Lecture 7a: Microbial Diversity in depth

Two ways to describe microbial diversity

Phylogenetic diversity and functional diversity;

Phylogenetic diversity

Grouping microbes into phyla by evolutionary relationships, most often using the 16S rRNA gene sequence;

Functional diversity

Grouping microbes by the activities they carry out;

Example of a function spread across several phyla

Anoxygenic phototrophy;

Example of a function found in a single phylum

Oxygenic phototrophy (cyanobacteria);

Why can't we study many prokaryotes in the lab?

Most cannot be cultured yet, so some phyla are known only from 16S or metagenomic sequences;

Tenericutes

Mycoplasmas: no cell wall, stain Gram negative, often pleomorphic, related to Gram positives

Actinobacteria

High GC Gram positives that include coryneforms, mycobacteria, propionic acid bacteria, and filamentous Streptomyces

Firmicutes

Low GC Gram positives that include lactic acid bacteria, staphylococci, and endospore formers (Bacillus, Clostridium)

Bacteroidetes

Large, varied Gram negative phylum (aerobes and anaerobes) with few unifying traits and dominant in the human large intestine

Acidobacteria

Poorly known, hard to culture phylum recognized only in the last ~20 years that makes up 20-50% of the soil microbial community

Chlamydiae

Gram negative wall type with no peptidoglycan and obligate intracellular parasites with two cell types

Planctomycetes

Budding, appendaged bacteria with a protein stalk and internal membrane-bound compartments, contain peptidoglycan

Cyanobacteria

Gram negative type wall, oxygenic photosynthesis in thylakoids, autotrophs, and some make heterocysts

Proteobacteria

Gram negative and the most metabolically diverse phylum, divided into 6 classes

Which phylum has no cell wall?

Tenericutes (Mycoplasmas)

Which phylum is the high GC Gram positives?

Actinobacteria

Which phylum is the low GC Gram positives?

Firmicutes

What are the two Gram positive phyla?

Actinobacteria (high GC) and Firmicutes (low GC)

Which phylum has elementary and reticulate bodies?

Chlamydiae

Which phylum does oxygenic photosynthesis?

Cyanobacteria

Which phylum is the most metabolically diverse?

Proteobacteria

Which phylum makes up 20-50% of soil microbes but is hard to culture?

Acidobacteria

Which phylum contains the endospore formers?

Firmicutes (Bacillus and Clostridium)

Which phylum is dominant in the human large intestine?

Bacteroidetes (Bacteroides thetaiotaomicron)

Alphaproteobacteria

Pathogens and non-pathogens, including Rhizobium (nitrogen-fixing root nodules) and Rickettsia (Rocky Mountain spotted fever)

Betaproteobacteria

Metabolically diverse class that includes the Neisseria species

Gammaproteobacteria

Metabolically and ecologically diverse class with many lab model organisms, including E. coli and Pseudomonas aeruginosa

Deltaproteobacteria

Class with strange behavior, including Myxococcus, Bdellovibrio, and Desulfovibrio

Epsilonproteobacteria

Small class famous for a few microaerophilic, spirillum-shaped pathogens like Campylobacter jejuni

Zetaproteobacteria

Barely studied class with only one known species, Mariprofundus ferrooxydans

Mycoplasma genitalium

Tenericutes: no cell wall, causes urethritis and pelvic inflammatory disease, first free-living bacterium with a sequenced genome, and one of the smallest genomes (~500 kbp)

Mycobacterium tuberculosis

Actinobacteria: acid-fast because of mycolic acids, slow growing (~24 h per generation), and causes tuberculosis

Corynebacterium diphtheriae

Actinobacteria: club-shaped coryneform whose exotoxin inhibits protein synthesis and causes diphtheria

Propionibacterium freudenreichii

Actinobacteria: found in milk and used for Swiss cheese, with flavour from propionate and holes from CO2

Propionibacterium acnes

Actinobacteria: lives on the human body and is non-pathogenic

Streptomyces griseus

Actinobacteria: filamentous soil aerobe that makes streptomycin, a protein synthesis inhibitor active against Gram negatives

Bacteroides thetaiotaomicron

Bacteroidetes: strict anaerobe that dominates the human large intestine and breaks down plant polysaccharides

Chlamydia trachomatis

Chlamydiae: obligate intracellular parasite that causes trachoma, leading to eye scarring and blindness

Gemmata obscuriglobus

Planctomycetes: its nucleoid is surrounded by a true unit membrane

Prochlorococcus

Cyanobacteria: one of the most abundant organisms on Earth and responsible for about half of ocean photosynthesis

Rhizobium leguminosarum

Alphaproteobacteria: forms root nodules on legumes and fixes nitrogen in a symbiosis

Rickettsia rickettsii

Alphaproteobacteria: obligate intracellular pathogen spread by insect bites, causes Rocky Mountain spotted fever, and is the closest relative to the mitochondrion

Neisseria mucosa

Betaproteobacteria: non-pathogenic commensal on mucous membranes

Neisseria gonorrhoeae

Betaproteobacteria: causes gonorrhea

Escherichia coli

Gammaproteobacteria: Gram negative facultative rod with peritrichous flagella that ferments lactose and indicates fecal contamination

Pseudomonas aeruginosa

Gammaproteobacteria: rod with polar flagella that does not ferment sugars, resists many antibiotics and disinfectants, and is an opportunistic pathogen

Myxococcus xanthus

Deltaproteobacteria: gliding predator that lyses other bacteria and forms fruiting bodies with myxospores when starved

Bdellovibrio bacteriovorus

Deltaproteobacteria: curved, motile predator that enters Gram negatives and multiplies in the periplasm

Desulfovibrio

Deltaproteobacteria: obligately anaerobic sulfate reducer linked to oil well souring

Campylobacter jejuni

Epsilonproteobacteria: microaerophilic, spirillum-shaped pathogen spread by undercooked chicken that causes gastroenteritis and bloody diarrhea

Mariprofundus ferrooxydans

Zetaproteobacteria: the only known species in its class

Lactobacillus delbrueckii

Firmicutes: lactic acid bacterium used in yogurt

Streptococcus pyogenes

Firmicutes: lactic acid bacterium that causes strep throat, scarlet fever, and flesh-eating disease

Staphylococcus aureus

Firmicutes: grape-like clusters on skin, halotolerant, frequent cause of nosocomial infections, and yellow on mannitol salt agar

Staphylococcus epidermidis

Firmicutes: normal skin commensal that stays pink on mannitol salt agar

Bacillus subtilis

Firmicutes: aerobic endospore former and a lab model for Gram positive structure and endospore differentiation

Clostridium botulinum

Firmicutes: strictly anaerobic endospore former that grows in canned foods and makes the neurotoxin that causes botulism

Thermus aquaticus

Source of Taq DNA polymerase, used in PCR

Deinococcus radiodurans

Extremely radiation resistant thanks to DNA repair, forms pairs or tetrads, and stains Gram positive despite a Gram negative wall type

Which bacterium causes tuberculosis?

Mycobacterium tuberculosis

Which bacterium causes diphtheria?

Corynebacterium diphtheriae

Which bacterium causes Rocky Mountain spotted fever?

Rickettsia rickettsii

Which bacterium causes gonorrhea?

Neisseria gonorrhoeae

Which bacterium causes trachoma?

Chlamydia trachomatis

Which bacterium causes botulism?

Clostridium botulinum

Which bacterium causes strep throat and scarlet fever?

Streptococcus pyogenes

Which bacterium in undercooked chicken causes bloody diarrhea?

Campylobacter jejuni

Which bacterium causes urethritis and pelvic inflammatory disease?

Mycoplasma genitalium

Mycoplasma vs Mycobacteria cell wall

Mycoplasma has no cell wall while Mycobacteria have a Gram positive wall with a mycolic acid layer

Bacillus vs Clostridium

Both are endospore formers, but Bacillus is aerobic and Clostridium is strictly anaerobic

E. coli vs Pseudomonas flagella

E. coli has peritrichous flagella and Pseudomonas has polar flagella

S. aureus vs S. epidermidis on mannitol salt agar

S. aureus makes acid and turns the agar yellow while S. epidermidis makes no acid and stays pink

Elementary body vs reticulate body

Elementary body is small, dense, and infective while reticulate body is larger, vegetative, and not infective

Cyanobacteria vs chloroplasts

Both photosynthesize in thylakoids, but cyanobacteria have cell walls with peptidoglycan

How must canning prevent botulism?

Reach above 120°C to destroy endospores or add enough acid or sugar to prevent germination

Why can phosphate cause cyanobacterial blooms?

Many cyanobacteria fix N2, so a phosphate imbalance alone can trigger blooms

Why might LUCA have been a hyperthermophile?

Several deeply branching bacterial phyla are hyperthermophili