BIOL 10511 Lecture 2 Prokaryotes and the origins of metabolic diversity

(“ways to make a living”)

Background reading for this lecture is Chapter 27 [for those who have not done
biology before, or who want reminders].

As we saw from the last lecture, the prokaryotes have been here the longest, and
are still the most abundant and successful organisms. As I stressed in that
lecture, there is no need to worry about detailed taxonomy. We will be taking the
simplest view possible and considering 3 domains, the first 2 of which (Bacteria
and Archaea) are prokaryotic [handout]. Both groups must have arisen from an
ancestor, but we don’t know anything about that or when the lines of evolution
arose/separated. The focus of this whole unit is “ways to make a living”, the aim
of this lecture is to introduce 4 basic ways – they apply to all organisms; today we
will concentrate on the prokaryotes.

Your handout, and Table 27.1 has 2 major categories for nutrition, each with 2
sub-divisions: autotrophs (self-feeding) and heterotrophs (different way of
feeding). Autotrophs can be sub-divided into those that use energy from
sunlight – photoautotrophs (most plants) and have carbon dioxide as their
carbon source; and chemoautotrophs that use inorganic chemicals instead of
light as their energy source. The latter are less familiar to almost everyone –
they are examined on the back of the handout for today, and I mentioned
hydrothermal vents last time. One sulphur-metabolising thermophile (heat-loving)
Archaean lives in 105C water and oxidises sulphur to get its energy e.g. in mid-
Atlantic ridge, up to 2 miles beneath the surface of the sea. [movie taken from the
ground-breaking 2004 BBC “Abyss” programme, broadcast live – we will come
back to this in later lectures and you can re-watch the movie by going into the
“movies from the lectures” area on Blackboard. If you are interested in deep sea
organisms you might like to see also some of the “additional movies” on the BB
site and New Sci 27th Sept 2006 “Mysteries of the Deep”
http://www.newscientist.com/channel/earth/deep-sea/dn9967 which has links to
articles that have added value in the form of their own links to further reading.
This particular article will be one to which I may refer again later in the course, so
it may be worth accessing – but how many of the additional links you explore, by
clicking on the underlined words and phrases, should depend on what
particularly interests you and how much time you have]

The “Abyss” programme also still has a game you can play if you have time:
http://www.bbc.co.uk/nature/blueplanet/alien/flash/main_game.shtml

The Archaea that can use the sulphides or hydrogen coming out of the black
smoker form the basis of an ecosystem that is entirely free from the sun’s
energy, and the Abyss programme script ended with the suggestion that
hydrothermal vent “bacteria” (Archaea used to be called Archaebacteria) could
be like ancestors of all forms of life on earth, but as I mentioned in last lecture,
there is also support for alternative scenarios.

Heterotrophs are sub-divided into photoheterotrophs – use light as energy

source but require organic form of carbon (few examples – more information and
examples in “Microbes, Man & Environment” unit next semester) and
chemoheterotrophs. The latter use organic compounds as both their energy
and carbon source. We are the most familiar example, but there are many
others eg Rafflesia, a parasitic plant (see Ennos & Sheffield plate 7) - more later
in this unit.

Energy and carbon sources are not the only aspect of metabolic diversity in
prokaryotes. Eukaryotes are very limited with regard to the forms of nitrogen
they can use, but there are some prokaryotes that can use just about any
nitrogenous compounds. You may have covered the nitrogen cycle at A level,
may also cover it in ‘Microbes, Man & Environment’ unit [no need to do it for this
unit!] but even if not, should know how important nitrogen is to all organisms –
some chemoautotrophic bacteria convert ammonium to nitrite, others ‘denitrify’
nitrite or nitrate and return nitrogen gas (N 2) to the atmosphere, yet a third group
can take the N2 and convert it into ammonium and other molecules.

This last process is unique to certain prokaryotes and is crucially important to the
environment, as it makes atmospheric nitrogen available to other organisms,
such as plants and animals, for incorporation into essential organic compounds
such as proteins and nucleic acids. Handout [27.14] shows Anabaena, a
prokaryotic photoautotroph “blue green” (“cyanobacterium” [next lecture for more
explanation of such names]) that can fix atmospheric nitrogen [Ennos & Sheffield
p39]. Specialised cells that fix nitrogen are heterocysts (or heterocytes in some
books) – paler than the other cells in the filament [handout]. These cells lack the
systems necessary to photosynthesise, so generate no oxygen. Nitrogenases
are enzymes that can fix nitrogen, and they are inhibited by oxygen – thick walls
and restricted connection to neighbouring oxygen-releasing cells means that the
atmosphere inside heterocysts is almost anaerobic, any oxygen that does get in
is quickly removed by respiration, carried out on the thylakoid membranes
[handout]. This means that this organism could be considered to be a
differentiated, “multicellular” organism as not all the cells are the same, and the
organism can react to changing conditions by forming smaller or greater numbers
of heterocysts. The best example of importance to man is rice. Used as ‘green’
solution to paddy fertility (sustainable, cheap and environmentally preferable
alternative to inorganic fertiliser [e.g. see New Scientist 23 Dec 2000, p14
http://www.newscientist.com/article/mg16822702.400-in-a-paddy.html ] – more
about this later in the unit).

Metabolic diversity in relation to oxygen

Anabaena is a photoautotroph – it uses light as energy source and CO 2 as
carbon source, just like “plants” (or as I like to consider it, “other plants”).
Although this is the most familiar story (green organisms with photosynthesis
generating sugars and oxygen), it is by no means the only way to do it. There
are many other forms of photosynthesis, one example is that based on pigment
like those in our retinas – (bacterio)rhodopsin [e.g. 27.1]. Seawater exaporating
ponds in San Francisco bay used for commercial salt production have dense
growths of Archaea with this photosynthetic pigment. These organisms all live in
environments where there is plenty of oxygen – aerobic, and they use O 2 for
respiration, but many are “extreme” (e.g. 4x more salty than sea water).

The earth’s environment was not always aerobic, and still isn’t in some
environments – familiar examples are the methanogens – Archaea that use CO 2
to oxidise H2, producing methane (CH 4) as a waste product. They live in guts of
animals, especially herbivores, which cannot digest cellulose [41.18]. It seems
likely that the earliest forms of life on earth may have been strict anaerobes like
these present-day organisms. It is thought that it was only when cyanobacteria –
photosynthetic photoautotrophs that generate oxygen – evolved, that the
atmosphere of the earth became aerobic. Some present day cyanobacteria
metabolise BEST at an air oxygen content of only 10%, but tolerate the 21%
level to which oxygenic photosynthesis has raised the current O 2 content of our
air.

Growth, reproduction and suspended animation

One consequence of the enormous versatility of prokaryotes is that there are

very few environments on earth that cannot be colonised by one sort or another.
They can grow and multiply (reproduce) extremely rapidly. Many have doubling
rates in the order of hours, some can double every 20 minutes in optimal
conditions. (More prokaryotes live in a handful of fertile soil or the mouth of a
human than the total number of people who have ever lived).

As you will learn from other units, prokaryotes do not reproduce sexually – i.e.
they do not mate in the conventional way, but they do pass on DNA to each
other. They have cell surface structures [27.12] that allow them to transfer genes
directly from one organism to another (e.g. antibiotic resistance genes).

They can also change form in response to stress – e.g. Camplyobacter [if
interested in Microbiology or food poisoning see October’s ereveiw and the BSR
article on Campylobacter on Blackboard] and some can enter a state of
completely suspended animation. This is switched on when environmental
conditions become too harsh to tolerate, e.g. when desert environments
completely dry out, sometimes for decades, in between rains. Cyanobacteria
can form resistant cells – large reserves of DNA and storage products, thick
walls, and dehydrate. As soon as it rains, they rapidly rehydrate and form
substantial mats very quickly (when the desert “blooms” so does the sand –
cyanobacteria can be very important in the binding together of fragile sandy soils
– “desert glue” – see handout). A similar process underlies use of anthrax by
bioterrorists – spores form inside the cells in response to harsh conditions [27.9],
can tolerate extreme heat or cold and most poisons when dehydrated. See also
http://www.bbc.co.uk/news/blogs-news-from-elsewhere-23710277

Prokaryotes are less robust when hydrated, hence autoclaves (or pressure
cookers) use steam heat, not dry heat, to kill off dangerous bacteria. This ability
is the basis of some explanations for life on earth starting from “Panspermia” (e.g.
http://leiwenwu.tripod.com/panspermia.htm) as Arrhenius (1903) showed with an
experiment that subjected bacterial spores and plant seeds to a near vacuum at -
198oC, then reheated them, that they “came back to life”.

Questions for (PASS) discussion

• Conjugation in bacteria involves the passage of variable amounts of DNA,

not equal contributions to a zygote (as when eukaryotes mate). So what
is the major source of genetic variation in prokaryotes? And how is it that
prokaryotes can adapt extremely rapidly to environmental change?
• Why can prokaryote cells divide so much faster than those of eukaryotes?