Survey of bacteria Bacteria: Planctobacteria Cyanobacteria

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1 Survey of bacteria Bacteria: Planctobacteria Cyanobacteria
Composed by Bas Kooijman Planctobacteria Cyanobacteria Endobacteria Proteobacteria Actinobacteria Eurybacteria Togobacteria Sphingobacteria Korarchaeota Bacteria: syn: Prokaryota, Monera flagella structurally different from eukaryotic flagella no nuclear envelope (exept in e.g. Gemmata); chromosome in a nucleoid, not in a nucleus; haploid DNA segregation by association to the cell surface, not a mitotic spindle respiratory chain in cytoplasmic membrane, not in mitochondria photosystem in cytoplasmic membrane or in free thylakoids, not in chloroplasts cell wall usually contains peptidoglycan no internal cytoskeleton of actin microfilaments and tubulin-containing microtubules no cytoplasmic motility mediated by ATPase molecular motors such as myosin and dynein no endoplasmic reticulum, Golgi complex and lysosomes no phago-, endo- or exocytosis recombination by parasexual processes, not by syngamy and meiosis no intracellular endosymbionts,spliceosomes, peroxisomes, hydrogenosomes presence of DNA gyrase (not in eukaryotes) Lipo- + Glycobacteria = Gram-negative bacteria + a few Gram-positive (Deinococcus) Crenarchaeota Heliobacteria Thaumarchaeota Spirochaetae Nanoarchaeota Hadobacteria Euryarchaeota

2 Lipobacteria outer membrane present, usually with murein wall between the two membranes; outer membrane of phospholipids acyl ester lipids; lipopolysaccaride absent no flagellar shaft outside membrane

3 Spirochaeta (Spirochaetae)
flagella in periplasmic space (2 to 200) murein walls with ornithine or diaminopimelic acid eco: marine, freshwater, deep muddy sediments, inside animal intestines. Some cause diseases: leptospirosis (Leptospira), syphilis, yaws (Treponema), lime-disease (Borrelia). Some are symbiontic in animals (Cristispira inhabits the crystalline style of clams and oysters which is used to grind their algal food; other pillotinas live in gut of wood-eating insects, or in association with bacteria or protists). They lack cellulase, however, but live in intimate contact with parabasilids, which produce cellulase. Spirosymplokos forms mats, and produces small offspring and membraneous bodies that may function as spores spec: Borrelia, Treponema, Leptospira, Leptonema, Spirochaeta, pillotinas (Pillotina, Hollandina, Diplocalyx, Clevelandia) From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

4 Chloroflexus (Chlorobacteria Hadobacteria)
murein walls with ornithine no diaminopimelic acid, cytochrome aa3 or RuBisCo small citrate synthetase Chlorobacteria eco: thermophilic gliders of hot springs Chlorosomes (in Chloroflexus, not in Heliothrix) membrane bound with bacteriochlorophyll g and g', cytochrome b, aliphatic caretenoids (alpha- and beta-) tendency to form filaments photosynthetic, they fix CO2 aerobically (not via Calvin-Benson cycle; binds 2 CO2 to acetyl CoA to form glyoxylate; also lack the TCA cycle) substrates: in light: CO2, H2, H2S, but also on organic matter in dark. Never produces oxygen (like cyanobacteria) spec: 3 genera: Heliothrix, Chloroflexus, Oscillochloris From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

5 Deinococcus (Deinobacteria Hadobacteria)
resistant with thick walls, Gram positive, coccoid eco: non-photosynthetic; strictly of facultatively aerobic; some Deinococcus grow in hypersaline environments substrates: sugars (glucose is metabolized by hexose monophosphate pathway, rather than by the Embden-Meyerhof pathway; small sugars by the TCA cycle)) spec: Deinococcus (radiation resistant, 3 Mrads, 500 rads is lethal for humans; also resistant for UV, dessication, mutagenic chemicals), Thermus (heat resistant, 60-80C) One cell from a tetrad From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

6 Heliobacteria Heliobacterium modesticaldum Heliorestis species
murein walls with ornithine (a nonprotein amino acid) no diaminopimelic acid, cytochrome aa3 nd b, RuBisCo, chlorosomes small citrate synthetase anaerobic photosynthesisers unable to fix CO2 Heliobacterium modesticaldum Heliorestis species

7 Glycobacteria outer membrane present, usually with murein wall between the two membranes; phospholipids in inner leaflet, lipopolysaccharides in outer leaflet acyl ester lipids small recognition RNA (in Proteobacteria) RuBisCo may be present if present, flagella pass through outer membrane

8 Selenomonas palpitans from sheep rumen liquor
Eurybacteria Selenobacteria Selenomonas, Sporomusa Fusobacteria Fusobacterium, Leptotrichia Fibrobacteria Fibrobacter Eurybacteria (poorly defined) non-photosynthetic no sphingolipids flagella: sometimes spec: Selenomonas, Sporomusa, Fusobacterium, Leptothrichia, Fibrobacter Selenomonas palpitans from sheep rumen liquor

9 Planctomyces (Planctomycetales)
Planctobateria syn:Pirellulae eco: freshwater, some cause diseases (parrot-transmitted human disease by Chlamydia psittaci, trchoma type of blindness by C. trachomatis) substrates: organic matter at very low concentration; some have appendices as hold fast to objects. Planktomyces can oxidize ammonia (plus nitrite) anaerobically into N2 (plus nitrate). reproduction by budding in Pirellula, Blastobacter, Planctomyces cells grow in polar region only. Internal membranes, carboxysomes, gas vesicles do not take part in cell division wall of protein, not murein peptidoglycan. Pirellula and Planktomyces are very rich in 2 animo acids (proline, cysteine) and have lipids typical eukaryotes (palmitic, oleic, palmitoleic). Gram-negative nucleoid membrane in Gemmata (without pores, chromatin attachment sites, microtubules) Chlamydia (parasites) form small desiccation-resistant propagules (elementary bodies). spec: Planctomycetales, chlamydias From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

10 Gemmata (Planctomycetales)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

11 Poribacteria Bacterial types in the sponge Aplysina aerophoba 1 Long rods with membrane-bound nuclear region and S-layer-type outer membrane, cell division by septation 2 Short fat rods with membrane-bound nuclear region and electron-dense cytoplasm 3 D-shaped cells with clear membrane-bound nuclear region and S-layer-type outer membrane 4 Rods with clear membrane-bound nuclear region and gram-negative outer membrane 5 Rods with clear, membrane-bound nuclear region and S-layer-type outer membrane 6 Rods with membrane-bound compartment that is devoid of DNA; the compartment contains most of the RNA, while the DNA is restricted to the cytoplasm; the outer membrane contains budding appendages; there is an unusually wide periplasmic space and a phenotypic resemblance to G. aurantiaca Fieseler,L, Horn, M., Wagner, M. and Hentschel1, U. (2004) Discovery of the Novel Candidate Phylum “Poribacteria” in Marine Sponges APPLIED AND ENVIRONMENTAL MICROBIOLOGY 70: 3724–3732

12 Anabaena (Phycobacteria Cyanobacteria)
S external layer (slime or sheath) OM outer memebrane PL peptidoglycan layer CM cytoplasmic membrane CW cell wall CY cytoplasma E cell envelope GV gas vesicle N nucleoplasmic region C carboxysome PP polyphosphate granule CP cyanophycin granule GG glycogen granules TH thylakoid PB phycobilisome Cyanobacteria syn: myxophyta, myxophyceae, cyanophyta, cyanophyceae eco: some form mats, or stromatolites (Persian Gulf, west coast of Mexico, Bahamas, western Australia, under Antarctic ice); some marine pelagic (Prochlorococcus, Synechococcus, Oscillatoria). Prochloron is endosymbiontic in tunicates (Didemnum, Diplosoma, Lissoclinum, Trididemnum) oxygenic photosynthesizers with cholophyll a or b (in chloroxybacteria), phycocyanin, allophycocyanin. Some have phycoerythrin and are red organelles: nucleoids, carboxysomes (which store RiBisCo), thylakoids in Phycobateria (Anabaena, Nostoc, Prochloron; often associated with phycobilisomes) no thylakoids in Gloeobacteria (Gloeobacter): phycobilisomes on cytoplasmic membrane no flagella spec: chloroxybacteria (Prochlorococcus, Prochloron, Prochlorothrix; no closely related), and thousants of others grouped into: Coccogonae (coccoid; Chroococales reproduce by binary fission, Chamaesiphonales by exspores, Pleurocapsales by propagules (Baeocytes)) and Hormogonae (filamentous; Nostocales with no true branches, and Stigonematales, with true branches) From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore

13 Prochloron (Phycobacteria Cyanobacteria)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

14 Pleurocapsa (Phycobacteria Cyanobacteria)
From: Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore

15 Chamaesiphon (Gloeobacteria Cyanobacteria)
From: Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore A bud enlarges B unequal fission C forming reproductive pole, r

16 Nitrobacter (Proteobacteria)
Proteobacteria (purple bacteria) no sphingolipids some are multicellular with cell differentiation. Some budding bacteria (hyphomicrobes) for, mycelia-like networks. Some form elaborate internal membranes; some form gas vacuoles flagella present or absent; some glide facultative aerobes most are chemoheterotrophic, Bdellovibrio and Daptobacter prey on Chromatium (reproduce inside cytoplasma). Many are enterics (Gram-negatives that live in intestines and plants, and cause diseases; Neisseria causes gonorrhea; Rickettsias are obligate intracellular parasites in animals and can cause Rocky Mountain spotted fever). Some are photosynthetic (Rhodomicrobium, Rhodospirillum, Rhodoferax, Rubrivivax, Chromatium, Amoebobacter). Some are chemolithoautotrophs that oxidize nitrogen compounds (Nitrobacter, Nitrispira, Nitrcystis, Nitrococcus, Nitrosomonas, Nitrosolobus), sulfur compounds (Thiobacterium, Macromonas, Thiovulum, Thiospira, Thiobacillus) or methane or methanol (Methylomonas, Methylococcus). Acetic acid bacteria (Gluconobacter, Acetobacter) oxidize ethanol to acetic acid. Some fix N2 (Azotobacter, Beijerinckia, Rhizobium, Bradyrhizobium, the latter to in endosymbiontic association with plants) some are bioluminescent (Photobacterium cultured by some marine fish in light organs, Beneckea lives free, Xenorhabditis associates with nematodes and nematode-eating insects) some are endosymbionts of ciliates (Caedibacter) some produce bright pigments: violet (Chromobacterium), red (Serratia, Beneckea), yellow, orange, red or brown (Aeromonas) Rhodobacteria photosynthethic purple bacteria plus colourless relatives no chlorosomes, phycobilisomes, thylacoids photo-machinery in cytoplasmic membrane invaginations contains bacteriochlorophyll c and d, purple carotenoid spec: Rhodospirillum, Rickettsia, Agrobacterium, Escherichia, Haemophilus, Spirillum, Chromatium Thiobacteria non-photosynthetic, often sulfur dependent spec: Desulfovibrio, Thiovulum, Bdellovibrio, Myxococcus From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

17 Azotobacter (Proteobacteria)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

18 Stigmatella (Proteobacteria)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

19 Bdellovibrio (Proteobacteria)
From: Prescott, L.M. et al 1996 Microbiology. WCB, Dubuque

20 Caulobacter (Hyphomicrobia Proteobacteria)
From: Dworkin, M. 1985 Developmental biology of the bacteria. Benjamin/Cummings Publ. Co, Reading Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

21 Ancalomicrobium (Hyphomicrobia Proteobacteria)
From: Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore

22 Pedomicrobium (Hyphomicrobia Proteobacteria)
1 mother cell with hyphae and buds 2 young bud 3 mature bud with flagellum 4 swarmer cell 5 young mother cell attached to surface 6 mature mother cell, beginning bud formation From: Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore

23 Myxococcus (Thiobacteria Proteobacteria)
From: Dworkin, M. 1985 Developmental biology of the bacteria. Benjamin/Cummings Publ. Co, Reading

24 Leucothrix (Thiobacteria Proteobacteria)
From: Staley, J. T. et al 1989 Bergey’s manual of Systematic bacteriology. William & Wilkins, Baltimore

25 Saprospira (Flavobacteria Sphingobacteria)
sphingolipids; no flagella, usually glide photosynthetic anaeorobes with chlorosomes (Chlorobium, Ancalochloris, Chlorochromatium, Chloherpeton, Chloronema, Pelodictyon, Prosthecochloris) or non-photosynthetic fermenting gliders (Flavobacterium, Cytophaga, Capnocytophaga, Saprospira, Sporocytophaga, Herpetosiphon) substrates: agar, cellulose, chitin, other arganic compounds phytosyntherizers use H2S or Na2S and produce S (intra- or extra-cellularly) or oxydized sulfur compounds; frequently associate with facultatively oxygen-respiring heterotrophic bacteria (mats, stromatolites) produce bright pigments: yellow, pink, green. From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

26 Chlorochromatium (Chlorobibacteria Sphingobacteria)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

27 Posibacteria (Gram-positive bacteria plus mycoplasmas, thermotogales)
single cytoplasmic membrane only, no outer membrane large signal recognition RNA acyl ester lipids; murein widespread

28 Streptomyces (Actinobacteria)
cell walls, if present, thick and with teichoic acids spores exospores (actinospores). The entire cell converts into a spore. Frankia and Actinoplanes have spores in sporangia (like fungi). At least one species of Micromonospora forms endospores, rather than exospores DNA high in guanine and cytosine. uniform morphology: coryneform (unicellular Gram-positives, straight or slightly curved rods with a tendency to form club-shaped swellings) and filamentous. Strong tendency to form colonies and multicellular organisms like fungi (septate or non-septate mycelium; earlier name: actinomyces) Mycelia of Dermatophilus can form flaggelated bacteria, that settle elsewhere while losing the flagella. Some stain Gram-variable substrates: cellolose (Cellulomonas), almost pure water (Arthrobacter), some fix N2 (Nocardia); produces propionic or acetic acids (Propionibacterium) eco: some are plant-symbionts (Frankia), some animal-pathogenes, in soils spec: e.g. Corynebacterium, Arthrobacter (till 20 spines), Cellulomonas, Propionibacterium, Streptomyces (500 spec), Mycobacterium, Actinoplanes From: Dworkin, M. 1985 Developmental biology of the bacteria. Benjamin/Cummings Publ. Co, Reading

29 Bacillus (Endobacteria)
cell walls, if present, thick and with teichoic acids; usually Gram-positive (insect symbiontic Sporomusa stain Gram-negative); no murein in mycoplasma's cell wall spores endospores (heat and desiccation resistent; in water or air; lives for years; rich in calcium dipicolinate; release by desintegration of the mother cell) eco: fermenting obligate anearobes (only Clostridium, Sporomusa) and obligate or facultative aerobes. Some require salt. Psychrophils grow obtimally at -3C, thermophils above 45C. Many species are animal symbionts, some very similar to Bacillus anthrax, which causes anthrax disease. substrates: organic matter, sometimes lichnin, cellulose, pectine; all can use glucose; Sporosarcina ureae transforms ureum into ammonium carbonate; Lactic acid bacteria (Lactobacillus, Streptococcus, Leuconostoc) ferment sugars in milk, producing lactic acid, acetate, formate, succinate, ethanol. Oxygen respiration in Bacillus, Sporosarcina, Sporolactobacillus; Clostridia can fix N2 flagella usually present (polar, peritrichous or laterally inserted) DNA low in guanine and cytosine some produce pigments: reddish brown or orange pulcherrinin, black or brown melanin Bacillus circulans continually rotates as a colony; mechanism unkown Mycoplasma have no cell wall (cannot produce diaminopimelic and muramic acids); no flagella shapes are irregular blobs, filaments, sometimes branched; many have a diameter less than 0.2 mu. Spiroplasma (in plants) are helical and motile (mechanism?) eco: many are symbiotrophs, and cause diseases in animals (tick mediated in Ehrlichia; pneumonia) and plants (``stubborn''); some have less than 500 genes. substrates: complex organic; frequently steroids, such as cholesterol is required (the membrane of Mycoplasma consists for more than one third of cholesterol); all require long-chain fatty acids; more ferment glucose or arginine, with lactic acid and sometimes pyruvic acid as fermentation products spec: Clostridea, Bacillus, Mycoplasma From: Margulis, L. & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY Prescott, L.M. et al 1996 Microbiology. WCB, Dubuque

30 Mycoplasmas (Aphragmabacteria Endobacteria)
From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

31 Thermogota (Togobacteria)
teichoic acids absent murein wall very thin external non-lipid toga eco: obligately anaerobic or microaerophilic thermophiles of sea bottom vents. Thermotoga grows optimally at 80C. substrates: organic matter. Aquifex oxidizes H2, elmental sulfur or thiosulfate by using oxygen (microaerophilic) or nitrate. spec: 4 genera: Thermotogales, Aquifex, Thermosipho, Fervidobacterium (all recently discovered; probably many more to come) From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

32 Archaebacteria single cytoplasmic membrane only, no outer membrane
large signal recognition RNA isoprenoid ether lipids; murein absent presence of N-linked glycoprotein (as in eukaryotes and some other bacteria)

33 Nanoarchaeum equitans (Nanoarchaeota)
Found at 90°C in submarin vents Epibiontic on Archaebacterium Ignicoccus, which grows anaerobically on S, H2, CO2 and produces H2S Intracellular membranes present Diameter 400 m, genome size 0.5 Mbp After: Huber, H., Hohn, M. J., Rschel, R. and others 2002 A new phylum of Archaea represented by a nanosized hyperthermophilic symbiomt, Nature 417:

34 Euryarchaeota Archaeoglobi Halobacteria Methanobacteria Methanococci
Methanomicrobia Methanopyri Thermococci Thermoplasmata Euryarcheota Unicellular Gram-positive and neative some have flagella energy metabolism various, not depending on elemental sulphur methanogens no flagella eco: marine sediments freshwater sediments, animal intestines (ruminants, wood-eating insects) substrates: formate, methanol, acetate; oxydise H2; anaerobic produce methane spec:Methanospirillum, Methanococcus, Mehanothrix extreme halophiles flagella present eco: hypersaline environments (salted fish); aerobic colours salt flats pink with carotenoids cell membrane with derivatives of glycerol diether, no diaminopimelic acid no spore formtion substrate: organic matter, produce methane spec: Halobacterium; Haloferax, Haloarcula, Natronobacterium theromophiles substrate: glutamate and other organic compounds eco: sulfurous hot springs, also in submarine volcanic eruptions; temp C; pH 1-2; aerobic and anaerobic DNA coated with proteins similar to histones (chromosomal proteins of eukaryotes) spec: Thermoplasma, Theromococcales, Archaeoglobales, Pyrodictium, Pyrolobus Methanobacterium From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY Halobacteria sp. strain NRC-1 each cell about 5 μm long.

35 Thermoplasma (Thermoplasmata Euryarchaeota)
Sulfobacteria syn: Crearcheota energy metabolism depends on elemental sulphur spec: Sulfolobales, Thermoproteales, Jim Black Pool thermophiles (Sulfolobus, Pyrobaculum) substrates: elemental sulfur eco: sulfurous hot springs, also in submarine volcanic eruptions; temp C; pH 1-2; aerobic and microaerophilic From: Margulis, L & Schwartz, K.V. 1998 Five kingdoms.Freeman, NY

36 (Thaumarchaeota) Cenarchaeales Nitrosopumilales Sulfobacteria
syn: Crearcheota energy metabolism depends on elemental sulphur spec: Sulfolobales, Thermoproteales, Jim Black Pool thermophiles (Sulfolobus, Pyrobaculum) substrates: elemental sulfur eco: sulfurous hot springs, also in submarine volcanic eruptions; temp C; pH 1-2; aerobic and microaerophilic

37 (Crearchaeota) Acidilobales Desulfurococcales Sulfolobales
Thermoproteales Sulfobacteria syn: Crearcheota energy metabolism depends on elemental sulphur spec: Sulfolobales, Thermoproteales, Jim Black Pool thermophiles (Sulfolobus, Pyrobaculum) substrates: elemental sulfur eco: sulfurous hot springs, also in submarine volcanic eruptions; temp C; pH 1-2; aerobic and microaerophilic

38 Korarchaeum (Korarchaeota )
Sulfobacteria syn: Crearcheota energy metabolism depends on elemental sulphur spec: Sulfolobales, Thermoproteales, Jim Black Pool thermophiles (Sulfolobus, Pyrobaculum) substrates: elemental sulfur eco: sulfurous hot springs, also in submarine volcanic eruptions; temp C; pH 1-2; aerobic and microaerophilic Korarchaeum cryptofilum