Growth and Kinetics I: Microbial morphology and structure Flashcards
Cell structure – general features
ALL Bacteria and Archaea have the following common features:
- cell membrane(s)
- cell walls in many cases but not all, and very variable. A glycocalyx [pl. glycocalyces]
may be present instead/as well, either as a well-formed capsule or irregular slime
layer. [Gr. masc. n. κᾰ́λῠξ (kálux), coating on a seed; L. masc. n. calyx] - cytoplasm, obviously – we often call this cytosol, it’s interchangeable.
- If they have two membranes (e.g. the Gram-stain-negative Bacteria), they will have a
periplasm too, in the periplasmic space between the two membranes. - respiratory chain is always on inner membrane (IF they respire at all – not all do!!!)
and Δp (proton-motive force) builds in periplasm (if present) or in membrane
invaginations if not). Note many respiratory Bacteria use ΔNa+ (sodium-motive
force) instead! - ribosomes, which vary by Domain of Life [S = Svedberg, a rate of sedimentation in a
centrifuge]. Both the Bacteria and Archaea have 70S ribosomes with about
ribosomal proteins. Each has a 50S subunit (23S and 5S rRNA plus ribosomal
proteins) and a 30S subunit (16S rRNA plus ribosomal proteins). Ribosomal proteins
c. 50 in the Bacteria, c. 60 in the Archaea. - circular genome. Sometimes other replicons too.
Cell structure – general features
Things some Bacteria and Archaea have too on the OUTSIDE:
- pili (pl. pili, sing. pilus) – either used in replicon transfer (‘sex pili’) or in gliding
motility (Type IV pili), particularly in Myxococcus spp.
[L. masc. n. pilus, a hair] - fimbriae (pl. fimbriae, sing. fimbria) used to be called ‘attachment pili’ (on this
module, we say “fimbriae” as that’s correct!) – used for sticking to surfaces and to
other cells.
[L.L. fem. n. fimbria, a fringe] - flagella (pl. flagella, sing. flagellum) fuelled by Δp directly, to provide movement.
Required for rapid tactic responses. Many organisms without flagella (atrichous cells)
are still motile by gliding or magnetotaxis and so on. Cells can have a flagella at one
end (monotrichous) or many at one end (lophotrichous). A single one at each end is
referred to as amphitrichous and cells with flagella all over are peritrichous.
[L. neut. n. flagellum, a whip, a lash, a scourge] - holdfasts– sticky regions for adhering to surfaces e.g. in Hyphomicrobium spp
Cell structure
Things SOME Bacteria and Archaea have too on the
INSIDE:
- membrane-bound nuclei/other regions – unique to the phylum “Planktomycetia”. Highly specialist cellcompartments used to protect DNA from metabolic intermediates. If interested, look at the anammoxosome in members of this phylum that grow autotrophically on ammonia as their electron donor and nitrite as their electron acceptor – the so-called ‘anammox’ Bacteria (we will do them in BIOL322Z next yr if you pick it!). Remember the whole “have no membrane-bound nuclei/organelles” thing you probably got told at some point? It’s not true
- proteinaceous cell compartments – examples include carboxysomes that we will meet in L06 and L07 in quite a lot of detail and enterosomes that maintain low-pH regions for diol metabolism (cf. Penrod and Roth (2006) J. Bacteriol. 188: 2865-2874 – N.B. they wrongly use the word “organelles” for them – strictly speaking, an organelle has a
membrane, but we were less fussy in 2006!)
Cell structure – general features
Things SOME Bacteria and Archaea have too on the INSIDE:
- storage granules– these are usually in the cytoplasm but sometimes in the periplasmic space
(sulfur granules only). - sulfur granules produced only by some chemolithoautotrophs when a lot of sulfide/thiosulfate around
this allows them to turn the sulfur into an insoluble form (mainly S8 rings and amorphous long chains) that
other organisms can’t get at and that they can then use themselves later on. Don’t stain – kind of “twinkle”
on light microscope (I’ll show you images in L06). Actual composition varies with taxon. - polyhydroxyalkanoate (PHA) granules – main types are poly-β-hydroxybutyrate (β-PHB) and poly-γ
hydroxybutyrate (γ-PHB) but longer ones also found. Long-term carbon storage – kind of like
triglycerides in adipose tissue in Homo sapiens L. Bioplastics – commercially very popular at present.
Older names “lipid bodies” and “sudanophilic granules” often used still. - glycogen granules produced in heterotrophic Bacteria are not like glycogen from the Animalia as they
don’t have a the same glycogenin glucosyltransferase (EC 2.4.1.186) enzyme at the core but they are the
same kind of D-(+)-glucose polymer. They are a form of carbon storage but they only last a few minutes so
do not
allow long-term survival during starvation (cf. Sekar et al. (2020) Appl Environ Microbiol 86:
e00049-20). Stain with periodic* acid-Schiff stain
[* “periodic” here is pron. “per-i-O-dic” like “perchloric” etc, not “PEER-i-oh-dic” like the table!]. - polyphosphate granules which we normally call volutin granules or metachromic granules– these are
really a means to storing up inorganic phosphate as an insoluble polymer when there is not much ADP
needing to be phosphorylated into ATP. That means that later on, if inorganic phosphate is less abundant,
they have a store. - insecticide crystals – e.g. δ-endotoxin in Bacillus thuringiensis– stains with any protein stain
like Coomassie brilliant blue R-250 (AB83) and looks like a cartoon diamond! - storage states/forms – like endospores, exospores, cysts etc– see L21 Storage States.
- internal membranes– common in methanotrophs (L09) and some autotrophs (L06).
Subcellular granules etc
Corynebacterium sp. from the class
Actinobacteria, stained to show volutin granules (polyphosphate granules) which are red-black against green cytoplasm. Stain is Albert’s stain which uses toluidine blue and malachite green.
Escherichia coli from the class
Gammaproteobacteria, stained to show polyhydroxyalkanoate granules using Sudan black III. Safranin O has been used as the counterstain to show the cytoplasm. Some people use Nile blue instead of Sudan black III.
Cell walls and membranes
- if a glycocalyx is present, it is on the very outside, and if it is jelly-like, we would
consider it a true capsule, and we can observe them by negative staining (as a wet
mount). Capsules sometimes contain polymers of amino acids, as well as the
polysaccharides. Generally we call the substance capsular polymeric substance
(CPS, also capsular polysaccharide). - India ink (lamp black (PBk7) particles in gum arabic and water) is excluded by the
capsule leaving a ‘halo’ around the cells. Nigrosin WS (ABk2) is also used – this is
water soluble violet-black dye used in most black marker pens, for example. It is a
big, lipophilic molecule so the hydrophilic/water rich slime layer excludes it. - if it is a looser slime layer form of glycocalyx or a thin layer of polysaccharide, we
can observe using Alcian blue 8G (IB1) staining, which picks up polysaccharides.
We generally refer to the substance slime is made of as extracellular polymeric
substance (EPS, also extracellular polysaccharide). Some slimes are very runny,
some are more stuff. - this will come back in the Diazotrophy lecture (L12) bigtime so go over it before
then!
[numbers in parentheses after stains are Color Index Names, which are universal and
can be helpful as stains are known by many alternative names…! They are always
“prefix colour number” so IB1 is Ingrain Blue 1, PBk7 is Pigment Black 7, ABk2 is
acid black 2, SBk5 is Solvent Black 5 etc– not for learning by rote, just helpful when
reading as sometimes differences are subtle e.g. nigrosin (SBk5) and nigrosin WS
(ABk2) are not the same thing at all. You may also see the Color Index Codes e.g. C.I.
50420 for nigrosin WS, but they’re not as user-friendly!]
The Gram stain and cell walls
invented by Gram (1884) and roughly divided the Bacteria into two
groups based on how they interacted with the stain.
Cells are dried and heat-fixed onto a microscope slide.
crystal violet oxalate (blue-violet) is applied in the presence of triiodide
(I3-) ions, which help trap the stain inside of cells.
[at this stage all cells are blue-violet]
Cells are washed with ethanol.
[some cells retain the blue-violet dye, some do not]
Cells are counterstained with either Bismarck brown (red-brown) or
safranin O (pink).
[cells that retained the blue-violet dye still look blue-violet; cells that lost
the blue-violet dye will now appear the colour of the counterstain used]
Cells are examined.
Cells that retained the violet dye are termed Gram-stain-positive.
Cells that lost the violet dye (and thus appear pink or brown) are termed
Gram-stain-negative.
Why does this happen? It relates to the structure of their cell wall.
Two wall types: Gram-stain-negative
. Lipopolysaccharides in outer membrane
. Outer membrane (a phospholipid bilayer with channel proteins etc)
. Periplasm (within the periplasmic space)
. Inner membrane (a phospholipid
bilayer with channel proteins and
respiratory chain (if present))
. Periplasm contains peptidoglycan (murein), which is anchored by proteolipids to the outer membrane.
* these proteolipids are often called Braun’s lipoprotein – the polypeptides are linked to the lipid by a cysteine residue.
Two wall types: Gram-stain-positive
. Sometimes an S-layer and
polysaccharides outside of wall
. Peptidoglycan layer – contains teichoic acids, unlike in Gram-stain-negative walls
. Single membrane (a phospholipid
bilayer with channel proteins and
respiratory chain (if present))
. Teichoic acids are backbones of
repeating sugar alcohols alternating with phosphate groups. Backbones are cross-linked by D-alanine and/or D-lysine.
(sugar alcohols are usually glycerol (C3) and D-ribitol (C5))
Cell walls in the Archaea
- Highly variable! Over 7 wall types.
- No convenient way to group organisms no generalisations one can really make!
- A good review to start your reading: Klingl (2014) Frontiers Microbiol 5: 624.
- We used to use “Gram positive Archaea” etc for some of the structures – stopped in
the 1990s, once it was realised more than 2 types but may see it in textbooks still! - Don’t try and learn them all by heart! But do use this figure to learn a bit more about some of the bugs I talk about in this module and think about ones you read about. Think about them when we do the various groups of extremophile Archaea in Extreme Environments.
