Micro-Bio test one Kebaara Baylor

Importance of microorganisms

most populous species, recycle essential elements, carry out photosynthesis, production of food, beverages, antibiotics, vitamins

what is microbiology

organisms and acellular entities too small to be clearly seen by unaided eye usually less than one millimeter, lack distinct tissue breakdown

cellular organisms include

fungi (yeast molds), protists (algae, protozoa, slime molds), bacteria(Escheria coli), archaea (methanogens)

Acellular organisms include

viruses (protein and nucleic acids), viroids (RNA), Satellites (nucleic acid with protein shell), prions(proteins)

5 kingdom system --> 3 domain sytem

Bacteria, Archaea, Eukarya

Bacteria Domain

- single celled

-cell wall with peptidoglycan

-lack membrane bound nucleus

-ubiquitous and can live in extreme environments

-cyanobacteria produce oxygen

Archaea Domain

-distinguished by rRNA gene sequences

-lack peptidoglycan in cell walls

-unique membrane lipids

-have unusual metabolic characteristics (produce methane)

-live in extreme environments

HMP (natural bacteria on our body)

nasal, oral, skin, gastro-intestinal, urogenital

Domain Eukarya

Protists

larger than bacteria and archaea, unicellular, protozoa/algaes/slime molds/water molds

-Algae

photosynthetic and produce much of planet's oxygen

- Protozoa

motile, hunters and grazers of microbial world, aid in digestion of cellulose

-Slime Molds

behave like fungi and protozoa, 2 separate life stages

-Water Molds

grow on freshwater and soil, have produced devastating plant infections/diseases

Fungi

range from yeasts to mushrooms and molds

-yeast

unicellular

-molds/mushrooms

multicellular, absorb nutrients from environment, antibiotics, bread rise, decompose dead organisms

Acellular Infectious Agents

-Viruses

smallest of microbes, requires host cell for replication, cause range of diseases

-Viroids

infectious agents composed of RNA

-Satellites

nucleic acid enclosed in protein shell, must coinfect host cell with a virus to complete life cycle

-Prions

infectious proteins

Tools used for study of microbiology

-microscopes, culture techniques, molecular genetics, genomics

Francesco Stelluti

Bees and weevils

Robert Hooke

published drawings of fungus in "micrographia"

Anton van Leeuwenhoek

first person to observe microorganisms accurately, handheld eye microscope

conflict over spontaneous generation

many thought microorganisms spontaneously existed from nonliving matter

Francesco Redi

disproved spontaneous generation for large animals, proved that maggots were coming from flied laying eggs not spontaneously generating from meats

Redi's experiments

1. placed meat in 3 containers

-uncovered

-covered with paper

-covered with fine gauze to exclude flies

generation of maggots by decaying meat resulted from presence of fly eggs

to find out whether or not spontaneous generation could be true for microorganisms, John Needham developed a broth experiment

mutton broth in flask--> boiled--> sealed = cloudy broth

Lazzaro Spallanzani

flasks with water and seeds--> sealed--> boiled

results: air carries germs to culture medium

Louis Pasteur

swan neck flask experiment. No growth on swan flasks because there was not easy access to outside

Final blow to spontaneous generation by John Tyndall

demonstrated dust carries microorganisms, showed if dust was absent, nutrient broths remained sterile, even if directly exposed to air, provided evidence for existence of heat-resistant forms of bacteria

Golden Age of Microbiology

1857-1914

microbiological techniques refined, microbial metabolism studies, disease producing organisms discovered, better understanding of immunity role

Ferdinand Cohn

showed evidence that heat resistant bacteria could produce endospores

role of microorganisms in disease

wasn't obvious at first, imbalance of 4 bodily fluids was thought to be the cause of disease

microorganisms and disease Agostino Bassi

showed that a disease of silkworms was caused by a fungus

MJ Berkeley

the great Potato Blight of Ireland was caused by a water mold

Heinrich de Bary

smut and rust fungi caused cereal crop diseases

Louis Pasteur

Pebrine disease of silkworms was caused by a protozoan, demonstrated microorganisms carried our fermentations helping with wine industry, developed pasteurization.

Joseph Lister

indirect evidence that microorganisms were the causal agents of disease, developed antiseptic surgery system to prevent organisms from entering wounds, less post-op infections and deaths

Robert Koch

relationship between bacillus anthracis and anthrax, used criteria from Jacob Henle, Koch's Postulates

Koch's Postulates

used for link between microorganism and particular diseases

Injected healthy mice with material from diseased animals, transferred anthrax by inoculation through . series of 20 mice, incubated a piece of spleen containing anthrax bacillus in beef serum, endospores were produced, isolated spores were injected into mice and anthrax developed

1. Microorganism must be present of every case of the disease

2. the suspected microorganism must be isolated and grown in a pure culture

3. Same disease must result when isolated microorganism is inoculated into healthy host

4. same microorganism must be isolated again from diseased host

limitations of koch's postulates

some organisms cannot be grown in pure culture, using humans is unethical, molecular and genetic evidence

koch's work led to developments for studying microbial pathogens

agar- fanny eilshemius hesse

petri dishes

nutrient broth and agar

methods for isolating microorganisms

Charles Chamberland

developed porcelain bacterial filters used by Ivanowski and Beijerinck to study tobacco mosaic disease, determined there were infectious agents smaller than bacteria that passed through the filters, these were shown to be viruses eventually

Pasteur and Roux

discovered incubation of cultures caused attenuation: pathogens lose their ability to cause disease after long intervals of time, developed vaccines for chicken cholera, anthrax, rabies

Immunology and Edward Jenner

used a vaccination procedure to protect individuals from smallpox

Emil von Behring and Shibasaburo Kitasato

developed antitoxins for diphtheria and tetanus

evidence for humoral (antibody-based) immunity

Elie Metchnikoff

discovered bacteria engulfing phagocytic cells in the blood, evidence for cellular immunity

Sergei Winogradsky and Martinus Beijerinck

studied soil microorganisms and discovered nixtrogen fixation, pioneered selective media

Basic aspects of microbiology

concerned with individual groups of microbes, microbial physiology, genetics, molecular biology, taxonomy

Applied aspects of microbiology

concerned with practical problems - disease, water, food and industrial microbiology

Molecular and genomics methods

led to a second golden age of microbiology, restriction endonucleases, first recombinant molecule, DNA sequencing methods, bioinformatics and genome sequencing and analysis

Major fields in microbiology

1)medical microbiology

2)public health microbiology

3)immunology

4)microbial ecology

5)agricultural microbiology

6)industrial microbiology

industrial microbiology

branch of microbiology in which microbes are manipulated to manufacture useful products, penicillin, antibiotics, vaccines, steroids, alcohols, vitamins, amino acids, enzymes, biofuels

Microbial evolution

cellular life discovered in 1977 Swartkoppie Chert, microbial fossils 3.5 billion years old

Definition of Life

cells and organization, response to environmental change, growth and development, biological evolution, energy use and metabolism, homeostasis and regulation, reproduction

First self-replicating entity

RNA, ribozymes in protists showed to be able to splice a section of their internal contents and excrete them necessary for protein and DNA synthesis, was able to perform actions for all three necessary components: DNA and protein and RNA

Ribozymes

RNA molecules that form peptide bonds for proteins, perform cellular work and replication, earliest cells may have been surrounded by liposomes (useful delivery system)

today's RNA

exists and is associated with ribosomes, RNA is catalytic in protein synthesis, may be a precursor to double stranded DNA, can regulate gene expression, ATP is the energy currency

early energy sources under harsh conditions were

inorganics like FeS

universal mushroom looking phylogenetic tree

based on comparisons of small subunit RNA (SSU rRNA) length of a branch is based on how related tow molecules are not time of when they were related, is molecular not organismal.

Last Universal Common Ancestor (LUCA)

the root or origin of modern life is on the bacterial branch but still controversial, archaea and eukarya evolved independently of Bacteria and diverged from common ancestry

Endosymbiotic Hypothesis

origin of mitochondria, chloroplasts, and hydrogenosomes from endosymbiont, SSU rRNa of chloroplasts and mitochondria show bacterial lineage, genome sequences are closely related to proteobacteria and prochloron

Hydrogenosomes

anaerobic endosymbiont

Endosymbiotic organelles

Mitochondria developed from proteobacteria and chloroplasts developed from cyanobacterium

Evolution of Cellular Microbes

mutation of genetic material led to selected traits, new traits and genotypes evolved producing mosaic of genetic info

Bacteria and Archaea increase genetic pool by

horizontal gene transfer within same generation

Hydrogenosomes information

asserts that alpha-proteobacterium endosymbiont was an anaerobic bacterium that produced H2 and CO2 as fermentation end products, hosts lacking external H2 source became dependent on endosymbiont which made ATP by substrate level phosphorylation, symbiont ultimately evolved into a mitochondrion or a hydrogenosome, pyruvate in hydrogenosomes reduces to acetate, H2, CO2 with ATP generated, similar to mitochondria

Microbial diversity

heritable gene changes in Archaea and Bacteria are introduced by mutation, lateral gene transfer

taxonomy definition

science of biological classification

parts of taxonomy

classification, nomenclature, identification

classification

arrangement of organisms into groups (taxa)

nomeclature

assignment of names to taxa

identification

determination of taxon to which an isolate belongs

Natural Classification

arranges organisms into groups whose members share many characteristics, first developed by Linnaeus based on anatomical characteristics, this doesn't provide information on evolutionary relatedness

polyphasic Taxonomy

used to determine the genus and species of a newly discovered microbe, incorporates information from phenotypic and genotypic analysis

Phenetic classification

groups organisms together based on mutual similarity of phenotypes, can reveal evolutionary relationships but not always (not all flagellated bacteria belong to the same phylum) best systems compare as many attributes as possible

Genotypic Classification

comparison of genetic similarity between organisms, individual genes or whole genomes can be compared, 70% homologous belong to the same species

Phylogenetic classification

also called phyletic classification systems, evolutionary development of a species, usually based on direct comparison of genetic material and gene products

Woese and Fox proposed

using SSU rRNA nucleotide sequences to assess evolutionary relatedness of organisms

Taxonomic Ranks

Microbes are placed in hierarchical taxonomic levels with each level or rank sharing a common set of specific features, highest rank is domain (bacteria+archaea=microbes only) (eukarya=microbes and macroorganisms) within domain there's phylum, class, order, family, genus, species, epithet, some microbes have subspecies

Strains

descended from a single, pure microbial culture. Vary from each other in many ways:

-Biovars: differ biochemically and physiologically

-Morphovars: differ morphologically

-serovars: differ in antigenetic properties

Type strains

usually one of the first strains of a species studied, often most fully characterized, not necessarily most representative member of species

Species

collecrtion of strains that share many stable properties and differ significantly from other groups of strains

Genus

well defined group of one or more strains, clearly separate from other genera, often disagreement among taxonomists about the assignment of a specific species to a genus

binomial system of nomenclature

devised by Linnaeus, each organism has 2 names, genus is italicized and capitalized, species epithet is italicized and lowercase, can be abbreviated after first use, a new species cannot be recognized until it has been published in the Journal of Systematic and Evolutionary Microbiology

techniques for determining microbial taxonomy and phylogeny

classical characteristics: morphological, physiological, biochemical, ecological

some physiological and metabolic characteristics used in classification and identification

-carbon, nitrogen, energy sources

-cell envelope constituents

-fermentation products

-motility

-oxygen requirements and tolerance

-pH and temperature optimum growth range

-photosynthetic pigments

-salt requirements and tolerance

-secondary metabolites formed

-storage inclusions

Ecological Characteristics

life cycle patterns, nature of symbiotic relationships, ability to cause disease in a particular host, habitat preferences (temp, pH, oxygen, osmotic concentrations), growth requirements

Molecular approaches

important because almost no fossil record was left by microbes, allow for collection of a large and accurate data set from many organisms, provides info for phylogenetic inferences on evolutionary background, compared to standards and type strains to phylogenetically identify

Nucleic Acid sequencing

SSU rRNAs are sequences of 16s and 18s rRNA most powerful and direct method for inferring phylogenies and making assignments at genus level

comparative analysis of 16s rRNA sequences

oligonucleotide signature sequences found, short conserved sequences specific for a phylogenetically defined group of organisms, signature sequences for a lower taxon may be found in the variable regions of a higher taxon like Pseudomonus in bacteria

Phylotype

any uncultivated microorganism identified solely on its nucleic acid sequence (or other observable, quantifiable phenotype)

whole genome comparison

identification to the species level requires detailed gene-by-gene comparison of its closest relatives

Average Nucleotide Identity (ANI)

uses pairwise alignments between all sequences shares between two genomes and calculates the fraction of identical nucleotides

DNA-DNA hybridization (DDH)

performed by mixing genomic data from two strains, heating to denature, then cooling; non-complementary regions remain unpaired and degree of renaturation is calculated

G+C content

percentage of the bases in DNA that G+C; G+C content of strains within a species is constant and varies little within a genus

Subspecies and strain identification

requires analysis of genes that evolve more quickly than rRNA encoding genes

Multilocus sequence analysis (MLSA)

seuquencing and comparison of 5 to 7 housekeeping genes is done to prevent misleading results from one gene; often performed from whole gneome sequences (wgMLSA) which enables extended gene by gene comparison

Single Nucleotide Polymorphism (SNP)

looks at single nucleotide changes or polymorphisms in specific genes, such as 16s rRNA , they reveal evolutionary changes

Restriction Fragment Length Polymorphism (RFLP)

uses restriction enzymes to recognize specific nucleotide sequences , cleavage patterns compared

Ribotyping

similarity between rRNA genes determined by RFLP

Phylogenetic Trees

show inferred evolutionary relationships in the form of multiple branching lineages connected by nodes, identified sequences at tips of branches, operation taxonomic unit, nodes represent divergence event, length of branch represents number of molecular changes between two nodes

creating phylogenetic trees from molecular data

align sequences, determine number of positions that are different, express difference, use measure of distance to create tree, organisms are clustered based on relatedness

Parsimony regarding phylogenetic trees

fewest changes from ancestor to organism in question

Phylogenetic tree topologies

unrooted tree: represents phylogenetic relationship but does not provide an evolutionary path, rooted tree: has node that serves as common ancestor

Phylogenetic trees and horizontal gene transfer

exntensive horizontal gene transfer has occurred within and between domains, patterns of microbial evolution is not as linear and treelike as once thought

Core and Pan genomes

core genomes: set of genes found in all members of a species, pan genomes: every gene in all strains of a species, includes core genome plus every additional gene found in at least one strain

concept and definition of microbial species

bacteria nad archaea lack sexual reporduction, enxtensive morphological features, and a dfossil record microbiologists are at a distinct disadvantage when defining species, gold standard for species assignment might not be applicable

Microbial evolutionary processes

bacteria and archaea are asexual, heritable changes occur, mutation, horizontal gene transfer not as important for initial evolution