrogenase)
• terminal reductases (cytochrome o complex, cytochrome d complex, nitrate reductase, fumarate reductase, trimethylamine oxide reductase)
• enzymes using proton motive force (PMF) (ATP synthase, flagellar motor, energy linked transhydrogenase, many permeases).
Although chemiosmosis occurs mainly in mesosomes, sometimes it involves non infolded plasma membrane.
• structural genomics
• nucleoid or nuclear region = the region in which the aploid genome is contained (not to be confonded with the nucleoid  in Eukarya peroxisome !). As they are aploid, every missense mutation in the genome become immediately detectable under phenotype analysis (e.g. Ames test for detecting mutagenic compounds). It usually consists of a single negatively supercoiled (by DNA gyrase and topoisomerase IV) circular dsDNA molecule, but in Streptomyces and Borrelia it is linear, while in Rhodobacter sphaeroides there are 2 chromosomes. Only polyamines and histone-like proteins (e.g. : HU and H in E.coli) are associated with DNA, but they are far less represented than in Archaea ("naked" molecule). All Bacteria genomes that have been sequenced at NCBI.
• chromosome : in bacterial genetics, a closed circle of double-stranded DNA that contains the genetic material of the cell and is attached to the cell membrane; the bulk of the material forms a compact bacterial nucleus (called also chromatinic body).
• genome size varies from 0.58 Mbp in Mycoplasma genitalium to 4.4 Mbp in Mycobacterium tuberculosis and Escherichia coli
• G+C percentage contents (melting point analysis) varies between 28% (in Clostridium) to 72% (in Sarcina).
• preferential positioning of bacterial genes in the leading strand was thought to result from selection to avoid high head-on collision rates between DNA and RNA polymerases. Here we show, however, that in Bacillus subtilis and Escherichia coli, essentiality (the transcript product), not expressiveness (the collision rate), selectively drives the biased gene distribution
• DNA duplication occurs via rolling circle (s structure) or via Cairns model (q structure). RNA primers are synthetized by RNA polymerase or by primase. Other required proteins are :
• DNA pol I aeqbtgd (secondary 5'=>3' polymerase, 3'=>5' and 5'=>3' exonuclease)
• DNA pol II (?)
• DNA pol III (main 5'=>3' polymerase, 3'=>5' and 5'=>3' exonuclease)
• type I and type II (a.k.a. DNA gyrase ab) topoisomerases
• DnaA (ori recognition), DnaB (helicase), DnaC (drives DnaB), DnaT (ter recognition)
• SSB proteins
• DNA ligase
It is often slower (10⁶ bp / 5 x 10⁴ bpm = 40' average) than cell cycle period and therefore new rounds of synthesis are initiated by the cell even though the previous copy has not fully replicated. Chromosomes origins are always plasma membrane-bound.
• modification : a mantainance methylase create N⁶-methylA and N⁴-methylC (less than 1%) during chromosome replication using SAM as donor.
• restriction : some plasmid or chromosome-coded restriction endonucleases specifically degrade viral DNA but not bacterial (modified) DNA.
• look here for plasmids and episomes.
• look here for bacteriophages
• look here for transposons.
• Bacteria parasexuality
• bacterial transformation : the exchange of genetic material between strains of competent Bacteria (i.e. expressing a DNA binding protein) by the transfer of a fragment of naked DNA from a donor cell to a recipient cell, followed by recombination in the recipient chromosome. DNAase sensitive.
• in Gram +ve Bacteria an ectoendonuclease degrades environmental DNA up to 7-10 kbp fragments : ssDNA molecules enter the cytoplasm
• in Gram -ve Bacteria dsDNA molecules enter the cytoplasm
Cotransformation assays after endonuclease digestion may be used to create genetic maps. Homologous or general recombination may occur if transferred DNA is homologous.
• transduction
• specialized transduction by temperate lysogenic (bacterio)phages (e.g. l) (once every 10^6-7 times prophage excision isn't precise and a deleted / substituted particle results, containing gene(s) adjacent one side of insertion site : when l transduces gal it loses the tail and b genes; when l transduces bio it loses int, xis and N)
• generalized transduction by virulent lytic (bacterio)phages (e.g. P₁) (after endonuclease digestion, a randomly chosen chromosome segment may be inserted into the capsid)
The recipient spectrum is extablished by host spectrum of the carrier virus. As next infected cell becomes a partial diploid (merozygote : homogenote if homozygotic; heterogenote if heterozygotic), some recombinations may occur between exogenote (the extra piece of genetic information introduced by transduction into the recipient cell by the donor cell) and endogenote (the recipient cell's own complement of genetic information).
• abortive or additional transduction (Campbell model : no recombination occurs and so the acquired DNA is lost in following generations)
• complete or substitutive transduction (homologous or general recombination occurs and so the acquired DNA is replicated and mantained in following generations)
• conjugation : in replicative transfer a nick in oriT creates a 3' end in a plasmid, which enter the pilus of the F⁺ (male) Bacteria and reaches pilus receptor OmpA on the F^- (female) cell (average speed : 40 Kbp / min at 37°C). Then pilus depolymerization allows cells to come nearer and the transfer occurs. At the end of the process both cells are F⁺. No recombination occurs with the host chromosome, except for site-specific integration (plasmid => episome) : if the latter occurs, the bacterium is named F'.
• F-duction = F' x F^-. If episome exiting is poorly precise, also chromosomal genes can be transuced. At the end of the process the F^- cell remains F^- because the tra genes can be transferred only after all the chromosome genes have been transduced : as such a process would require an average total duration of 1h 40', it has a very low likelihood to occur. Interrupted conjugation may be used to create a map (in minutes) of the chromosome genes. As the recipient Bacteria becomes a partial diploid (merozygote : if homozygote : homogenote; if heterozygotic : heterogenote), homologous or general recombination may occur between esogenote and endogenote.
• functional genomics
• Bacteria contain one only kind of RNA polymerase with abb'sw subunits coded respectively by rpoA, rpoB, rpoC and rpoD genes. Promoters contain -35 and -10 (Pribnow box) consensus sequences. Transcription occurs at an operon level and higher-than-operon regulatory networks exist => polycistronic mRNAs. E.g. :
• lac operon : lacZ (b-galactosidase), lacY (lactose permease), lacA (thiogalactoside transacetylase), lacI (aporepressor). The lactose catabolite allolactose acts as and inducer preventing the repressor from binding the operator, but anyway, when glucose is available, [cAMP]_i is too low to activate CAP and so the latter cannot activate the promoter (see also diauxia).
• trp operon : trpE, trpD, trpC, trpB, trpA, trpR (aporepressor)
• transcription ending may be poly-A dependent or Rho-(stem-loop)-dependent. mRNA average life is 40" at 37°C (degraded by RNAase III). Few kinds of RNA processing (no gene contains introns).
• DNA invertases segregate into 2 evolutionarily distinct families of site-specific recombinases : Tyr-specific recombinases (Tsrs) and Ser-specific recombinases (Ssrs). They can modulate gene expression at multiple loci scattered throughout the genome.
• ribosomes = about 10⁴ per Bacteria cell (less than in Archaea), sometimes membrane-attached in a polysome-like manner. 70S complexes [30S subunit (= 21 S proteins, 16S rRNA (about 1542 nucleotides)) + 50S subunit (= 34 L proteins, 23S rRNA (about 2900 nucleotides))]. The initiator amino acid in protein synthesis is N-formylMet, obtained by formylation of Met-tRNA^Met. 40÷60 different tRNA^Aaa exist. The translation framing is ensured by interaction between Shine-Dalgarno sequence at 5' end of mRNA and 3' end of 16S rRNA.
• post-translational modifications : few kinds
• N-deformylation of Met
• adenilylation
• deamination
• acetylation
• proteolysis ...
• accessory apparatuses
• inclusion bodies (not surrounded by membranes, on the contrary of Eukarya inclusion bodies !) =
• volutin : a complex molecule containing large amounts of orthophosphate polymers (polymetaP_i), nucleoprotein, and lipid, occurring as cytoplasmic granular inclusions (granules) in certain bacteria (e.g. Babes-Ernst granules in Corynebacterium spp.), yeasts, yeastlike fungi, and protozoa, and serving as an intracellular phosphate reserve. Because volutin granules stain red with blue basic dyes they are sometimes called metachromatic granules
• polar bodies : metachromatic granules located at one or both ends of a bacterial cell.
• poly-b-hydroxybutirate (PHB) or other b-alkanoic acids
• glycogen
• S = only in some photosynthetic Monera
• mesosome = a localized infold in the plasma membrane (more abundant in Gram +ve). This is the site for chemiosmosis in nitrifying Bacteria, chromatophores in purple sulfur Bacteria, cylindrical vesicle in green Bacteria and multilayered membrane thylakoids in Cyanobacteria. They bind the chromosome and, like the latter, duplicate themselves during binary fission, when an accessory septal mesosome appears.
• ectocellular components
• cell wall = the multilayered sacculusthat surrounds the plasma membrane (absent constitutively in Mycoplasma, Ureaplasma, Spiroplasma and Anaeroplasma genera and temporarily in L-phase variant of certain bacteria, induced by osmotic shock, temperature shock, or the presence of antibiotics, and consisting of a spherical or ellipsoidal body without a rigid cell wall. The cells are capable of growth and multiplication; they may be stable or may revert to a normal bacterial cell)

It confers resistance to osmotic shock allowing intracellular concentration up to 1 M, corresponding to an osmotic pressure p = s ^. M ^. R ^. T ~ 1 ^. 10^{3 .} 8,31 ^. 310 ~ 15÷20 atm. It is mainly made up of peptidoglycans (PGN) / mureins / mucopeptides, whose synthesis occurs as follows :
• cytosolic phase (N-acetylmuramylpeptide synthesis) : note that assembly is reversed relative to direction in protein synthesis (please note often GlcNAc and MurNAc are wrongly referred as NAG and NAM, respectively).
• Fru-6-P + Gln ===> Glu + GlcN-6-P
• GlcN-6-P + acetyl-CoA ===> GlcNAc-6-P
• GlcNAc-6-P ===> GlcNAc-1-P
• GlcNAc-1P + UTP ==> UDP-GlcNAc + PP_i
• UDP-GlcNAc + PEP =PEP transferase===> UDP-GlcNAc-enol pyruvyl ether
• UDP-GlcNAc-enol pyruvyl ether + NADPH + H⁺ ===specific reductase===> UDP-MurNAc (i.e. : 3-O-lactyl-GlcNAc) + NAD⁺
• UDP-MurNAc + L-Ala-tRNA^L-Ala ===specific ATP-dependent ligase===> [ ]² + L-Ala-tRNA
• [ ]² + D-Glu-tRNA^D-Glu===specific ATP-dependent ligase===> [ ]³ + D-Glu-tRNA
• [ ]³ + diaminoacid-tRNA^diaa ===specific ATP-dependent ligase===> [ ]⁴ + diaminoacid-tRNA. Diaminoacid is Lys in Gram +ve and mesoDap in Gram -ve Bacteria.
• L-Ala ==Ala racemase===> D-Ala
• D-Ala + D-Ala ==D-Ala-D-Ala synthetase==> D-Ala-D-Ala
• [ ]⁴ + D-Ala-D-Ala ===specific ATP-dependent ligase==> UDP-MurNAc-L-Ala-D-g-isoGlu-diaminoacid-D-Ala-D-Ala
• UDP-MurNAc-L-Ala-D-g-isoGlu-diaminoacid-D-Ala ===specific amidotransferase===> UDP-MurNAc-L-Ala-D-g-isoGln-diaminoacid-D-Ala-D-Ala (muramyl pentapetide)
• membrane phase (GlcNAc-MurNAc-peptide synthesis by the bactoprenol / undecaprenol / C₅₅-prenol-P cycle)
• UDP-MurNAc-L-Ala-D-g-isoGln-diaminoacid-D-Ala-D-Ala + undecaprenol-P ===> UMP + undecaprenol-P-P-MurNAc-L-Ala-D-g-isoGln-diaminoacid-D-Ala-D-Ala (Park and Strominger nucleotide)
• undecaprenol-P-P-MurNAc-L-Ala-D-g-isoGln-diaminoacid-D-Ala-D-Ala + UDP-GlcNAc ===> UMP + undecaprenol-P-P-MurNAc(-GlcNAc)-L-Ala-D-g-isoGln-diaminoacid-D-Ala-D-Ala (lipid pentapeptide or lipid II)
• [undecaprenol-P-P-MurNAc(-GlcNAc)-L-Ala-D-g-isoGln-Lys-D-Ala-D-Ala + 5 Gly-tRNA^Gly ====> undecaprenol-P-P-MurNAc(-GlcNAc)-L-Ala-D-g-isoGln-diaminoacid(-L-Gly)₅-D-Ala-D-Ala+ 5 tRNA^Gly ] (only in Gram +ve Bacteria, see below)
• membrane flippase (?)
• parietal phase (formation of crosslinks among base unit and peptidoglycan chains). The cross-linking reaction occurs outside the cytoplasmic membrane where there is no supply of ATP : energy comes from hydrolysis of terminal D-Ala-D-Ala bond. The outermost D-Ala is lost and the inner D-Ala is bound either to the 5^th glycine (Gram +ve Bacteria) or to the side chain carboxyl of DAP (Gram -ve Bacteria). In Gram -ve multiple random cross links between many chains occur. In Gram +ve relatively few cross links occur and many side chains are not cross-linked : DD-carboxypeptidase I removes terminal D-Ala "inactivating" some side chains. In E.coli there are at least 6 different penicillin-binding proteins (PBPs) : p91^PBP1 and p66^PBP2 have only transpeptidase activity, p60^PBP3 has both transpeptidase and transglycosylase activities, p49^PBP4 has endopeptidase and carboxypeptidase activities, p42^PBP5 and p40^PBP6 are DD-carboxypeptidase.
• NAM in lipid II is linked by the transglycosylase activity of PBP to a NAG in the peptidoglycan
• undecaprenol-P-P-MurNAc(-GlcNAc)-L-Ala-D-g-isoGln-diaminoacid(-L-Gly)₅-D-Ala-D-Ala + (peptidoglycan)_n ===transpeptidase activity of PBP===> (peptidoglycan)_n+1 + undecaprenol-P-P + D-Ala
• undecaprenol-P-P + H₂0 ==specific phosphatase==> undecaprenol-P +P_i
Autolysins or endopeptidases reshape cell walls in actively growing cells by breaking specific bonds in peptidoglycans and offering reactive groups to transpeptidase activity of PBPs.
On the basis of Gram differential stainingBacteria are divided in .. :
• Gram +ve Bacteria. Theircell walls are thick, consisting of
• about 50 layers of highly cross-linked peptidoglycan. NAM is linked to a L-Ala-D-g-isoGlu-L-Lys-D-Ala-(D-Gly)₅ peptide, which then transpeptidase cross-links to L-Ala in another peptide via e-Lys amino group. The (D-Gly)₅ bridge allows binding among different layers of peptidoglycan : it is absent in Micrococcus spp..
• ... non-peptidoglycan components :
• teichuronic acids (uronic acid b-polymers)
• teichoic acids
• (glycerolphosphates)_20-30 (e.g. Staphylococcus epidermidis)
• (ribitolphosphates)_20-30 (e.g. Staphylococcus aureus)
... a- and/or b-phosphodiesters : the latter forms an ester with the C-6 OH- in NAM of peptidoglycan. Absent in Micrococcus spp..
• lipoteichoic acid (LTA) (in Streptococcus spp.) : it arise from the outer layer of the plasma membrane.
• polysaccharide C (in Streptococcus spp.)
• protein M (in Streptococcus spp.)
• protein A (in Staphylococcus spp.) : binds to Fcg preventing binding to FcgRs.
Please note that although some Mycobacterium spp. and some Nocardia spp. are classified as Gram +ve Bacteria (due to their thick peptidoglycan layers), they often give a weak or a variable gram reaction caused by the presence (in the cell wall) of lipids :
• mycolic acids ...
• glucose-6-monomycolate (GM)
• mycoside C
• trehalose -6-monomycolate (TMM)
• trehalose-6,6'-dimycolate (TDM, a.k.a. cord factor)
... covalently linked to ...
• arabinogalactan (AG)

... to form ...
• mycolarabinogalactanpeptidoglycan
• lipoarabinomannan (LAM)
• glycopeptidolipid (GPL)
• phosphatidylinositolmannosides (PIM)
• sulfatides
• wax D
• C₂₇-phtyenoic acid
Such a cell wall resists many stainings, but not alcohol- and acid-fast Ziehl-Neelsen differential staining. In peptidoglycan MurNAc is substituted by MurNglycolyl and tetrapeptide is L-Ala-D-g-isoGlu-mesoDap as in Gram -ve Bacteria (see below), but, on the contrary of these,peptide crosslinks may occur even between mesoDap residues.
Protoplast = a Gram +ve Bacterium which appears as Gram -ve because deprived of its cell wall (by using lysozime) and maintained in hypertonic solution to prevent osmotic shock. It is still alive but cannot undergo repliction.
• Gram -ve Bacteria. Theircell walls consist of ...
• ... outer (or parietal) membrane that confers negativity at Gram staining. On the contrary of the common biological membranes, it is unpermeable to lipophilic compounds and permeable to hydrophilic compounds. It contains :
• in both the inner and the outer layers
• protein A : binds peptidoglycan
• phospolipids : more PE and less PG than in the inner membrane
• trimeric porins
• non-specific
• p38^OmpF decreases in high p (receptor for TuIa, T2 and ColA phages)
• p37^OmpC increases in high p (receptor for TuIb, Mel and 434 phages)
• p34^OmpD in Salmonella typhimurium
• specific
• PhoE porin favorites entry of phosphate (or similar anions) during phosphate limitation (receptor for TC45 phage)
• LamB porin is induced by Mal  (receptor for l phage)
Porins cover approximately 60% of cell surface. They are often named according to electrophoresis migration pattern (protein B, C,...) : sometimes wrongly named matrix proteins. Their pore have Ø ~ 1 nm ; they have no contact with peptidoglycan. They are also present in the outer membrane of mitochondria in Eukarya cells, supporting endosymbiotic theory.
• minor proteins are mostly receptors for molecules too large to get through pores formed by porins. Most are also receptors for phage and colicins (as are the major proteins), or are involved in iron transport.
• siderophores : biological iron chelators
• catechols :
• enterochelin / enterobactin is a cyclic trimer of 2,3-dihydroxybenzoylserine (DHBS), OM receptor is p81^FepA protein (also a receptor for ColB and ColD phages). The FepB protein is the inner membrane permease. The Fes protein is an esterase which hydrolyses Fe³⁺ - enterochelin into DHBS-Fe³⁺monomers. Such monomers may be easily reduced to the Fe²⁺ form which is used in biosynthesis. E. coli synthesizes enterochelin. Iron-laden enterochelin (or dihydroxybenzoyl-serine, a breakdown product of enterobactin) is bound by lipocalin 2
• hydroxamates :
• ferrichrome is not synthetized by E. coli but only by Fungi, e.g. Penicillium. Despite this, many Bacteria have receptors for Fe³⁺/ferrichrome, hence stealing the fungal siderophores. Albomycin is an antibiotic analog of ferrichrome, made by the Fungi to kill such dishonest Bacteria ! OM receptor is p78^FhuA/TonA (also a receptor for  Tl, T5, f80 and ColM phages), while inner membrane receptor is FhuB.
• aerobactin and its receptor system are made by E. coli carrying the ColV plasmid (also coding for colicin V, which eliminates competing E. coli by binding to the p74^Cir, a carrier for Fe³⁺ which is also a receptor for ColI and ColV phages). Such E. coli are often virulent - due, in part, to aerobactin which can scavenge Fe from transferrin, while most other bacterial siderophores bind iron less strongly.
• The 2 siderophore variants produced by M. tuberculosis, the cell-associated and soluble mycobactins (MBTs), and the Y. pestis siderophore, yersiniabactin (YBT)^ref, all have salicyl-capped non-ribosomal peptide-polyketide hybrid scaffolds


• p26^Tsx : carrier for nucleosides; receptor for T6 and ColK
• gp66^BtuB/Bfe : carrier for vitamin B₁₂; receptor for BF23 and ColE
• p75^Iut: carrier for Fe-aerobactin, receptor for CloacinDF13 (on ColV plasmid)
• p76^FhuE : carrier for Fe-coprogen
• p81^FecA : carrier for Fe-citrate
• p83^Fiu : carrier for Fe³⁺
• in the inner layer only :
• p7^{lipoprotein (Braun protein)} : it is bound via its -NH₂ group of C-terminal Lys to carboxyl group of every 10-12^th (on average) Dap residue in peptidoglycan. N-terminus is glyceryl-Cys : 2 fatty acids are attached to glycerol moiety by ester links and a fatty acid is bound to Cys by amide bond. Only one lipoprotein out of 3 is linked to peptidoglycan.
• in the outer layer only :
• enterobacterial common Ag (ECA) is an acidic polysaccharide of GlcNAc, ManUANAc and 4-acetamido-4,6-dideoxy-D-Gal, covalently bound to a phospholipid.
• K antigens are specific capsular polysaccharides made by most Enterobacteriaceae. Some are anchored by lipid tails.
• colanic acid contains Glc, Gal, Fuc and GlcUA. It is made in response to adverse environmental conditions (high p, low T, or dessication).
• OmpA protein is the receptor for the F-pilus during mating.
• phospholipase
• lipopolysaccharides (LPS) / endotoxins are synthetized on the inner membrane via the undecaprenol-P pathway and then transfered in the outer one. Look here for purification methods, dosing methods and biological effects. Assembly occurs on cytoplasmic membrane: then it is translocated to OM via the Bayer patches. LPS covers approximately 30% of cell surface. It is made up of ... :
• lipid A (the immunogenic portion of LPS)
• class I  (GlcN-b(1->6)-GlcN-glycophospholipid). C-4' and C-1 bind P groups, C-3' binds KDO, N binds 3(or b)-hydroxymiristic acid (BHM), C-4 and C-6' bind lauritic, palmitic or D³-miristoxymiristic acid
• class II (3-aminoGlcN-b(1->6)-GlcN-glycophospholipid). No phosphate groups. It is less immunogenic than class I.
• polysaccharide
• constant R core (-2-keto-3-deoxyoctonic acid (KDO)-L-glycero-D-mannoeptose-GlcNAc-Gal-Glc-). Ra, Rb, Rc, Rd and Re mutants have defective R cores due to different mutations in the rfa operon.
• variable side chain or somatic O antigen (D-Abe(a1->3)Man(a1->4)L-Rha(b1->3)Gal(b1->3))_n-40. Stabilized by Ca²⁺ and Mg²⁺. Other sugars in the side chain may be Fru, Tet, 4-aminoAra, GlcU, GalU : sometimes the side chain is immunogenic (Bacteroides fragilis), alternatively it may be substituted by haptens (e.g. Ag T1 (polyRib+polyRibGal), Ag T2 (GlcA) and the enterobacterial common Ag (ECA : poly(GlcNAc-ManUANAc-4-acetamido-4,6-dideoxy-D-Gal),  partially esterified with palmitic acid)) : the latter may become immunogenic). When LPS has no O chain, the strain is called R  for the aspect of their colony (rough), otherwise S (for smooth) : not to be confused with R and S definition for capsule absence/presence ! The transfer of the O chain from the lipid carrier to the core-lipid A complex is mediated by rfbT (in rfb operon) and rfaT (in rfa operon)
Both LPS and OMPs may act as receptors for bacteriophages. Receptors for P1, T4, and T7 include both protein and LPS components. Mutants defective in LPS sugars change their phage susceptibility. Thus E. coli O8 adsorbs phage Omega8 (binds to the O8 O-antigen) whereas E. coli K-12 (no O-antigen) does not. E. coli K-12 phages specific for the LPS include : U3 (it requires presence of Gal at the end of core), C21 (it only adsorbs if final Gal is absent => exposure of Glc), Br10 (it requires phosphate on heptose), Br2 (it requires inner Glc(Gal)-Glc in core) and FP1 & T4 (they require heptose in inner core).
• periplasm or periplasmic space/gel = the region (5-7 nm) between the inner and the outer membranes (please note sometimes it is wrongly defined as the region between the inner membrane and the peptidoglycan layer). It contains :
• the monolayered cell wall : NAM units are linked to a L-Ala-D-g-isoGlu-mesoDap-D-Ala peptide, which then transpeptidase crosslinks to L-Ala in another peptide via the remaining mesoDap amino group.
• osmotical shock-sensitive binding protein transports, functionally linked to the specific porins (e.g. : in E.Coli Mal enters through LamB, MalF, MalG and MalK; also transport systems for Ara, Gal, His, Leu, several other amino acids and sugars, phosphate, sulfate, vit B₁₂ and vit B₁ exist)
• scavenging enzymes such as asparaginase, acid phosphatase, alkaline phosphatase, carboxypeptidase-II, endonuclease-I, 5'-nucleotidase (UDP-glucose hydrolase).
• protective enzymes which inactivate antibiotics
• membrane derived oligosaccharides (MDO) contain 8 to 10 Glc residues linked by b(1->2) and b(1->6) bonds and carrying phosphoglycerol side chains. They increase when osmolarity of the medium drops.
• Bayer sites : temporary discontinuities in peptidoglycan allow limited regions of adhesion between outer and inner membrane. These are sites of entry for phage DNA in many cases. Uncertain structure  - also unknown whether they are short lived or permanent. Observed under EM by phage attachment and by binding of antibody/ferritin complex to newly made O-antigen.
Spheroplast = a Gram -ve Bacteria partially deprived of its cell wall by using lysozime (and maintained in hypertonic solution to prevent osmotic shock)
Secretion systems in Gram -ve Bacteria(exporting molecules through both inner and outer membranes)
• type I
• type II (the main terminal branch of the general secretory pathway)
• type III (injects toxins directly into target cells through a needle or translocon)
• type IV
• type V

• cytoskeleton : in bacteria, the cell wall is generally considered to be the primary determinant of cell shape. However, this has been called into question, most recently by the discovery of the Mollicutes (Mycoplasma, Acholeplasma, and Spiroplasma). Mollicutes are the smallest and simplest free-living and self-replicating cells within prokaryotes, and they are enveloped only by a cholesterol-containing cell membrane. Despite the lack of a cell wall, these cells have distinct morphologies, and their peculiar mode of movement that occurs in the absence of appendages normally implicated in motility (e.g., flagella or secretion organelles) makes the existence of an internal cytoskeleton likely. Williamson^ref first reported the isolation of a cytoskeleton upon cell lysis and sodium deoxycholate extraction of Spiroplasma isolated from Drosophila. Cytoskeletal elements have also been released from Spiroplasma cells by repeated freezing and thawing^ref. Townsend et al.^ref also developed methods for purification of the membrane-associated fibrils from S. citri and suggested that they may be involved in motility. Electron microscopy and SDS gel electrophoresis have shown that S. melliferum possesses a cytoskeletal ribbon comprosed of 4- to 5-nm-wide fibrils with an axial repeat of 9 nm; these fibrils form pairs within the ribbon and are composed of the 55-kD fibril protein^{ref1, ref2}. Townsend and Plaskitt^ref further used immunogold staining of thin sections with an antibody to p55 to localize the ribbon built of the fibril protein within S. melliferum cells. More recently, the structure and localization of this cytoskeleton was described as a flat, monolayered, membrane-bound ribbon composed of 6 or 7 pairs of fibrils following the inner, shortest helical path of the cell^{ref1, ref2}. The fibril protein, which is completely unrelated to any other eukaryotic or prokaryotic protein and has been found exclusively in the genome of Spiroplasma^ref, was identified as the only component of this ribbon^ref. Because this protein would have a diameter of about 5 nm, assuming a spherical shape, it was proposed that the subunit of the fibrils is a tetramer and that the filaments form pairs to give the 10-nm axial and lateral spacings in the cytoskeletal ribbon^ref. Tomographic studies^ref of intact vitrified S. melliferum cells, however, reveal a more complex pattern of filamentous structures just underneath the cell membrane. 2 types of filaments (thin and thick) are arranged in parallel, anchored to each other and to the cell membrane, and jointly form three ribbons that span the entire cell from the blunt to the tapered end. By calculating the Hough transformation of the filament regions in several tomograms and finding the position of the highest contrast, we determined the number and spacings of the individual filaments. The 2 outer ribbons consist of five thick filaments with a spacing of 11 nm. These 2 ribbons are joined together by nine thinner filaments with a spacing of 4 nm. Depending on the extent of twisting of the cell and the position of the filaments with regard to the direction of the electron beam during data acquisition, five or locally fewer than five thick filaments are visible in the tomograms. Using 3D visualization, the arrangement and path of the 2outer ribbons underneath the cell membrane through the entire cell body was illustrated. Although the ribbons cannot be visualized as continuous bands along the cell membrane of the whole cell because of the "missing wedge" problem^ref, it becomes clear that the ribbons follow, in parallel, a helical path from one end of the cell to the other. By calculating the geodetic line^ref (i.e., the fastest connection between two arbitrary points on the 3D cell membrane), we could also show that one of the two outer ribbons is locally shorter; indicating differential length changes of the 2 ribbons. What is the protein composition of the ribbons? We have been able to show that isolated and purified filaments composed of the fibril protein exist in pairs with a total thickness of about 10 nm; hence, we suppose that the two outer ribbons of the S. melliferum cytoskeleton are made of the fibril protein. Our structural data showing two different filaments in the cytoskeleton of S. melliferum raises the question of the identity of the second protein. Until recently, there has been an ongoing controversy about the existence of actin or actin-like proteins in prokaryotes, including Mollicutes^ref. Bacterial homologs of actin were first identified when the cell-shape determinants MreB and Mbl (MreB-like) were shown to assemble into helical filamentous structures that run in spirals around the periphery of the cell under the cytoplasmic membrane in Bacillus subtilis^ref. Depletion of MreB induced the formation of rounded inflated cells that was ultimately lethal. This phenomenon was also reported for Escherichia coli^{ref1, ref2}. MreB has been found only in bacterial species with rod-shaped, filamentous, or helical cells^ref. Consistent with this, the helical cells of S. citri have five MreB homologs. Using Western blot and sequence analysis, we showed that both the fibril protein and MreB exist in S. melliferum cells and both are homologous to the sequenced fibril and MreB proteins of S. citri. Hence, the inner ribbon of the S. melliferum cytoskeleton is composed of MreB. Because of the instability of MreB filaments, the isolation of intact triple ribbons proved difficult and therefore, direct and unambiguous proof for this assignment by immunolabeling was not possible. Nevertheless, there is evidence supporting our assumption about the protein composition of the cytoskeleton. Purified MreB from Thermotoga maritima has been shown to form 4-nm-wide protofilaments in vitro^ref, and a linkage between an actin-like protein and the fibrils in Spiroplasma cells was already proposed by Williamson et al.^ref but has not yet been proven. How does this cytoskeleton enable the movements of S. melliferum cells? Trachtenberg and Gilad^ref suggested that the filaments can change their length in a coordinated manner, driven by conformational changes of their tetrameric subunits from nearly circular to elliptical. In this regard, the assumptions for our computer simulations, which are based on light microscopy experiments and the existence of three ribbons, are (i) the ribbons are connected to each other, (ii) the inner thin filament ribbon functions elastically during cell movement, and (iii) length changes of the five filaments of the outer 2 ribbons occur simultaneously by switching between two conformational states of the filament subunits. Hence, we can simulate on a molecular level how the different motility modes are generated. If length changes in the 2 outer ribbons are coordinated such that one ribbon becomes gradually tense by shortening while the second one concurrently relaxes, the cell would alternate handedness between left- and right-handed, with handedness switching at the position where the state of tension and relaxation of the ribbons reverses. This point of transition between left- and right-handedness travels throughout the whole cell, leading to a motion that resembles that of a bacterial flagellar bundle or of a single eukaryotic flagellum or cilium. A similar motion can be generated if the distance between the two outer ribbons is changed locally, thereby creating a deformation or kink, which propagates throughout the cell body. Thus, the whole Spiroplasma cell functions as a dynamic helical propeller. Coupling of a biochemical cycle (e.g., adenosine 5'-triphosphate hydrolysis) to the dynamics of the filaments could enable these filaments to propagate deformations that generate propulsive forces which, in turn, can drive cell motion^ref. MreB filaments give the cell a rodlike shape by forming the inner, elastic ribbon, whereas the outer filaments composed of the fibril protein enable the formation of a helix, as well as movement, by interaction with the MreB ribbon^ref
• Bacteria also produce bacteriocins (coded by defective phages or by (un)conjugative plasmids), antibiotics with a very narrowed spectrum of action :

bacteriocin	produced by	bactericidal by/to
lactocin F	Lactobacillus acidophilus	Enterococcus faecalis
lactocin S	Lactobacillus sakei	Gram-positive Bacteria
colicin	Escherichia coli	colicins A, E1, Ib and K form membrane ion channels; E2 and E3 are intracellular enzyme (the latter cleaves rRNA 16S); V2; IIb  Escherichia coli and its close relatives
piocin	Pseudomonas aeruginosa
plantacin	Lactobacillus plantarum	inhibits endospore germination
mesenterocin 5	Leuconostoc mesenteroides	Listeria monocytogenes
pediocin	Pediococcus acidilactici	Gram +ve Bacteria; inhibits endospore germination
hiraecin S	Enterococcus hirae	Listeria monocytogenes
propionicin	Propionivibrio thoenii	Gram-negative Bacteria
epidermin	Staphylococcus epidermidis	other skin Bacteria
	Bacillus megaterium
	Yersinia pestis
	Serratia marcescens
cloacin DF13	Enterobacter cloacae	Escherichia coli
	Clostridium butyricum
lysostaphin	Staphylococcus simulans bv.  staphylolyticus	other Staphylococcus spp.
staphylolysin / LasA protease : cleaves peptide bonds following Gly-Gly pairs in peptides or proteinsref1, ref2, and as in the case of lysostaphin, its ability to lyse staphylococci results from cleavages within the pentaglycine cross-links in the peptidoglycan of S. aureus cellsref. LasA protease	Pseudomonas aeruginosa	can cause lysis of a wide range of Staphylococcus aureus strainsref, and it has also been shown to inhibit the growth of S. aureus cells in vitroref. This favors LasA protease as another useful agent in enzyme-based treatment of S. aureus infections

Colicin-producing strains cannot coexist with sensitive or resistant strains in a well-mixed culture, yet all three phenotypes are recovered in natural populations. Recent in vitro results conclude that strain diversity can be promoted by colicin production in a spatially structured, non-transitive interaction, as in the classic non-transitive model rock–paper–scissors (RPS). In the colicin version of the RPS model, strains that produce colicins (C) kill sensitive (S) strains, which outcompete resistant (R) strains, which outcompete C strains. Pairwise in vitro competitions between these three strains are resolved in a predictable order (C beats S, S beats R, and R beats C), but the complete system of three strains presents the opportunity for dynamic equilibrium. Here we provide conclusive evidence of an in vivo antagonistic role for colicins and show that colicins (and potentially other bacteriocins) may promote, rather than eliminate, microbial diversity in the environment^ref.
In Bacillus subtilis (the model sporulating Gram-positive bacteria), cells at the beginning of the sporulation pathway may delay entering the dormant phase by killing their siblings and feeding on the released nutrients In mutants in which the genes controlled by Spo0A, a protein that regulates sporulation, had been altered, 2 operons are strongly induced at the start of sporulation : their mutations accelerated spore formation
• sporulation killing factor (skf) is a group of 8 genes that govern the synthesis of a peptide antibiotic and the production of an export pump that confers resistance to the toxin
• sporulation delaying protein (sdp) comprises 3 genes and controls the production of an extracellular-signaling protein that delays spore formation, probably by increasing energy production by the cell. In addition, the signaling protein causes enhanced cell sensitivity to the sporulation killing factor
Acting synergistically, the B. subtilis killing factor and the signaling protein thus prevent sporulation in sister cells and cause them to lyse, releasing nutrients that permit the cannibals to keep growing and to delay committing to spore formation. Because sporulation becomes irreversible after its earliest stage, delaying spore formation as long as possible might be beneficial as a cell that is committed to spore formation could be at disadvantage relative to other cells should nutrient deprivation prove to be fleeting
• antibiotic-producing bacteria have evolved a range of mechanisms to escape the lethal effects of their own chemical warfare; self-protecting mechanisms have contributed to the widespread resistance of pathogenic bacteria to clinically important antibiotics
• antibiotic elimination through specific efflux pumps
• antibiotic inactivation by modification of its chemical structure
• modification of the antimicrobial target
• antibiotic sequestration
• self-sacrificing : detoxification is accomplished at the expenses of both the metabolite and the resistance protein. Enediynes, a set of antibiotics that are among the most potent cytotoxic antitumoral agents to have been discovered in the past decade. Following prodrug activation, the enediynes undergo cycloaromatization reactions resulting in formation of highly reactive diradical intermediates that destroy bacteria by engaging in atom-transfer chemistry to produce neutral arene products, in the process abstracting hydrogen atoms from the backbone of DNA and induce permanent damage to the key macromolecule. Enediynes are so active that many of the 20 or so naturally occurring substances identified so far are in clinical trials, and efforts using chemical synthesis to improve the target specificity of designed enediynes are ongoing. CalC, a Micromonospora gene, confers resistance to calicheamicinin vivo by attracting the activated calicheamicin molecule, which in turn abstracts a single hydrogen from a specific glycine residue in the protein backbone—in a manner consistent with its action on DNA—and causes irreversible protein cleavage. CalC acts within the enediyne-producing microorganism by capturing and detoxifying activated antibiotics that escape the biosynthesis-exportation system before they attack and damage bacterial DNA
• adhesion accessory apparatuses
• glycocalyx = it binds cell together forming multicellular aggregates on rocks, animal tissues, ... Its molecules are said capsular Ags, in contrast with the molecules of the remaining part (bacterial body), who are called somatic Ags. It varies among species and may consist of one of the following forms :
• S layer = a paracrystalline (i.e. : non-covalent bonds, self-assembling in vitro) (glyco)protein layer found outside the cell walls of some Gram +ve Bacteria or outside the outer membrane of some Gram -ve Bacteria. It presents pores with Ø ~ 2÷3 nm.
• capsule = homopolysaccharides (levan in Streptococcus salivarius, dextran in Leuconostoc mesenteriodes, cellulose in Acetobacter xylinum, mannan in Bacillus circulans ... ), heteropolysaccharides (in pneumonia causing pathogens : Streptococcus pneumoniae, ..) or (D-Glu)_n (in Bacillus anthracis, Bacillus subtilis, Bacillus megaterium, ...) tightly bound to the S layer or to the cell wall (directly if the latter is positive-charged or through cations if the latter is negatively-charged) : at least in Bacillus megaterium, Staphylococcus aureus and type 6 Pneumococcus some covalent bonds are present between cell wall and capsule. Smooth-rough (S-R) variation : a genetic mutation or an adaptation seen in bacteria, most often evidenced by a change in the surface of colonies from smooth (S, glossy) to rough (R, dull).
• bacterial or microbic dissociation : the change, due to mutation and selection, in colonial morphology (usually from mucoid (M) or smooth sapsulated variants to rough) of bacteria in culture on laboratory media;
The cells in S colonies have polysaccharide capsules and are more antigenically complete; R cells contain little or no capsule. The term may also refer to changes in other cell structures such as flagella and somatic antigens, as well as susceptibility to bacteriophage. Variations are often reversible and tend to result in mixed types on repeated subculture. The change correlates with pathogenicity, S strains being generally more virulent and R strains of the same species less so because :
• its polysaccharides inhibit alternative pathway for complement cascade activation : group B type III Streptococci have Sia residues that attract factor H, while type VII and XII Streptococci prevent factor B from binding C3b on cell wall: in both cases the formation of the C3bBbP complex and subsequent complement-mediated phagocytosis are prevented.
• as it is hydrophilic, it protects against hydrophobicity-mediated non-immune phagocytosis (but not against opsonin-mediated phagocytosis which occurs late in infections !), preventing adhesins from binding phagocyte receptors Anyway surface phagocytosis in pulmonary alveoli (rough surface) remains functional.
• it confers resistance to desiccation
• it represents a nutrient storage
As they exclude stains, they can be observed only by negative staining. When the capsule is monolayered it is called microcapsule (e.g. in Salmonella) : it becomes observable at TEM only after the Neufeld reaction. The capsule-building ectoenzymes are inherited (in classical 1928 Griffith's bacterial transformation experiments with Streptococcus pneumoniae strain 3, the R variants lacked UDP-Glc dehydrogenase, needed to transform UDP-Glc in UDPGlcA, which is a sugar for the cell wall disaccharide cellobiuronic acid) but their activity is subordered to nutrient availability (e.g. : carbohydrates for Aerobacter, sucrose for Leuconostoc, CO₂ for Bacillus anthracis (CO₂ + Pyr => OAA => aKG => D-Glu)) and growth phase (elder Streptococci A and C produce hyaluronidase which degrades hyaluronic acid in cell walls to GlcUA and GlcNAc, causing cell death in colony center) so that a reversible S => R transition is possible. The cell wall precursors may be exported from cytoplasm through secretion systems or (only for some Gram +ve Bacteria with ectomembrane-bound transglycosylase) come from environment (e.g. : diet sucrose in oral cavity for Streptococcus mutans => dextran or levan => biofilms (dental caries) => pH lowering => enamel decalcification). While some biofilms are useful—sewage treatment plants, for instance, rely on them to remove contaminants from water—they are estimated to be involved in 65% of human bacterial infections : when microbes band together in a biofilm they are 1,000 times more resistant to killing by antibiotics, biocides and disinfectants than free-floating bacteria. ndvB gene is required for the production of periplasmic glucans, glucose polymers that prevent antibiotics from reaching sites of action.
• slime layer = similar in composition to capsules but less tightly bound to the cell wall. E.g. in Staphylococcus epidermidis and Pseudomonas aeruginosa.
• adhesins (lectins whose synthesis doesn't occur if T < 20 °C) protruding outward ...
• ... fimbriae = inherited trait, much shorter and more numerous than flagella. They often contain adhesins and receptors for bacteriophages.
• ... pili = protein scaffolds of pilin (convergent evolution : chaperone and usher pilus family, type IV pilus family, ...) packed tightly into an helical array. They are longer and fewer (sometimes only one per cell) than fimbrae. They act as :
• sex pilus for bacterial conjugation (F type for F plasmids and R plasmids, I type for colicin plasmids and R plasmids)
• attachment to host tissues (act as haemagglutinins)
• receptor for bacteriophage(s).
• ... outer membrane : invasin in Yersinia pseudotuberculosis, intimin in EPEC, LTA.

Biofilms / microcolony, densely-packed microbial communities develop when free-swimming (planktonic) cells attach to a surface and form mushroom-like structures containing stalks, a meshwork of channels, and encased in a layer of slime comprising proteins, polysaccharides, and DNA. Consequently, this bacterial fortress is notoriously resistant to antimicrobial agents, rendering biofilms virtually untreatable : they are responsible for something like 65% of all infections in the West.
Pseudomonas aeruginosa biofilm development occurs in 5 stages during which >n 800 proteins (> 50% of the proteome) showed a sixfold or greater expression level change^ref :
• reversible attachment: cells transiently affix to substratum, and surface induced gene expression results in a protein profile significantly different from planktonic bacteria.
• irreversible attachment: cells reorient themselves, clusters develop, motility is lost, and the las quorum sensing regulon becomes activated.
• maturation I: cell clusters become thicker than 10 mm and the rhl quorum sensing system becomes active.
• maturation II: cell clusters reach maximum thickness (100 mm) with a protein profile most different from planktonic cells.
• dispersion: cluster structures change, and pores and channels form. Motile and non-motile bacteria are present as the protein profile begins to resemble planktonic cells once again.

Upregulated proteins included those involved in anaerobic processes, denitrification, many efflux pumps, and some quorum sensing proteins. One major player they found upregulated was a known transcriptional regulator that turns on antibiotic resistance by inducing transcription of efflux pumps. Microbiologists have tended to define microbial physiology based on planktonic bacteria, but in nature bacteria exist almost exclusively in biofilms : the only time they are planktonic is when making the transition from one biofilm to another. If bacteria in biofilms are physiologically different from planktonic bacteria, then all the work done right back to Louis Pasteur has to be repeated. Within biofilms, cell-cell communication occurs through quorum sensing, in which signaling molecules called autoinducers, specific for that species, are produced and exchanged among bacterial neighbors.
Web resources : Center for Biofilm Engineering
• positive or negative motility or taxis accessory apparatuses
• magnetosomes = membrane-enclosed magnetite (Fe₃O₄) or greigite (Fe₃S₄) crystals that create permanent magnetic dipole in anaerobic or microaerobic Bacteria living in marine and freshwater sediments

... magnetotaxis : in the northern emisphere evolution selected Bacteria that move "north-seekingly" according to Earth magnetic field, down to the sediment, where P_O2 is low. In the southern emisphere evolution selected Bacteria with reverse polarization. The orientation process is passive, while movement along the field is an active process.
The chromosomal 'magnetosome island' contains genes connected with magnetosome synthesis : gene deletion in Magnetospirillum gryphiswaldense show that magnetosome alignment is coupled to the presence of the mamJ gene product. MamJ is an acidic protein associated with a novel filamentous structure, as revealed by fluorescence microscopy and cryo-electron tomography. A mechanism in which MamJ interacts with the magnetosome surface as well as with a cytoskeleton-like structure has been proposed : magnetosome architecture represents one of the highest structural levels achieved in prokaryotic cells^ref
• chemoreceptors =

... chemotaxis : changes in ligand concentrations are sensed by a protein assembly consisting of transmembrane receptors, a coupling protein (CheW) and a histidine kinase (CheA). In Escherichia coli, these components are organized at the cell poles in tight clusters that contain several thousand copies of each protein. Assemblies of bacterial chemoreceptors work in a highly cooperative manner, mimicking the behaviour of allosteric proteins. Conditions that favour steep responses to attractants in mutants with homogeneous receptor populations also enhance the sensitivity of the response in wild-type cells. This is consistent with a number of models that assume long-range cooperative interactions between receptors as a general mechanism for signal integration and amplification.
• photoreceptors =

... phototaxis
• flagella (completely different from the structure of Eukarya flagella !) = 100÷200 mm length, a motile organelle made up of
• flagellar motor embedded in the cell membrane
• M protein (in the basal body or motor)
• S protein (in stator)
• flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. The hook is made of about 120 copies of a single protein, FlgE, and its function as a nano-sized universal joint is essential for dynamic and efficient bacterial motility and taxis. It transmits the motor torque to the helical propeller over a wide range of its orientation for swimming and tumbling. FlgE31 is a major proteolytic fragment of FlgE lacking unfolded terminal regions^ref.
• flagellar filament : flagellin (a fibrous helicoidal dextrogire protein which also acts as a type II T-independent Ag and binds to TLR5). Flagellin subunits held together by hydrophobic interactions assemble into so-called protofilaments in 2 different conformations : L-type and R-type. Supercoiled bundles of 11 protofilaments can form left-handed or right-handed helices. In the L-type protofilament the central channel of the flagellum is lined with polar residues : this could be relevant to export of unfolded proteins through the flagellum - like flagellin, which is exported then added to the growing filament tip - and for type III virulence protein secretion through a needle complex that is similar to the flagellum.
“Run and tumble” movement controlled by the direction of the flagellar spin (counterclockwise spin => left-handed helix => straight run; clockwise spin => some of the protofilaments switch to form a right-handed helix => the cell stops and reorientates in a random manner (tumble)). Escherichia coli and Salmonella swim fine in water at a neutral pH of 7.0. And without the weak acids present to lower their internal pH, they also swim fine in acidic water at pH 5.0. But, with the weak acids and a lower internal pH - as the outside water becomes more acidic - they slow and ultimately stop. The flagellar apparatus may secrete virulence factors. It may be stained with tannic acid. The flagellum may be absent  (atrichous), single (monotrichous), double (if at opposite poles : amphitrichous) or multiple (if grouped at both poles : lophotrichos, if diffused on all surface : peritrichos).
• cilia =
• axial filaments / endoflagella / axistyles / flagellar apparatuses are the spirochetae equivalent of flagellum. The endoflagella are contained within the periplasmic space between a rigid peptidoglycan helix and a multi-layer, flexible outer membrane sheath. When the filaments rotate within this space, the spirochetes move in cork-screw fashion. This mode of motility in spirochetes is thought to be an adaptation to viscous environments such as aquatic sediments and the intestinal tracts of animals. For pathogens, this allows the spirochetes to hide their flagella, which are normally antigenic, from the host immune defenses.
• gas vacuoles =
• pseudopodia =
• cellulosome : an extracellular enzyme complex which consists of a scaffolding protein and many bound cellulases. Anaerobic microorganisms have evolved a system to break down plant cell wall materials, including cellulose, the most abundant carbohydrate polymer in nature. Although anaerobic fungi as well as anaerobic bacteria are believed to produce cellulosomes, so far full genetic evidence for their presence has only been obtained in anaerobic bacteria. To date, cellulosomes have been identified in 12 different bacterial species, and this list is expected to continue growing. Cellulosomes comprise a fibrillar protein known as the scaffolding protein or scaffoldin with cellulosomal enzyme subunits positioned periodically along the fibrils. Typically, the scaffoldin contains enzyme-binding sites known as cohesins, and a cellulose-binding domain (CBD) or carbohydrate-binding module (CBM). The enzyme subunits bind to the cohesins via cohesin-binding sites known as dockerins. The properties of the scaffoldins vary between species. Additionally, cellulosomes can contain either one or several different scaffoldins that can bind different combination of enzymes. This variation and the presence of many cellulosomal enzymes means that any single microorganism can secrete a variety of cellulosomes with many different compositions. The cellulosomal enzymes include cellulases, hemicellulases, pectinase, chitinase and many ancillary enzymes that can degrade plant cell wall materials. In biotechnology, there is great interest in exploiting the properties of cellulosomes. 'Mini-cellulosomes' can be created, which, because they contain specific cohesins, will only bind to specific enzymes. These constructs have been used to great effect in cellulosome research in the study of the synergistic effects of cellulosomal enzymes and the cohesin–dockerin interaction, for example, but it is also hoped that mini-cellulosome constructs could be used in the future to develop artificial metabolic pathways that allow the synthesis of any desired product. There is also great interest in the heterologous expression of cellulosome genes, such that non-cellulose degrading organisms can be converted to cellulose degraders. Cellulosomes have many potential biotechnological applications as the conversion of cellulosic biomass into sugars by cellulosomes could result in the production of high-value products such as ethanol or organic acids from inexpensive renewable resources.
• cell-cell communication in bacteria is accomplished through the exchange of chemical signal molecules called autoinducers. This process, called quorum sensing, allows bacteria to monitor their environment for the presence of other bacteria and to respond to fluctuations in the number and/or species present by altering gene expression to coordinate particular behaviors. Most quorum-sensing systems are species- or group-specific (eg see Pseudomonas aeruginosa), which presumably prevents confusion in mixed-species environments. However, some quorum-sensing circuits control behaviors that involve interactions among bacterial species. These quorum-sensing circuits can involve both intra- and interspecies communication mechanisms. Finally, anti-quorum-sensing strategies are present in both bacteria and eukaryotes, and these are apparently designed to combat bacteria that rely on cell-cell communication for the successful adaptation to particular niches. The AI-2 autoinducer, unlike all other known autoinducers, which are species-specific, is produced by > 50 bacterial species and believed to be a universal signaling molecule : its receptor is LuxP sensor protein^ref. It contains boron in the molecule : despite ubiquitous in the biosphere, especially in oceans, the only well-defined reference to boron in biology is its role in stabilizing cell wall structures of plants. Millimolar quantities of borate are found in seawater, meaning that a role for boron in communication among the marine V. harveyi, makes sense in hindsight.


Bacteria communicate with each other in multiple ways, including the secretion of signaling molecules that enable a cell population to determine when it has reached a certain density or that a potential partner is present for conjugation^{ref1, ref2}. Cellular communication can also occur through contact between cells, as has been shown for Myxococcus xanthus, which undergoes a complex developmental pathway^{ref1, ref2}. Certain Escherichia coli, including uropathogenic strains, contained a bacterial contact-dependent growth-inhibition (CDI) system that uses direct cell-to-cell contact. Inhibition was conditional, dependent upon the growth state of the inhibitory cell and the pili expression state of the target cell. Both a large cell-surface protein designated Contact-dependent inhibitor A (CdiA) and 2-partner secretion family member CdiB were required for growth inhibition. The CdiAB system may function to regulate the growth of specific cells within a differentiated bacterial population. Many UPEC strains contain fim (type 1 pili), pap (P pili), and sfa (S pili) operons^{ref1, ref2}. The expression of these pili types is normally subject to reversible off/on switching, generating diversity within bacterial populations by a differentiation mechanism^{ref1, ref2}. Such a mechanism might play a role in the temporal control of the differentiation observed for UPEC strains inside bladder cells, during which the bacteria progress through distinct developmental stages, including a quiescent growth state^ref. E. coli K-12 cells inhibited by CDI appear to be nonviable because of their lack of growth on agar medium. However, CDI-inhibited cells appeared to be viable because they excluded propidium iodide, a standard criterion for distinguishing viable cells from nonviable cells^ref. The identification of this sophisticated mechanism in E. coli, with possible homologs in a broad range of species, opens the door for exploration of the potential roles of CDI in controlling bacterial development and pathogenesis^ref.
• cell cycle
• vegetative form : exogrowth and division by binary fission (formation of septal mesosome). Cell cycle period is average 20' long, but varies (also according to growth conditions) from 10' (in Beneckea) up to > 24 hrs in Mycobacterium leprae. Please note often in vitro doubling times are shorter than in vivo ones !
• the bacterial septum-located DNA translocase FtsK coordinates circular chromosome segregation with cell division. Rapid translocation of DNA by FtsK is directed by 8-base-pair DNA motifs (KOPS), so that newly replicated termini are brought together at the developing septum, thereby facilitating completion of chromosome segregation. Translocase functions reside in three domains, a, b and g. FtsKab are necessary and sufficient for ATP hydrolysis-dependent DNA translocation, which is modulated by FtsKg through its interaction with KOPS^ref.
• quiescent form : no exogrowth => no division.
• structures for survival under unfavourable growth conditions (protection and dispersion)
• (endo)spores : mainly in Gram +ve genera (Bacilli(aerobic rods), Clostridii, Thermoactinomyces and Desulfotomaculum (anaerobic rods), Sporosarcina (aerobic cocci)) but also Gram -ve (Coxiella burnetii). They arise in 6÷8 hrs after post-logarithmic phase in culture growth ...
• depletion of environmental energy sources causes a fall in [GTP]_i and accumulation of ppGpp, ppGppp (stringent factors) and ppAppp : such events cause the chromosome to relax itself into an axial filament and duplicate itself, duplicating even its origin. At this stage some species produce antibiotics. All these modifications are reversible. Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with 2 highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel (the "backdoor of gene expression") to coordinate a ppGpp bound Mg²⁺ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors^ref.
• before the terminus of the chromosome is duplicated, an asymmetric membranaceous sporal sept irreversibly divides the cell into a major (sporangium) and a minor (forespore) compartment.
• the sporangium endocytes the prespore (then called anterior chamber of the spore), that in such a way becomes surrounded by 2 bilayers whose inner layers are facing up. Such a polarity guarantees the deposition of peptidoglycan in the intermembrane space. DPA is synthetized in the sporangium and actively imported into the future spore : acting as a buffer, it drives the passive influx of Ca²⁺. 80 genes (grouped into 4 families : spo, ger, ssp and cot) are needed for sporulation. Spore specific proteins are synthetized thanks to specific s subunits in RNA polymerase : s^E and s^F => s^G in the forespore & s^K in the sporangium.
They may be cylindrical, ellipsoidal or spherical in shape with size ...
• ... smaller than the originary bacterium (from 1 to 5 spores per cell)
• central (bactridium type sporulation) (e.g. in Bacillus anthracis)
• terminal(plectridium type sporulation) (e.g. : in Clostridium)
• sub-terminal (e.g. : in Bacillus cereus)
• ... larger than the originary bacterium (distends the cell)
Within 24 hrs the sporangium undergo lysis and mature spore(s) are free. From inner to outer you find :
• core-containing sporoplast or protoplast : spore strome (a gel matrix) is made up of nucleoid, calcium dipicolinic acid (CDPA or pyridin-2,6-dicarboxylic acid : it replaces H₂O in the manteinance of the quaternary structure of its binding partners as they're as thermosensitive as the proteins expressed in the vegetative forms are (except for NADH oxidase in Clostridium botulinum and aldolase in Bacillus cereus)), polyamines, amino acids and 3-phosphoglycerate. Refracting index : 1.54.
• cortex (peptidoglycans) : its anisotropic expansion confers impermeability (unstainable !) => low water content structures viewable after Wirtz staining) => low metabolic activity and biopolymers more resistant to hydrolysis. Refracting index : 1.47.
• inner cortex or spore wall (20% of the cortex)
• outer cortex (80% of the cortex): only 20÷32% peptidoglycan units are similar to those in cell wall (but containing mesoDmp !). The remaining 50÷60% units present MurNAc modified to form N-acetylmuramyl-lactame, while 18÷20% of MurNAc are linked to L-Ala instead of the usual tetrapetide. Such modifications are driven by a membrane-bound Glu-mesoDmp hydrolase and a cytosolic Ac-Ala-Glu-mesoDmp lyase.
• pericortical membrane
• coats (Cys-rich proteins similar to keratins)
• exosporium : present only in some Bacillus species, made up of proteins, lipids and polysaccharides.
Endospores are heat and dry stable, resisting in amber for more than 1 million years : anyway endospore-forming cells are not always very heat-resistant (e.g. : Bacillus anthracis requires only 1-2 minutes at 100 °C to be killed), but Clostridium botulinum requires 2÷6 hours at 100 °C to be killed compared to the only 30' at 70 °C for non-endospore formers ! Spores can be killed with 10'÷20' at 120 °C in wet heat or 90'÷180' at 160÷200 °C in dry heat (Pasteur oven) autoclaving. From soils into wounds or on vegetables (ingested as aliments, wooden choping boards, ...). Some strains are used as bioweapons (Bacillus anthracis), some others as biopesticides (GE vegetables expressing the Bt toxin transgene from Bacillus thuringiensis var.israelensis against mosquito and blackfly larvae). Newer spores need activation (coat destabilization by 5÷10' at 70÷85 °C) before germination in a favourable environment : high [Ca²⁺], P > 10 MPa, L-Ala, Ado and Ino activate (while D-Ala, MgCl₂, PMSF inhibit) a receptor that cleaves and activates a pre-formed p68 => p29^{spore lytic enzyme or corticohydrolase} that depolymerizes the outer cortex allowing H₂O income during exogrowth. Finally the spore comes back to the vegetative form, dividing itself 2 hours after the germination.
• cysts : resting stage formed by some Azotobacter and Myxobacteria in which the whole cell is surrounded by a protective layer. They arise from deposition of cell wall layers around the cell and are resistant to dehydratation but not to heat : they are mainly involved in nitrogen fixation and protection.
• cell shapes & arrangements : they are established by cell wall but environmental conditions can change them.
• coccus (from the Greek kokkox = berry; plural : cocci): cells that are spherical in shape.
• streptococcus (from the Greek streptox = necklace) : arranged in chains, like beads on a string.
• Diplococcus : arranged in pairs. (e.g. : Streptococcus pneumoniae, Neisseriae)
• staphylococcus : arranged like clusters of grapes. Random planes of division.
• tetrad : arranged in a group of 4, looking almost like a square under the microscope. 2 planes of division.
• sarcina (plural : sarcinae) : arranged in a group of 8. Sarcinae look like small cubes and may be difficult to distinguish from tetrads. 3 planes of division.
• bacillus (plural : bacilli) : rod-shaped cells. A single plane of division.
• Diplobacillus : arranged in pairs.
• Streptobacillus : arranged in end-to-end chains (e.g. : Mycobacteria, Bacillus anthracis)
• Coryneform bacillus : arranged at angles to form V- and L-shaped arrangements (e.g. Corynebacterium)
• coccobacillus (e.g.: Gardnella vaginalis) : intermediate to coccus and bacillus
• spiral-shaped & no arrangement.
• Spirillum (plural: spirilla) : rigid
• Spirocheta : flexible
• vibrio : a bacterium with curved or comma-shaped cells. No arrangement.
• pleiomorphic : do not display a constant shape even during growth in an otherwise unchanging, homogeneous environment
• fruiting body : macroscopic reproductive structure produced by some bacteria, including Myxobacteria. Fruiting bodies are distinctive in size, shape, and coloration for each species.
• Escherichia coli concentrates Zn and Fe by several orders of magnitude relative to the concentration in a typical growth medium until they achieve a quota of about 2 ^. 10⁵ atoms per cel, which is equivalent to a total concentration of about 0.1 mM. Metals such as Cu and Mn are maintained in the 10 to 100 mM range. Other metals are also concentrated by the E.coli cell to a narrow, fixed, total concentration as follows : K and Mg, 10⁸ atoms per cell, > 10 mM, Ca, Zn, and Fe, 10⁵ atoms per cell, 0.1 mM; Cu, Mn, Mo, and Se, 10⁴ atoms per cell, 10 mM; V, Co, and Ni, low abundance.
• Understanding the life strategy of highly motile Bdellovibrio bacteriovorus, which preys on other gram-negative bacteria, including plant, animal, and human pathogens^ref, could lead to the identification of novel antimicrobials. This extremely small bacterium—it averages 0.2–0.5 by 0.5–2.5 mm—has a relatively large genome of over 3.7 Mb, encoding 3584 predicted genes. There is no indication of horizontal gene transfer from its prey, even though B. bacteriovorus has easy access to its prey's genomic information. Additionally, the genome lacks the genes to synthesize 11 and to degrade 10 amino acids, suggesting it relies on its prey for some essential amino acids. The bacterium also harbors a huge contingent of lytic enzymes, numbering over 200 genes, that are potential new antimicrobial substances. Bdellovibrio has been considered for use as a living biocontrol agent reduce or modify populations of pathogenic microbes (e.g. plant pathogenic Erwinia : most of the field uses stain 109 J, and not HD100)^ref
• satellite phenomenon : the more luxuriant development of a colony of microorganisms when in the neighborhood of a foreign colony, as shown by Haemophilus influenzae when contaminated by Staphylococcus aureus
• Twort-d'Herelle phenomenon : the phenomenon of transmissible bacterial lysis; bacteriophagia. When to a broth culture of typhoid or dysentery bacilli there is added a drop of filtered broth emulsion of the stool from a convalescent typhoid or dysentery patient, complete lysis of the bacterial culture will occur in a few hours. If a drop of this lysed culture is added to another culture of the bacilli, lysis will take place exactly as in the first. A drop of this culture will then dissolve a third culture, and so on through hundreds of transfers. d'Herelle attributed this phenomenon to the action of an ultramicroscopic parasite of bacteria, which he named the bacteriophage
• researchers studying ageing in cells focus on 2 key characteristics: asymmetric cell division and the stage of the life cycle leading up to reproduction. The bacterium Escherichia coli, however, lacks both. The single-celled organism splits into 2 apparently identical daughter cells, which in turn divide, and so on. As a result, many scientists believed that it, and similar bacteria, were immortal. The bacteria's apparently symmetrical division makes it difficult to track cells. Stewart and his teammates tackled the problem by taking pictures of a group of rectangular E. coli cells every 2 minutes. Their complete record included over 35,000 cells. In the lab, E. coli reproduces in half an hour. A custom-made computer program analysed the snapshots. The computer identified and tracked the tips of each bacterial cell. E. coli divides down the middle, giving each daughter cell one newly regenerated tip. But the cell's other tip is passed down from its mother, or grandmother, or some older ancestor. The bacteria inheriting the older end reproduced 1% more slowly than their counterparts with each cell division^ref. Stewart's group was unable to follow bacteria until death, as after 10 generations the dish became too crowded to spot individuals. Single-celled organisms that divide asymmetrically, such as yeast and the bacterium Caulobacter vibrioides (a.k.a. Caulobacter crescentus), were recently also revealed to reproduce more slowly as they grow old.

Web resources :
• E. coli blog
• Ageing in E. coli
• bacterial microcompartments are primitive organelles composed entirely of protein subunits. Genomic sequence databases reveal the widespread occurrence of microcompartments across diverse microbes. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. 3D crystal structures of multiple carboxysome shell proteins have been revealed, revealing a hexameric unit as the basic microcompartment building block and showing how these hexamers assemble to form flat facets of the polyhedral shell. The structures suggest how molecular transport across the shell may be controlled and how structural variations might govern the assembly and architecture of these subcellular compartments^ref.

Please note this was the old Gibbons-Murray taxonomy :

• division I - Gracilicutes (Gram -ve Eubacteria)
• division II - Firmicutes (Gram +ve Eubacteria)
• class I - Firmibacteria (cocci and Bacilli)
• class II - Thailobacteria (Actinomycetae)
• division II - Tenericutes (cell wall-less Eubacteria)
• class I - Mollicutes (i.e. Mycoplasmatales)
• division IV - Mendosicutes
• class I - Archaeobacteria, now named Archaea

• phosphobacterium : Bacterium that is especially good at solubilizing the insoluble inorganic phosphate in soil.
• akinete : thick-walled resting cell of Cyanobacteria and Algae.
• heterocyst : differentiated cyanobacterial cell that carries out dinitrogen fixation.

Web resources :

• Academic Info Microbiology & Virology
• Bacteriamuseum.org
• Biocatalysis/Biodegradation Database : biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds from the University of Minnesota
• Cyanosite
• Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) GmbH Bacterial Nomenclature up-to-date
• dmoz Open Directory Project (ODP) : Microbiology
• Dr. Kaiser's microbiology website
• Genome Information Broker (GIB)
• Ela BacteriaWeb Directory
• Enhanced Microbial Genomes LIBrary (EMGLIB), Université Claude Bernard, Lyon
• GenoList genome browser
• Higher-than-operon regulatory networks
• List of Bacterial Names with Standing in Nomenclature
• Microbes.info : the microbiology information portal
• MicrobeWorld
• MicrobeWorld.org
• MicrobeLibrary.org
• Microbe.org
• Microbial Genome Database (MBGD) for Comparative Analysis
• Microbiological Garden by Heribert Cypionka
• Microbiology and immunology at University of Leicester
• Microbiology Direct - Reviewed Microbiology Web Directory
• Microbiology links on LabExplorer.com
• Microbiology study guides
• Microbiology Webbed Out : Microbiology textbook
• MuseumStuff.com Microbiology Resources
• Netherlands Culture Collection of Bacteria (NCCB)
• Suite101: Microbiology by Neal Rolfe Chamberlain
• The Microbiology Network
• The Virtual Library - Microbiology and Virology
• The Institute for Genome Research (TIGR)
• Microbial Database (MDB)
• Comprehensive Microbial Resource (CMR)
• ViruloGenome at the University of Birmingham
• WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)
• Yahoo! Microbiology
• Associations :
• Japanese Society for Bacteriology (JSB)
• Federation of European Microbiological Societies (FEMS)
• Journals
• International Journal of Systematic and Evolutionary Microbiology (IJSEM)
• Journal of Bacteriology

• The Prokaryotes: A Handbook on the Biology of Bacteria, Second Edition, Vol. 1-4, 1991. Springer-Verlag, New York NY. A. Balows, H. Truper, M. Dworkin, W. Harder & K.-H. Schleifer
• Bergey's Manual of Systematic Bacteriology, 1^st Edition, Vol. 1-4, 1989. Williams & Williams, Baltimore MD. John Holt (editor-in-chief).
• Bergey's classification : a system of classification of bacteria in which the organisms are grouped according to Gram reaction, metabolism, and morphology, with each group being further subdivided into orders, families, genera, and species.

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