10-taxonomy and major groups of bacteria.ppt

Taxonomy and Major Groups of Prokaryotes Dr. Akepati S. Reddy School of Energy and Environment Thapar University Patiala (PUNJAB) – 147001 INDIA

Taxonomy Taxonomy • A system of cataloging organisms • A science of classification organisms (preferably based on their evolutionary relationships) with the goal of showing relationships amongst them • Viewed to include 3 separate but interrelated areas: – Identification – Classification – Nomenclature

Identification • Involves characterization or knowing the properties of organisms – cell wall composition, morphology, differential staining, biochemical testing, etc.

• Determining to which species the organism belongs through direct comparison with known taxonomic groups • Bergey‟s Manual of Deterministic bacteriology is the standard reference for laboratory identification of bacteria

Taxonomy Classification • Process of arranging organisms, on the basis of shared properties, into similar or related groups (taxa) – Arrangement according to their phylogenetic relationships (phylogeny: evolutionary history from a common ancestor) is preferred – for determining the phylogenetic relationships molecular biology techniques are used In prokaryotes and fossil records are mainly used in eukaryotes

• Historically prokaryotes were classified on the basis of their phenotypes (morphology, staining reactions, biochemistry, substrates/products, antigens, etc.) • Modern classification is based on the genome (genetic information carried in genes) which provides information on the phylogenetics of organisms – homologous genes (genes having common ancestor), specially orthohomologs (genes belonging to different species but retained their original function), are used – 16S rRNA gene present in the small sub-umit of the ribosome (SSR) in prokaryotes and 18S rRNA gene present in the SSR of eukaryotes has been used

Taxonomy Approach followed in the classification • Defining a group of bacteria derived from a single cell as a strain – Strains have small genetic differences (may be in nutrition, antibiotic resistance, toxins, etc.)

• Grouping together of closely related strains into a specie • Grouping related species into a genus, related genera into a family, related families into an order, related orders into a class, related classes into a division or phylum and related phyla into a kingdom – cataloguing organisms into a taxonomic hierarchy! Taxon (a group or category of related organisms) • Species, genus, family, order, class, phylum, kingdom each one of these is known as a taxon (pl. taxa) • species is taxon at the lowest level and domain or kingdom is taxon at the highest level • Lower level taxa become included in the higher level taxa – members of a lower level taxon (e.g., species) are more similar to each other than those of higher level taxon – members of a taxa are more similar to each other than to those of a different taxon at the same hierarchical level – If two organisms are members of a same taxon, one can infer certain similarities between the two organisms

Taxonomy Definition of species • Species concept applicable to eukaryotes is not applicable to prokaryotes • A eukaryotic species is a group of organisms that interbreeds but does not breed with individuals of another species • Definition of a prokaryotic species is quite difficult – organisms belonging to the same species must share many properties with eachother than with organisms of any other species – Must have similar molar percentage of G+C – DNA must show a minimum of 70% reassociation

Whittaker‟s classification places all the prokaryotes under one kingdom, Monera 3 domain classification places prokaryotes under two domains (bacteria in one domain and Archaea in the another) – This classification is based on sequence of rRNA in ribosomes, tRNA, plasma membrane lipid structure and sensitivity to antibiotics

Bergey‟s Manual of Systematic Bacteriology provides a standard reference for the classification of prokaryotes

Taxonomy Using dichotomous key • • •

Involves use of specific criteria posed as questions for assigning an organism to a specific taxon Criteria are arranged as a dichotomous key and the questions are hierarchically arranged just as the taxonomical categories Each of the questions must only have two possible answers – answer for one question decides path for the next question

Numerical taxonomy • • •

• •

•

A method of classification of organisms using a pool characteristics Larger number of characteristics increase accuracy of detection of similarities among organisms – choosing genetic characteristics enable understanding even the of evolutionary relationship No one characteristic is considered as more important than others all characteristics are weighted equally Similarity Coefficient is found between the compared strains and used in the classification The organism is compared against several control species for a multitude of characteristics and results are presented in the form of scores – based on the shared properties grouping is carried out Greater the similarity coefficient, closer relatedness is inferred.

Taxonomy Nomenclature The system of assigning names to organisms and to taxa • Names can be from any language but they must be latinized (name is italized to indicate that it is latinized) • Name can be either descriptive or it can be in honor of a related scientist – Staphylococcus aureus (staphylococcus refers to the clustered arrangement of cocci cells and aureus refers to the colour of the colony) – Escherichia coli (Escherichia refers to the name of the discoverer Theodor Escherich and coli refers to the intestinal habitat of the organism)

Scientific nomenclature (binomial nomenclature) of organisms • Linnaeus is responsible • Each organism is assigned with two names (two lower level taxa, genus and species)

Viruses are exceptions for binomial nominclature

Taxonomy Rules for assigning names are established/published by • International Committee on Systematic Bacteriology for bacteria • International Code for Botanical Nomenclature for fungi & algae • International Code of Zoological Nomenclature for protozoa

Rules for the binominal nomenclature • In the name genus name comes first, & then the species name • First letter of genus name should be capitalized and rest of the name should be written in lower case letters • Entire name should be either italicized or underlined (Escherichia coli) • Genus name can be abbreviated by its first letter (capitalized) – can be abbreviated only if used in conjunction with species name (i.e., E. coli) – for avoiding ambiguity prior to the abbreviated name, when used first, the name without abbreviation must be used

• Genus name can also be used alone, but not the species name (i.e., "Escherichia," alone is legitimate while "coli" is not) • Strains are indicated by adding number and/or letter (E. coli K12; E. coli 0157:H7)

Hierarchical Classification Taxon

Name

Name

Domain Phylum

Bacteria Proteobacteria

Bacteria

Class

Gammaproteobacteria

Order

Enterobacteriales

Family

Enterobacteriaceae

Genus

Escherichia

Species

coli

Strain:

O157:H7

Spirochaetes Spirochaetes Spirochaetales Spirochaetaceae Spirochaeta plicatilis

Taxonomic hierarchy shows evolutionary or phylogenetic relationships among organisms

Characterization of Prokaryotes Prokaryotes are characterized by morphological, physiological, metabolic and genetic features

Morphological features: • • •

Features of organisms visually perceived through staining and microscopic examination For prokaryotes morphological diversity is very limited Size and shape of cells; size and shape of colonies; spores; sheaths, capsule and appendages; staining (gram and acid fast) characteristics, etc.

Physiological features: • • •

Range of physical and chemical environmental conditions under which organisms survive or live For prokaryotes physiological diversity is very high Temperature, light, pressure, oxygen, pH, etc.

Metabolic features: • •

Refer to how organisms make their living (carbon source, energy source, electron donors and acceptors, etc. for them) Fermentation of selected nutrients; Photoautotrophy and photoheterotrophy (unique for prokaryotes); chemoautotrophy (unique for prokaryotes) and chemoheterotrophy; etc.

Characterization of Prokaryotes Genetic features • Represent true and heritable characters of organisms present in genes (DNA sequences) • All morphological, physiological and metabolic features are manifested in genetic features • For knowing genetic features sophisticated equipment and molecular biology techniques are required

Phenotypic and genotypic features • Morphological, physiological and metabolic features are phenotypic • Phenotypic features depend on the patterns of gene expression • Genetic differences among organisms do not always manifest into phenotypic differences (differences in gene expression possible) – Phenotypic differences observed may not always be due to genetic differences – Phenotypic differences among organisms may not always be measurable

Methods for Characterization of Prokaryotes Characterization for morphological features • Do not require sophisticated equipment, and can be known through staining and microscopy; and through culturing on culture media in the laboratory • Laboratory culturing helps in knowing colony morphology (size, shape, colour, outline, elevation, refractivity, etc., features)

Characterization for physiological features • Observation of parameters like activity, growth, survival, community diversity under a range of conditions like – temperature, light, pressure, pH, oxygen concentration, salt concentration, antibiotics, metals, etc.

Characterization of metabolic/biochemical features • A battery of biochemical tests (serological tests, fatty acid analysis, etc.) can be used – Determination of possession of various enzymes – Serological tests involving reactions of microorganisms with specific antibodies – Phage typing (determination of susceptibility to various phages)

Methods for Characterization of Prokaryotes Characterization/assessment for genetic features Phylogenetic analysis through • Genetic homology studies (similarity of the DNA or RNA between two organisms) • Comparison of nucleic acid sequences of the genome and of the SSU-rRNA (the conserved sequences are used to capture variable signature sequences to establish phylogeny)

Phylogenetic analysis has resulted in the development of „phylogenetic tree‟ or „tree of life‟ or „cladograms‟ Cladogram: • A branching treelike diagram in which the endpoints of the branches represent specific species of organisms • It is used to illustrate phylogenetic relationships and show points at which various species have diverged from common ancestral forms

Universal phylogenetic tree as determined from comparative ribosomal RNA sequencing.

Rampant gene-swapping is believed to have occurred within early communities of prokaryotes, and first eukaryotes - All the three domains seem to have genomes that are mixes of DNA transferred across the domain boundaries - Some researchers suggest replacing the classical phylogenic tree with a web-like phylogeny

Genetic homology Homology is similarity between two organisms - Genetic homology is similarity of the DNA or RNA between two organisms • Genetic homology (because of minimal interference from phenotype) explains better the evolutionary relationships and can be used for classifying organisms • If two organisms are closely related evolutionarily then their genetic homology is higher • Genetic homology can be determined by determining – base composition – nucleotide sequence – DNA hybridization rates

Base composition • Chargaff‟s rules state adenine is equal to thymine and cytosines to guanines in any organism • Organisms differ in A+T to C+G ratio – the ratio is similar to closely related organisms

Genetic homology (contd..) Determining DNA or RNA nucleotide sequence • Determining the nucleotide sequence information is time consuming and costly • Genomics – study of organisms from genome sequence up rather than from phenotype down DNA hybridization • Heating splits DNA double helix into two strands of DNA and cooling allows the strands to reform into double helices (reannealing) • Mixing of DNA of two organisms and bringing about hybridization will result in different degrees of reannealing depending on the similarities between the two organisms DNA sequence

DNA-DNA Hybridization

Identification of Strains Category below the level of species, such as strain is not usually not considered as a taxon Strains are identified through comparing with type strains/standard strains (usually first example of the strain) Methods available for making these comparisons include • Protein profiling • Immunological reactions • Phage typing

Distinguishing strains can also be done on the basis of differential staining and various other biochemical tests Here phenotypes are being compared and hence not very precise for determining evolutionary relationships

Protein profiling • Involves isolation of proteins of an organism and describing them in terms of their size, charges, etc. • Comparisons are made between the profiles constructed for organisms • More similar organisms display more similar protein profiles

Species and strains (contd..) Immunological reactions • Microorganisms differ in their susceptibility to bind with antibodies and/or to get inactivated as a consequence • This property is used as basis for determining evolutionary relationships

Phage typing • Different strains of organisms may have different surface receptors or restriction enzymes and hence differ in binding of phages to cells and replication of phages in host cells • These differences are used as basis for strain identification

Phage Typing

Bergey’s Manuals Bergey‟s Manuals act as mirror for the world of bacteria First edition of Bergey’s Manual of Determinative Bacteriology was initiated by Society of American Bacteriologists by appointing an Editorial Board for which David H. Bergey was chairman First edition of the Bergey‟s Manual was brought into print in 1923 Subsequent 7 editions were brought out during 2nd –1925; 3rd – 1930; 4th – 1934; 5th – 1939; 6th – 1948; 7th - 1957 and 8th - 1974 Upto 7th edition, the Manual continued to be American classification for bacteria 8th edition in 1974 acquired international character 9th edition, printed in 1994, is different from the earlier editions Parallel to Bergey‟s Manual of Determinative Bacteriology a new manual “Bergey’s manual of systematic bacteriology” was started Second edition of the Bergey’s manual of systematic bacteriology is now available

Bergey’s Manuals 9th edition of Bergey's Manual of Determinative Bacteriology (1994) • A new manual “Bergey’s manual of systematic bacteriology” was started • Different from earlier editions - Included only determinative information white earlier one‟s included both systematic and determinative information • Compiled by abstracting the phenotypic information contained in the first edition of Bergey‟s Manual of Systematic Bacteriology • No attempt was made to offer natural higher classification – arrangement of the book was strictly phenotypic – the bacteria were divided into 35 groups • Introductory material concerning identification and a key to the groups were added • Supposed to serve as reference to aid in the identification of unknown bacteria

Bergey's Manual of Systematic Bacteriology Included information dealing with ecology, enrichment, isolation, preservation and characteristics of bacteria First Edition: included 4 volumes: (1984) - Gram-negative Bacteria of general/medical/industrial imp. (1986) - Gram-positive Bacteria other than Actinomycetes (1989) - Archaeobacteria, Cyanobacteria, & remaining Gram(-) Bacteria (1989) - Actinomycetes

Second edition: includes 5 volumes and 2 kingdoms: Archaeota and Bacteria Volume 1. (2001) 2. (2005) 3. (2006) 4. (2007) 5. (2007)

Contents Archea, cyanobacteria, phototrophs and deeply branching genera Proteobacteria

High G+C gram positives

Notes Includes the domain Archaea and some gram negative bacteria Phylum proteobacteria (related gram negative bacteria) Phylum firmicutes and phylum mycoplasmas Includes actinomycetes

Chlamydiae, Spirachaetes, bacteroidetes and fusobacteria

Each od these distinct phyla have unique r RNA sequence

Low G+C gram positives

Phylogenetic Tree of Life

• Phylogenetic tree of life divides prokaryotes into 2 domains: Archaea and Bacteria • Bergey’s manual of Systematic Bacteriology (2nd edition) follows phylogenetic scheme of classification • ssrRNA analysis indicates Archaea to include three phylogenetically distinct groups • Bergey’s Manual of Systematic Bacteriology recognizes 23 phyla of bacteria

Major groups of Prokaryotes Archaea – Methanogens – Extreme halophiles – Extreme thermophiles

Bacteria – Photosynthetic purple and green bacteria – Cyanobacteria – Spirochetes – Spirilla – Myxobacteria – Lithotrophs – Pseudomonads and their relatives

Bacteria – – – – – – –

Enterics Vibrios Nitrogen fixing organisms Pyogenic cocci Lactic acid bcteria Endospore forming bacteria Actinomycetes and related bacteria – Rickettsias and chlamydiae – Mycoplasmas – Plant pathogenic bacteria

Archaea On the basis of ssrRNA analysis, Archaea are considered to include 3 phylogenetically-distinct groups: Crenarchaeota, Euryarchaeota and Korarchaeota – Crenarchaeota consists mainly of hyperthermophilic sulfurdependent prokaryotes – Euryarchaeota contains the methanogens and extreme halophiles – In case of Korarchaeota only nucleic acids have been detected and no organisms have been isolated or cultured

Archaeal features that distinguish Archaea from Bacteria include no murein in cell wall, ester-linked membrane lipids, etc. Archaea exhibit other unique structural or biochemical attributes which adapt them to their particular habitats Based on the physiology, Archaea can be organized into 3 types – Methanogens – extreme halophiles – extreme (hyper) thermophiles

Archaea 1. Methanogens • Obligate anaerobes - do not tolerate even brief exposure to O2 • Have a type of metabolism that can use H2 as energy source and CO2 as carbon source for growth and in the process produce methane (CH4) • normal inhabitants of the rumen (fore-stomach) of cows and other ruminant animals (cow belches about 50 liters per day of methane) • Methanogens represent a microbial system that can be exploited to produce energy from waste materials

2. Extreme halophiles • Live in environments with very high salt concentrations (5 molar or 25%) - require salt for growth (actually the cells lyse at low NaCl concentrations) • Their cell walls, ribosomes, and enzymes are stabilized by Na+. • These organisms are heterotrophs that are normally aerobic – however high concentration of NaCl limits availability of O2

Archaea 2. Extreme halophiles (contd..) • Capable of supplementing ATP production capacity by converting light energy into ATP using bacteriorhodopsin – light harvesting pigment in the plasma membrane that forms proton gradient across the membrane on reaction with light – potential across the membrane allows ATP synthesis

3. Thermophiles and extreme thermophiles or "hyperthermophiles" • inhabitants of hot, sulfur-rich environments (hot springs, geysers and fumaroles, and thermal vents and cracks in the ocean floor) • Require very high temperature (80 to 105°C) for growth • Membranes and enzymes are unusually stable at high temp. – Thermus aquaticus is a source for taq polymerase used in PCR • Most need elemental sulfur for growth - Some use sulfur as an electron acceptor - Some are lithotrophs (oxidize sulfur as an energy source) – Sulfur-oxidizers grow at low pH (100°C) and salt concentration (about 5%) Phylogenetic analysis has demonstrated existence of at least eleven distinct groups of bacteria Bergey's Manual of Systematic Bacteriology (2001) recognizes 23 distinct phyla of bacteria Bergey‟s Manual of Determinative Bacteriology (1994) (based on morphology, physiology, or ecology) divides bacteria into 35 groups – only 17 major groups are discussed here

Bacteria 4. Photosynthetic purple and green bacteria Conduct bacterial photosynthesis • Occurs under anaerobic conditions and produce no oxygen • Has only one photosystem (photosystem-1) – Phycobilins characterisitc of cyanobacteria are absent – Use chlorophyll other than chlorophyll a (bacterial chlorophylls and carotenoids absorb light)

• Electron donor is not water but sulfur, hydrogen, hydrogen sulfide or organic compounds like succinate or malate • Many store elemental sulfur – may be byproduct of photosynthesis when sulfide is used as electron donor – may use as electron donor in photosynthesis

The bacterium that became an endosymbiont of eukaryotes and evolved into mitochondria may be a purple non-sulfur bacterium

Bacteria 4. Photosynthetic purple and green bacteria Includes purple (sulfur and non-sulfur) bacteria and green (sulfur and non-sulfur) bacteria Purple bacteria: Pigmented with bacteriochlorophylls a or b and carotenoids • Purple sulfur bacteria (Chromatium) – Use hydrogen sulfide as electron donor and produce elemental sulfur granules (external and internal) – further oxidized to sulfurate

• Purple non-sulfur bacteria (Rhodospirillum): – Can not use elemental sulfur as electron donor (Use hydrogen and also organic electron donors, like, succinate, malate, etc.)

Green bacteria: Have bacteriochlorophylls c,d & e – present in vesicles attached to membrane known as chlorosomes • Green sulfur bacteria (Chlorobium) – Use hydrogen sulfide as electron donor and granules of elemental sulfur are deposited outside the cell

• Green non-sulfur bacteria (Chloroflexi/Thermomicrobia) – Typically filamentous and move about through bacterial gliding

Bacteria 5. Cyanobacteria These are prokaryotic cells with gram negative cell walls • Though some form branched filaments and irregular plates or irregular colonies, cells continue to be independent units of life • In the filaments/plates/colonies individual cells are joined together by walls or mucilagenous sheath • From the filaments, fragments (called hormogonia) can break away and develop into new colonies

Most of these have deeply pigmented mucilaginous sheath These have chlorophyll a, carotenoids and phycobilins (phycocyanin and phycoerythrin) • These pigments are present on numerous layers of membrane (comparable to thylakoids of chloroplasts) in the cytoplasm • These utilize photosystem-2 and perform plant type or oxygenic photosynthesis • Glycogen inclusions are present in the cytoplasm as the main storage product

Bacteria 5. Cyanobacteria Cyanobacteria are one of the most significant free-living nitrogen-fixing prokaryotes In filamentous forms nitrogen fixation occurs in heterocysts (specialized, enlarged cells with capabilities to fix nitrogen) • Nitrogen fixation is mediated by the enzyme nitrogenase and occurs only under anaerobic conditions – Thick, specialized, glycolipid cell wall of the heterocyst slows down the rate of oxygen diffusion into the cell – Any O2 diffused into the cell is rapidly reduced by hydrogen, a byproduct of N2 fixation – These are low in phycobilin pigments and have only photosystem-I (must not be producing oxygen)

• These have intercellular connections with adjacent vegetative cells (involved in material exchange!)

Certain cyanobacteria form spores (akinetes: enlarged cells with thickened outer walls), which resistant to heat, freezing and drought – help survival in unfavorable environmental conditions

Bacteria 5. Cyanobacteria Cyanobacteria are aerobic and frequently found in planktonic community – Can grow under fairly extreme environmental conditions (high temp. and salinity), but do not favour acidic waters

Some are symbionts and live in association with eukaryotes (liverworts, ferns, cycads, flagellated protozoa, and algae) – in certain lichens cyanobacteria photosynthetic partners

Cyanobacteria has great ecological importance - play important role in the global carbon, oxygen and nitrogen cycles Cyanobacteria also have evolutionary significance in relationship to plants • Believed as evolutionary forerunners of modern-day plant and algal chloroplasts – believed to have given rise to eukaryotic chloroplasts through endosymbiosis – cyanobacteria are similar to the chloroplasts of red algae

• One group of phototrophic prokaryotes, prochlorophytes, must be a link between cyanobacteria and chloroplasts • Prochlorophytes resumble cyanobacteria on one side (prokaryotic and have chlorophyll a); & with plant chloroplasts on the other side (have chlorophyll b not phycobilins)

Bacteria 6. Spirochetes: Have a unique cell morphology and mode of motility • Cells are very thin, flexible, spiral-shaped • Move by axial filaments/endoflagella (contained within a sheath between cell wall peptidoglycan and an outer membrane) • Endoflagella flex or rotate within their sheath – this causes cells to bend, flex and rotate during movement

Most are free living (in muds and sediments) Some live in associations with animals (in the oral cavity or GI tract) A few are pathogens (leptospirosis in dogs, syphilis in humans and lyme disease in dogs and humans) Leptospirosis: • An infectious disease in dogs, caused by Leptospira • Characterized by jaundice and fever • Transmitted to humans by contact with the urine of infected animals.

Bacteria 6. Spirochetes: Syphilis: • A STD caused by Treponema pallidum • Characterized by three clinical stages: primary secondary and tertiary or late syphilis • primary syphilis is manifested by a skin ulcer called a chancre • secondary syphilis involves infection becoming chronic • During tertiary or late syphilis virtually any tissue in the body can be damaged • If left untreated (by pencillin and another antibiotics), can cause blindness, mental illness, and death Lyme disease: • An inflammatory disease caused by Borrelia burgdorferi that is transmitted by ticks • Characterized initially by a rash followed by flu like symptoms including fever, joint pain, and headache • If left untreated, the disease can result in chronic arthritis and nerve and heart dysfunction

Bacteria 7. Spirilla: Spiral shaped, gram-negative aerobic heterotrophic bacteria inhabiting microaerophilic environment Have rigid cell wall and motility is by polar flagella Some contain magnetosomes and exhibits magnetotaxis (property of movement in relation to earth‟s magnetic field) Metabolize by respiration and never by fermentation Some are oceanic and can grow at high NaCl concetrations (Oceanospirillum grows at 9% NaCl level) Some (Azospirillum) are N2-fixing and enter into mutualistic symbiosis with certain tropical grasses and grain crops • Azospirillum is N2-fixing, plant rhizosphere bacteria – also known to protect the plant against pathogens and immobilize the applied chemicals fertilizers Campylobacter jejuni and Helocobacter pilori are human pathogens (former causes bacterial diarrhea in children and the latter causes peptic ulcers)

Bacteria 7. Spirilla Helicobacter pylori: • Spiral bacterium living in the human stomach (highly acidic environment) • Infects (2/3 of the world population are infected) mucus lining of the stomach and causes peptic ulcers • Has been categorized as group I carcinogen by the International Agency for Research on Cancer (IARC) – associated with gastric cancer and gastric MALT lymphoma • Standard first-line therapy is a one week triple-therapy of amoxicillin, clarithromycin and omeprazole • In many antibiotic resistance is appearing and human immune system is not able to eradicate it

Campylobacter jejuni: • Curved, rod-shaped bacterium commonly found in animal feces (chickens and many bird species) • Cause bacterial diarrhea especially in children • Normally no antibiotics are given - the disease is self-limiting

A chemical is considered a carcinogen if: o It has been evaluated by the International Agency for Research on Cancer (IARC), and found to be a carcinogen or potential carcinogen; or o It is regulated by the Occupational Safety and Health Administration (OSHA) as a carcinogen (22 are regulated).

IARC list of carcinogens o Group 1 Carcinogens: Materials known to be carcinogenic to humans (70) o Group 2A: Materials that are probably carcinogenic to humans (57) o Group 2B: Materials that are possibly carcinogenic to humans (224)

Bacteria 8. Mixobacteria (a group of gliding bacteria): A group of fruiting gliding bacteria inhabiting soils (gliding across substrate and obtaining nutrients) Vegetative cells are typical gram-negative rods These exhibit the most complex behavioral patterns and life cycles among the known prokaryotes When nutrients become exhausted, cells aggregate together and differentiate into multicellular fruiting bodies with mixospores • Myxospores are a type of dormant cells descended from differentiated vegetative cells • In Stigmatella, myxospores are packed into secondary structures (cysts) developing at the tips of the fruiting body Eukaryotic counterparts of these in nature are Myxomycetes or slime molds

Stigmatella

Myxobacterium: Life cycle and Fruiting body

Bacteria 9. Lithotrophs Lithotrophy: a type of metabolism requiring inorganic compounds as sources of energy and is found in both Archaea and Bacteria • Most of these are autotrophs • inorganic substrates utilized include H2, NH3, NO2, H2S, S, Fe++, and CO • Methanogens utilize H2 many extreme thermophiles utilize H2S or elemental sulfur as a source of energy Lithotrophic metabolism does not extend to eukaryotes Typically Gram-negative species Important in the biogeochemical cycling of elements Ecologically important lithotrophic Bacteria include • Nitrifying bacteria (Nitrosomonas and Nitrobacter together convert NH3 to NO2, and NO2 to NO3) and • Colorless sulfur bacteria (Thiobacillus): oxidize H2S to S and S to SO4)

Bacteria 10. Pseudomonads and their relatives Bacteria that morphologically and physiologically resemble members of the genus Pseudomonas Very diverse group of gram-negative rods with strictly respiratory mode of metabolism In Bergey‟s manual these are unified as gram negative aerobic rods and cocci Morphology and habitat of many pseudomonads sufficiently overlaps with the enterics - differences with enterics include • Pseudomonads move by polar flagella (enterics by peritrichous flagella) • Enterics ferment sugars such as glucose - pseudomonads generally do not ferment sugars • Most pseudomonads have an unusual cytochrome in their respiratory electron transport chain (detectable by oxidase test) - oxidase positive! Most are free-living in soil and water and play important role in the decomposition, biodegradation, and Carbon and Nitrogen cycles

Bacteria 10. Pseudomonads and their relatives These are known for their ability to degrade very wide variety of organic compounds • Can degrade insecticides, pesticides, herbicides, plastics, petroleum substances, hydrocarbons and other of the most refractory molecules in nature • But, unable to degrade biopolymers like cellulose and lignin • Further, their role in anaerobic decomposition is minimal

Relatives of pseudomonads • Rhizobium and Bradyrhizobium – Can fix nitrogen in association with leguminous plants but not independently – root nodules are formed – Supply ammonia or amino acids to plants and receive organic acids as carbon and energy sources

• Agrobacterium – Motile rods capable of reducing nitrates (can not fix nitrogen) – Cause tumors (galls) in the host plant – has ability to transfer DNA between itself and host plant (can not infect all plant spp.)

Bacteria 10. Pseudomonads and their relatives Relatives of pseudomonads • Methanotrophs – Use methane & other 1-carbon compounds as source of both carbon and energy – methane combine with oxygen to form formaldehyde and this is incorporated into organic compounds – Occur in soil near methane producing environs – Special interest for researchers studying global warming

• Azotobacters – Rod shaped or spherical non-pathogenic, non-symbiotic, freeliving, nitrogen-fixing bacteria found in soil and water – Can form thick walled cysts and can produce large quantities of capsular slime

• Acetobacters – Have ability to convert alcohol into acetic acid in the presence of air - used in the manufacture of vinegar

Bacteria 10. Pseudomonads and their relatives Most have normal existence in soil, water, on the surfaces of plants and in animals Pseudomonas syringae and Xanthomonas species cause a wide variety of plant diseases • Xanthomonas – Gram negative flagellated rod shaped bacteria – Grow exclusively in plants and cause diseases like citrus canker and black rot – lisions on leaves, fruit and stems and twig dieback occur

Some are very important pathogens in animals and humans (have lesser inclination as pathogens than enterics) • Pseudomonas aeruginosa – Opportunistic pathogen of immunocompromised individuals and infects pulmonary tract, urinary tract, burns, etc. – 1/10th of hospital-acquired infections are by pseudomonas and common cause for burn infections – Resistant to penicillin

Bacteria 10. Pseudomonads and their relatives • Bordotella pertussis (agent of whooping cough) – Fatal disease in children of developing countries -two stages • Catarrhal stage: cough, sneezing and running nose are symptoms • Paroxysmal stage: fits of cough followed by inspiratory whooping sound are symptoms – vomiting may follow the fits

– It is vaccine preventable disease – but, vaccine offers protection only for shorter time • Require immunization at 2, 4, and 6 months, 15-18 months and 4-6 years of age • Immunization after 7 yrs. age, due to side effects not favoured

• Legionella pneumophilia (legionaires‟ pneumonia) – Aquatic organism thriving in warmer environs (25 to 45°C) – cooling towers are important place to find – Affects middle aged and older persons, specially smokers – Severe form of infection is pneumonia – while milder form is known as pontiac fever (a mild respiratory illness)

Bacteria 11. Enterics (Escherichia coli and its relatives) Gram negative rods with facultative anaerobic metabolism – can ferment glucose into acidic end products Live in intestinal tracts of animals – consistent members of the normal flora of humans (have medicinal importance) Phenotypically related to Pseudomonas, but are physiologically quite unrelated E. Coli, type species of enterics, is a regular inhabitant of human intestine Include intestinal pathogens – Shigella dysenteriae (cause of bacillary dysentery) – Salmonella typhimurium (cause of gastroenteritis) – Salmonella typhi (infects via intestinal route and causes typhoid fever)

Some don't have an intestinal habitat but resemble E. coli – Protius is a common saprophyte of decaying organic matter – Yersimia pestis causes bubonic plague – Erwinia is a plant pathogen

Bacteria 11. Enterics Escherichia coli • Live in lower intestines of mammals as part of intestinal flora considered as necessary for proper digestion of food – human being discharges 0.1 to 10 trillion cells/day in fecal matter • Coliform bacteria: All aerobic and facultative anaerobic nonspore forming, gram negative, rod shaped bacteria that can ferment lactose and produce gas within 48 hours at 35°C – Includes fecal coliforms and bacteria similar to fecal coliforms but living in the ground

• Usually harmless but can cause illness specially when they get out of intestinal tract – Cause honeymoon sickness when escape into the urinary tract (into the bladder) – Cause fatal peritonitis when escape into the abdomen (inflammation of peritonium – inner surface of the abdominal cavity and membrane covering of organs of the abdomen)

Bacteria 11. Enterics Escherichia coli • Some strains are toxicogenic and can cause food poisoning (from eating contaminated meat) – harbor both heat stable and and heat labile enterotoxins • Some strains are enteropathogenic and can cause (acute but uncomplicated) intestinal tract infections, uncomplicated UT infections and neonatal meningitis • Growing antibiotic resistance is a problem • Considered as model organism of bacteria and is most studied in biology – Among the first for entire chromosomal DNA base sequence determination – used as indicator of fecal pollution of water – total and fecal coliform counts are used – can sometimes be misleading (also found in environments other than intestine, paper mills – used in the experiments in cell biology, physiology, and genetics and considered as the workhorse of molecular biology – Plays important role in modern biological engineering – Often used as factories for producing substances like insulin

Bacteria 11. Enterics Salmonella typhi Causes typhoid - an extremely serious gastrointestinal tract infection with symptoms of – High or intense spiking fever that raises slowly and chills – Brady cardia (slow heart beat), unrelenting headache and myalgia (muscle pain) – lack of appetite, constipation, and stomach pain – flat rose coloured spots on the trunk – Becoming delirious and suffering intestinal hemorrhage – Delusions and confusion

Has long (about 2 weeks) incubation period – Food or water borne (fecal contamination from infected person – The bacteria multiply in blood stream and get absorbed into digestive tract and then eliminated from body as waste – Recoverers are chronic carriers (harbor salmonella in gall bladder)

Diagnosis: by blood, bone marrow and stool culturing and Widal test (serological test) Treatment: Antibiotics like amphicillin, chloramphenicol, trimethosulfa-methoxazole and ciproflaxacin – development of resistance is a problem (multidrug resistant typhoid fever)

Bacteria 11. Enterics Salmonella typhimurium • Causative of gastroenteritis - also called stomach flu/gastric flu • Non-inflammatory infection of upper bowel or inflammatory infection of colon – infection limited to stomach is gastritis and infection limited to small bowel is enteritis • Acute but self-limiting infection (lasts 3 weeks, chest pain and hemoptysis – systemic symptoms include fever, chills, night sweats, appettite loss, weight loss and easy fategability

Bacteria 17. Actinomycetes and related bacteria Tuberculosis (Mycobacterium tuberculosis) Transmission – Aerosol droplets generated through cough, sneeze, speech or spit spreads the infection – can occur only from people with active TB disease – quantity expelled as aerosol droplets, environment and duration of exposure, virulence of the pathogen also influence infection

Treatment – Multi-drug resistance (resistance to the two first line drugs, rifampicin and isoniazid) and extreme drug resistance (resistance to front line drungs and to 3 or more second line drugs) are emerging as problems – Resistance can be primary (infection by resistant bacilli) or secondary (resistance developed during therapy from inadequate treatment)

Protection – Exposure to non-tuberculous mycobacterium offers some protection – BCG vaccination specially for infants – DNA TB vaccine together with conventional chemotherapy accelerates disappearance of the bacilli and offers protection against reinfection (still in the developing stage)

Bacteria 17. Actinomycetes and related bacteria Streptomyces • Predominantly found in soil and decaying vegetation • Most produce spores – chains of spores are produced on aerial filaments called sporophores at maturity • Unlike other bacteria (which have single circular chromosome), these have single linear chromosome – Genome is the largest of all the known bacteria

• Metabolically very diverse – Produce extracellular hydrolytic enzymes – Degrade all types of substances (sugars, alcohols, amino acids, organic acids, and aromatic compounds) – Considerable interest in these as agents for bioremediation

• Have medicinal and industrial importance – synthesize antibiotics – over 50 different antibiotics have been isolated – more than half of world‟s antibiotics are from streptomyces – streptomycin, neomycin, chloramphenicol and tetracyclines

• Streptomycin – an aminoglycoside – stops bacterial growth by damaging cell membrane & inhibiting protein synthesis

Bacteria 18. Rickettsias and Chlamydiae These are obligate intracellular parasites of eukaryotic cells

Rickettsias • Non-motile, gram negative, non-spore forming, highly pleomorphic (cocci, rods or thread like) bacteria • Have leaky membrane and can not obtain enough nutrients outside the host cell – hence, like virus, grow only in living cells Can be cultured in tissue or embryo cultures • Live in gut lining of arthropods (ticks, fleas, lice, etc.) and transmitted to vertebrates by arthropod bite • Cause diseases like typhus fever, rocky mountain spotted fever, Q fever, and canine ehrlichiosis • Majority are susceptible to tetracycline group of antibiotics

Bacteria 18. Rickettsias and Chlamydiae Rickettsias Typhus fever • Disease is endemic in rodent hosts and spreads to humans through mites and fleas • Symptoms: Fever and headache and smokey or hazy state of mind • Often in tropical countries mistaken for dengue fever

Rocky mountain spotted fever • Originally called as black measles • Serious and potentially life threatening disease of Americas caused by Rickettsia rickettsii • Symptoms: sudden onset of fever, headache anfd muscle pain and development of rash • The causative is maintained in nature by a complex cycle involving ticks and mammals – humans are accidental hosts

Bacteria 18. Rickettsias and Chlamydiae Chlamydiae • Unable to produce sufficient ATP to sustain metabolism outside the host cell (energy parasites!) • Intracellular parasites or endosymbionts of animals, insects and protozoa and colonise and infect tissues of eye and UT in humans • Life cycle includes intracellular replicative form (reticulate body, RB) and extracellular infectious form (elementory body, EB) – – – – –

EB is endocytosed by eukaryotic cell to form vacuole Inside the vacuole EB is transfomred into RB RB takes up nutrients and multiply by binary fission After several multiplications RB transform back into EB EBs are released outside through host cell rupture or through fusion with plasma membrane

• Spread by aerosol or by contact and require no vector • Chlamydia trachomatis causes chlamydia (a prevalent STD) and trachoma (leading cause for blindness) diseases

Bacteria Chlamydia (A STD caused by Chlamydia trachomatis) >50% of the infected do not develop symptoms and about 40% of the infected develop pelvic inflammatory disease Cervix, fallopian tubes, urethra, epidymis, prostate gland, anus, throat and eyes get affected – in case of newborns of infected mothers lungs & eyes are affected – Fail to conceive and tubal pregnancy (development of fertilized egg in the fallopian tubes) can be consequences

Symptoms – Burning pain during urination and more frequent urination – Abnormal vaginal discharge, bleeding between periods and after sex, heavier menstrual bleeding and more painful periods – Dull pelvic pains – Redness at penis tip and white or yellow discharge from penis

Trachoma (Highly contagious eye disease - result in blindness) • Spreads by direct contact with eye, nose and throat secretions and with objects like towels and/or wash cloths • Symptoms: conjunctivitis or irritation similar pink eye – Eye discharge, swollen eyelids, turned-in eye lashes, swollen lymph nodes in front of the ears and corneal scarring

• Treatment: oral antibiotics (sulfanamide) and eye drops • Adequate hygiene and education can prevent infection

Bacteria 19. Mycoplasmas • Resumbles bacteria but lacks cell wall – Cells have a more stable triple layered membrane – Sterols (responsible for stabilityand obtained cholesterol of the hosts) may be present in the membrane

• Smallest known cells (0.2 to 0.3 µm diameter) – have smallest known genome (about 650 genes) and low G-C ratio (18-40%) • Can be free living and saprophytic (in soil and sewage) or parasitic (some are commensals) or pathogenic – Tend to inhabit environments of high osmolarity

• Some are pathogenic in animals and plants – Mycoplasma pneumoniae - causative of pneumonic and other respiratory disorders – M genitalium - one of the causatives of pelvic inflammatory diseases – Mycoplasma by definition is restricted to vertebrate hosts and require cholesterol for growth – Spiroplasma citri - causative of citrus stubborn disease and corn stunt disease

Bacteria 19. Mycoplasmas • Most are resistant to the antibiotics that target cell wall synthesis (penicillin) • Use an alternate genetic code, wherein UGA codon is preferred for tryptophan in place of the usual opal stop Mycoplasma pneumoniae • Genome and proteome are fully characterized • Uses unique genetic code (similar to mitochondria than to other bacteria) • Lacks cellular machinery needed for making essential compounds – similar to viruses than bacteria and live as obligate parasite • Spreads through respiratory droplets • Through attaching to upper and lower respiratory tract causes pharyngitis, bronchitis and pneumonia • Infection caused is known as atypical pneumonia (infection of mild to moderate severity) • Chronic mycoplasma infections are implicated in the pathogenesis of rheumatoid arthritis

Bacteria 20. Plant-pathogenic bacteria • • • •

1/8th of crop is lost to diseases caused by bacteria/ fungi/ insects Most are gram negative bacteria in the families Enterics, and Pseudomonads Very few are gram negative and still fewer are fastidious (mycoplasmas, and rickettsias) Symptoms of bacterial diseases in plants include – – – – – –

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spots (of various sizes) on stems, leaves, flowers and fruits Bacterial blights (rapidly developing necrosis, dead and discoloured areas) on stems leaves and flowers Soft rots of fresh vegetables and fruits during post-harvest stage Wilts (affecting herbaceous plants) from interference to the movement of water and inorganic nutrients causing wilting and death Black rot Galls (swellings formed at the site of infection, usually near the soil line) – affect ornamental plants and fruit stock

Strains that cause plant diseases usually do not infect animals or humans

Bacteria 20. Plant-pathogenic bacteria Erwinia - Enterics isolated from plants – several are pathogens and some are opportunistic pathogens and a few are saprophytes Pseudomonads – causative of leaf spots and cankers with extremely wide host range – grow epiphytically on plant surfaces – some are saprophytes Ralstonia – causative of wilts in solanaceous members Xanthomonas – pseudomonads producing unique yellow pigment and xanthan gum – causative of leaf spots and wilts – very hostspecific Agrobacterium – causative of galls by genetically transofrming normal plant cells into tumer cells – plasmid genes are transferred from the bacterium to the plant cell and incorporated into plant chromosomes