Please enable JavaScript.
Coggle requires JavaScript to display documents.
Chapter 2: Microorganism Biodiversity - Coggle Diagram
Chapter 2: Microorganism Biodiversity
:two: :large_blue_circle: :one: Classification and identification method
:red_circle: :one: Conventional
:large_blue_circle: :two: Morphological
useful for identifying eukaryotes
dichotomous key: paired statements describing characteristics of organism
:large_blue_circle: :three: Staining
gram staining, acid-fast staining
:large_blue_circle: :one: Biochemical
determines presence of bacterial enzymes (enzymatic activity)
eg: API KIT, ENTEROTUBE, VITEX
:red_circle: :two: Advanced
:large_blue_circle: :two: Serology
:black_circle: :one: Latex agglutination
combine known antiserum plus unknown bacteria
slide agglutination slide
Agglutination assay to detect antigens
:black_circle: :two: ELISA
enzyme-linked immunosorbent assay
known antibodies
unknown type of bacterium
antibodies linked to enzyme
enzyme substrate
ELISA test principles animated HD
direct sandwich ELISA
indirect ELISA
:large_blue_circle: :three: Genetic
:black_circle: :one: PCR
to detect small amounts of microbial DNA in a sample
amplify a few copies of DNA across several orders, generating thousands copies of particular DNA sequence
amplification used for
DNA fingerprinting
,
sequencing
and
detection of specific nucleotide sequence characteristics of specific organism
Polymerase chain reaction (PCR)
:black_circle: :two: DNA fingerprinting
DNA typing: isolating & making images of sequences of DNA
electrophoresis
:black_circle: :three: metagenomic
study of metagenomes, genetic material recovered directly from environmental samples
based on recent development of high through put sequencing technology
identify
one colony
, isolate and send the
colony
for sequencing
identify
more colony
, repeat operations for each
single colony
provides a clear picture of the microbial community
:large_blue_circle: :one: FISH
Fluorescent In Situ Hybridization
FISH
bacteria do not grow well in lab, use FISH
FISH detect directly the presence of the suspect in small sample
technique used to detect chromosomal abnormalities
DNA probes annealing to specific target sequence of sample DNA
attached to probes, fluorescent reporter under fluorescence microscopy
Taxonomy: science classification of living forms.
Taxonomy obj
to establish
relationships
between one group of organisms and another and differentiate them
to provide
universal names
for organisms
to provide a common
reference
for identifying organisms
Three domain system
Bacteria
Archaea
Eukarya
Scientific nomenclature
common names
vary with languanges
vary with geography
binomial nomenclature
[genus noun :heavy_plus_sign: specific epithet (species adj)]
eg:
Homo
(man)
sapiens
(wise)
eg:
Rhizopus
(root)
stolonifer
(shoot or long hyphae)
Taxonomic hierarchy
domain, kingdom, phylum, class, order, family, genus, species, (common name)
aphykofags
Methods
classification
placing organisms in groups of related species.
list of characteristics
of
known
organisms
identification
matching characteristics
of an
unknown
organism to lists of
known
organisms
clinical lab identification
:two: :large_blue_circle: :two: Microbes
Bacteria
begin with van Leeuwenhoek's first examination of tooth scrapings
characteristics
single-celled
shape, arrangement
spherical
rod
spiral
filamentous
lack cell nucleus
lack membrane-enclosed intracellular structure
absorb nutrient from environment
Peptidoglycan rRNA signature cell wall
types, phylum
proteobacteria, gram :heavy_minus_sign:
Alphaproteobacteria
Betaproteobacteria
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
nonproteobacteria, gram :heavy_minus_sign:
Cyanobacteria
Chlamydiae
:purple_heart: & :green_heart: photosynthetic bacteria, gram :heavy_minus_sign:
Chlorobi
Chloroflexi
firmicutes, gram :heavy_plus_sign: :arrow_down: G+C
Clostridia
Mollicutes
Bacili
actinobacteria, gram :heavy_plus_sign: :arrow_up: G+C
Streptomyces
role
Nitrogen fixation
Azospirillum
grow in soil, using nutrients excreted by plants
fix nitrogen
Rhizobium
fix nitrogen in the
roots
of plant
decomposer: sewage treatment
food industry: lactic acid as preservatives, acetic acid as vinegar
probiotic: digestion systems
medicine & cloning: insulin, hormone, antibiotics
microbial diversity
1 :spoon: of garden soil - 100,000 microbes
1L seawater - 1billion microbes
only named 0.5%
not identified because
haven't been cultured
need special nutrients
part of complex food chains require the products
need to cultured to understand their metabolism and ecologicale role
MacConkey agar
pink, gram :heavy_minus_sign:, lactose fermenter
Escherichia coli
colorless, gram :heavy_minus_sign:, non-lactose fermenter
Serratia marcescens
News
Listeria costaricensi
not harmful
lead to discovery of antibiotics
could help treat people facing bacterial infections
Archaea
types
hyperthermophiles @ extreme thermoacidophiles
grow in extremely
hot
environment
Pyrodictium
Sulfolobus
obligate aerobe, facultative aerobe,@ obligate anaerobe
hot springs, geothermally heated marine sediments, submarine hydrothermal vents
eg: Grand Prismatic Spring of Yellowstone National Park
methanogens
Methanobacterium
strict anaerobes that produce
methane
(CH4) from CO2 & H2
waterlogged soils, lake sediments, G.I. tracts of animals and human
extreme halophiles
require :arrow_up: concentrations of
salt
for survival
Halobacterium
obligate aerobe
Great Salt Lake, salt-preserved food
eg:
Pyrodictium abyssi
found in deep-ocean sediment temp 110C
Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN)
discovered in acid mine drainage
characteristics
Pseudomurein rRNA signature cell wall
news
Candidatus Methanothrix paradoxum
(microbes producing methane)
Lake Erin wetland
scientists showed that microbes produce methane in an oxygen-rich environment
this finding disproves the long-accepted idea that O2 limits microbe's ability to produce methane
Fungi
types
mold
fungal body (thallus) consists of long
filaments
(hyphae) [plural hyphae: mycelium]
aerial hyphae: reproduction
vegetative hyphae: obtaining nutrients
pathogenic dimorphic 25C
yeast
non filamentous
unicellular
fission yeasts: divide symmetrically
budding yeasts: divide asymmetrically
replicating yeasts
budding yeasts
Saccharomyces cerevisiae
pathogenic dimorphic 37C
Mycology - study of fungi
characteristics
chemoheterotroph
multicellular, except yeast
arrangement
unicellular
filamentous
fleshy
absorptive food acquisition method
sexual & asexual spores
:red_cross: embryo form
fungal dimorphism
conversion of certain fungi from one phenotype to another (change environment)
advantages
Saccharomyces cerevisiae
(bread, wine, HBV vaccine)
Trichoderma
(cellulase enzyme)
Taxomyces andreanae
(taxol drug)
Entomophaga maimaiga
(biocontrol)
Paecilomyces
(kills termites)
disadvantages (Mycoces-fungal diseases)
systemic mycoses (deep within body)
subcutaneous mycoses (beneath the skin)
superficial mycoses (localized, hair shafts)
cutaneous mycoses (affect hair, skin, nails)
opportunistic mycoses (caused by
normal
microbiota @ environmental fungi)
news
fungal spores + nutrients placed together in concrete matrix (mixing process)
when cracking occurs, H2O and O2 find their way in
the dormant fungal spores will germinate, grow & precipitate CaCO2 to heal the cracks
Protozoa
types, phylum
archaeazoa
:red_cross: mitochondria
multiple flagella (
Giardia lamblia
,
Trichomonas vaginalis
no cyst stage)
Trichomonas vaginalis
Giardia
trophozoites
Giardia
cyst
amoebozoa
move by pseudopods
Entamoeba
amebiasis
Acanthamoeba
chronic granulomatous amoebic encephalitis (GAE)
apicomplexa
:red_cross:motile
intracellular parasites
Plasmodium
(Malaria)
complex life cycles
Babesia
(Babesiosis)
Cryptosporidium
(Cryptosporidiosis) - diarrheal disease cryptosporidiosis
Cyclospora
(Cyclosporiasis) - intestinal illness by Cylospora cayetanensis, consuming food @ water with that parasites
ciliophora
move by cilia
complex cell
Balantidium coli
is the only human parasite
euglenazoa
move by flagella
Euglenoids
photoautotroph - harmless
Trypanosoma
African trypanosomiasis @ sleeping sickness
characteristics
kingdom - protist
chemoheterotroph
:red_cross: multicellular
unicellular arrangement
absorptive & ingestive food acquisition method
motility, some form cysts
:red_cross: embryo formation
moist habitats (freshwater, marine environment, soil)
asexual reproduction (fission, budding, schizogony - multiple fission)
sexual reproduction (conjugation)
some parasites for plants & animal
vegetative form - trophozoite (growing stage)
news
Cryptosporidium parasite potentially endangering the health of the general public
at Blountsville pool
Algae
types
diatom
pectin & silica cell walls
unicellular
store their energy mostly as fat & oil in large globules
fossilized diatoms formed oil
produce domoic acid - toxin in mussels that can cause diarrhea & memory loss
phytoplankton
@ dinoflagellates
cellulose in plasma membrane
unicellular
store starch
some are symbionts in marine animals
neurotoxins cause paralytic shellfish poisoning
characteristics
kingdom - protist
photoautotroph
some multicellular
arrangement
unicellular
colonial
filamentous
tissues
diffusion food acquisition method
features characteristics - pigments
none embryo formation
by color
brown
kelp
:red_circle:
grow at deeper levels
:green_heart:
similar to plants
diatoms unicellular produce neurotoxins
dinoflagellates cause neurotoxins
algal habitats
role in nature
primary producers in aquatic food chain
produce most of molecular O2
much of our petroleum is fossil remains of plankton
many unicellular algae are symbionts in animals
news
diatoms - microalgae that produce the O2 for every 5th breath we take
survive their harsh environment
EPS protect cells from environment
helping them move and float & influence the formation of sea ice
can trap bubbles & get carried into atm
get eaten by bacteria & enter food chain @ get buried in sediment
Virus
characteristics
intracellular parasites
contain DNA @ RNA
contain protein coat (capsid)
some enclosed by envelope
some have spikes
most viruses only infect specific types of one host cells
host determined by specific host attachment sites & cellular factors
virus sizes
structure
nucleic acid (DNA @ RNA)
capsid (capsomeres)
option envelope
option spikes
types
helical virus
influenzavirus
herpesvirus
ebola virus
classification
modern
nucleic acid type
replication strategy
morphology
classical
presence @ absence of lipid membrane (envelope)
Cyctoviridae
-
Kystic
bladder, sack
size of the virion
Parvoviridae
-
Parvus
small
nature of the nucleic acid in the virion (DNA @ RNA)
Hepadnaviridae
whether @ not the genome is segmented
symmetry of the protein shell (capsid)
Baculoviridae
-
Baculum
stick
type of nucleic acid single stranded @ double stranded
Baltimore
developed by David Baltimore
types of genome (DNA, RNA, single-stranded, double-stranded)
method of replication
growing viruses
embryonated eggs
cell culture
lab animal
news
3 people in Uganda & Kenya died from an extremely rare
caused by Marburg virus
virus related to another notorious virus, Ebola virus
both members of the "filovirus"
