Still small – Cnidaria Part 1

This will be a short post, as I am in the middle of that annoying revision period for exams.  I haven’t written for several days due to writing a report on enzyme kinetics (far too abstract, and too much maths for my taste!), and am now revising for next weeks zoology exam.

There will be several posts about various species within Cnidaria, as this is a wide phylum which has a ton of amazing organisms in it.

This post will be about the general attributes life cycle of organisms in this phylum.  Later posts will focus on specific organisms within this phylum, such as sea anenomes, corals, sea pens, and colonial swimming organisms like the Portuguese Man’o War.

There are two distinct forms of organisms within Cnidaria, and many of the members use both forms throughout their life, whilst others are found in one formonly.

Polyps are the stationary (sessile) part of the life-cycle, and whilst in corals this is the adult stage, in jellyfish and other organisms which have a free-swimming adult stage, this is the juvenile part of their life cycle.

A Hydra in the polyp stage. Image from SARS centre for Marine Molecular Biology

Diagram of a Cniadarian Polyp.

Image from structure of cnidarians

These are effectively tube-like structures, with tentacles around the mouth to direct food into the gastrovascular cavity (Also called a blind gut, as it has no exit).  Many jellyfish polyps form symbiotic relationships with corals, and some species even attach to larger, mobile creatures, the image below shows a hermit crab covered in polyps.

Polyps from Hydractinia echinata covering a hermit crab shell. Image from
http://www.vattenkikaren.gu.se/fakta/arter/crustace/decapoda/pagubern/pagube1e.html

Whilst in this form, the organism reproduces asexually by a process known as budding.  This is where a lump of tissue forms on the side of the polyp, and develops its own mouth and tentacles.  Once this has been achieved, one of two things occurs.  The newly developed polyp can break off as a clone, or it can stay attached to the parent polyp, and then a colony is formed, often with one shared gastrovascular cavity.  Colonial budding allows for different polyps to perform different tasks.  In Hydrozoan polyps, some retain tentacles and become feeding polyps (hydranths) whereas others do not retain tentacles, and become reproductive polyps (gonangia).  There are variations on this stage of the life cycle, and these will be covered as we go into more specific organisms.

Life cycle of Aurelia aurita. The polyp phase is at the bottom. Image from Black Sea Education

As can be seen in the diagram, the polyps can keep budding new polyps, but if the conditions are favourable, then these polyps produce Ephyrae, which are immature medusa (medusa is the term for the free swimming form). These mature into adults, which reproduce sexually to produce the larva which makes new polyps on the sea floor, and the cycle begins again.

There are some jellyfish which are able to bud directly from themselves, but the vast majority bud from polyps.  Sexual reproduction is usually done by the mass release of sperm and eggs from the adults.  As can be seen from the diagram below, medusa are essentially upside down polyps, but able to swim, rather than being attached to the sea floor.

Medusa diagram. Image from
http://www.ucmp.berkeley.edu/cnidaria/scyphozoamm.html

Why would this phylum have such distinct life cycles, instead of just reproducing to directly form immature medusa?

One reason is that this allows for the organisms to coexist in the same area of ocean without directly competing with each other for resources.  Polyps occupy the benthic (bottom of the ocean) zone, whilst medusa live in the pelagic zone (The open water zone).  The polyps are also afforded some protection from open ocean predators whilst in the juvenile form.  Finally, and for me, most important, it allows for the organism to not become adult until the conditions are right.  This is one cause of the blooms of jellyfish seen in coastal regions.  The asexual reproduction of polyp budding to new polyp can continue until the conditions are right for production of ephyra.  When these conditions arise, the polyps will switch to production of ephyra, and so vast quantities of medusa will appear at once.

As a final point of interest, there is one species of jellyfish Turritopis nutricula which is able to switch between polyp and medusa forms.  This involves some amazing cellular acrobatics, and means that theoretically, the organism is biologically immortal.   First, the umbrella of the jellyfish inverts itself, then the tentacles and the mesoglea (the jelly in jellyfish) gets absorbed into the body. Once this has been achieved, the end opposite the mouth attaches itself to the ocean floor, and begins producing polyps.  The process by which it does this is known as transdifferentiation whereby one type of cell turns into another.  This occurs very rarely in nature, and so is quite an interesting process.

Next time, we will start looking at some specifics of this phylum, and I can get further into showing you the really cool stuff that these organisms do.

Starting small – Dinoflagellates

This is the first in series of posts which will work through David Attenboroughs Life on Earth series, taking interesting parts and going into them in greater depth, to try and explain, and make accessible, what it is that excites me about nature, and about the history of life on Earth.

Previously I have written about cyanobacteria, and the theories on how eukaryotes arose, so this series will start with protists and micro-algae.  This clip shows the amazing differences in structure among these organisms, as well as the reproductive differences.

In this video there are a number of different single celled organisms, so let’s take a peek into the structure of some of them:

Dinoflagellates (Dinophyta) are the organisms responsible for the “red tide” effects when some species undergo rapid growth in numbers due to a change in conditions.  They come in a variety of different shapes, and I often mistake some of them for diatoms, which are a different group of organisms.  They are also responsible for the colours in coral, and for many forms of food poisoning from fish and shellfish

Ornithocercus thumii, a dinoflagellate

Image from
http://www.mnh.si.edu/highlight/sem/dinoflagellates.html
  (Also a LOAD more amazing photos of dinoflagellates on there)  VERY recommended viewing for awesome pictures!

Ceratium, a genus of Dinoflagellates

(Image from
http://www.biologycorner.com/resources/dino.jpg
)

Dinoflagellates also produce the bioluminescence you see at night on the ocean….this alone makes them fairly awesome in my opinion, but I really love their structure, it is so unexpected.  They have a whole range of shapes and forms, and many appear almost man-made.   One group is responsible for the colours in coral, where they live in symbiosis with the colonial organisms which make up the coral….there is discussion about whether the coral is actually parasitic towards the dinoflagellates, as the benefits to the coral are clear, but because they capture the dinoflagellates, incorporate them into their own systems, and then reject them when conditions change, it appears that the coral is the dominant partner in this relationship (Much more to come on this when I get to corals)

Dinoflagellates can be autotrophic (Generating their own carbohydrates from photosynthesis), heterotrophic (obtains carbohydrates from other organisms, like us), or, mixotrophic (This means they can do both, so depending on environmental conditions, they use photosynthesis, or are predators)

During their life cycles, some species are able to form cysts if conditions are not suitable for growth, these cysts fall to the bottom of the lake or ocean where the organsism is, and can be transported by currents to a more suitable location, or can lay dormant until conditions are favourable.  When conditions improve, the cysts germinate, causing the blooms that we see in our lakes and oceans. (see
http://www.whoi.edu/redtide/page.do?pid=18215
for more details on the general life-cycle of dinoflagellates, with an interactive image)

Bloom off of the coast of California (image from wikipedia)

There is one species of dinoflagellate, Pfisteria piscidia, which is thought to have a particularly complex and interesting life cycle.  When it is in cyst form, the presence of fish appears to trigger germination, and the organism then produces a toxic substance which paralyzes the respiratory system of the fish, causing it to suffocate.  As the fish decomposes, the cells extend a tube, and digest the fish flesh.  Once the fish is consumed, they turn back into cysts, and sink to the ocean floor once again. Investigation into this, and whether there are other organisms involved in the process, and the exact nature of the toxin used is still ongoing, and the subject of debate among researchers.

Finally, I will leave you with an image of bioluminescence from dinoflagellates.  This is caused when the water around them is disturbed.  They release a chemical known as luciferin. Further information on how bioluminescence occurs is here
http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioChem_p033.shtml

Bioluminescence on a shore in California

Carl Sagan

Still working on the post about development of life and awesome nature, but, here is an awesome video I came across tonight.  Carl Sagan is always good to watch, but this one is one of the best videos I have seen.

Greatest Show on Earth!

Been busy with exams for two days, so not done any posts, but will start tomorrow on the series of posts inspired by David Attenborough!   Here is a little video to get you in the mood!

Eukaryotes – Or, why we love bacteria part II

Ok, so following on from the post on photosynthesis, this post will be about eukaryotes and endosymbiosis.  As with photosynthesis, this is a HUGE topic that I could happily write 5 posts on, but will try to keep it to one, shortish post.

The next 10 or so posts will be inspired by the series which led me into Biology.  David Attenborough’s “Life on Earth” (Which is what inspired me to get up at 1am to write the photosynthesis post), basically I will take particularly awesome organisms and moments from the series, and go into greater depth on them, with diagrams, links to videos etc.  The aim of this will be to a) get people to watch the awesome series as I will mention the episode each post is inspired by, and link to the video, and b) to give more detail on each one, and hopefully show why I am so excited by the natural world.   By the way, David Attenborough got me into university, and through the first 2 years! I did not go to college, but got into university with a letter of motivation, and what I learned from Attenborough, and the research online that it led me to do, got me through the first 2 years of courses, without it, I would have felt more lost than I did, with having a 16 year gap between school and university, all the maths, physics and chemistry can seem scary!

Finally, before we jump into endosymbiosis, I would like to share two thoughts for the day that have occupied my mind on my 1 hour train journey each way to uni and back today to pick up my essay exam question:

1) Never mind made of star stuff….There are atoms in your body which have most likely been part of the sort of animals you see in fossils…there may be part of me that was once part of a carnivore, and another which was part of an animal which it preyed on, and another which was part of a plant eaten by that animal!….part of me may once have been one of the sulfur bacteria I wrote about last time!  Thinking about the journey that molecules and atoms made to go into me sitting here today just blows my mind.

2) I am more closely related to some archaea than they are to bacteria, despite them both being prokaryotes, and often thought of as one group, and I am more related to fungi than some bacteria are to each other!

Bacteria are blue, Archaea are green, Eukaryotes are red

Ok, so, onto todays post: How eukaryotes arose, and a bit about endosymbiotic theory.

First we need to define some terms which will be used constantly through this post:

Prokaryotes are organisms which do not have a nucleus in their cell. These are found today in bacteria, and single-celled organisms known as Archaea.

Eukaryotes are organisms with nuclei, that is, a membrane surrounds the centre of the cell, containing the genetic material.  This is found in all organisms apart from archaea and bacteria.  We are eukaryotes.

Comparison of Eukaryote and Prokaryote cells

Image is from
http://www.daviddarling.info/encyclopedia/E/eukarycell.html
  which also has a nice comparison of eukaryotes and prokaryotes.

Mitochondria: These are organelles, which exist outside of the nucleus of the cell.  They perform some important functions in the cell, including providing ATP which is vital to the processes within the cell. They also control things such as cell growth.  The important thing to note is that although I just wrote that the genetic material is inside the nucleus, mitochondria have their own DNA.  You may be familiar with the term Mitochondrial DNA, which is used for tracing genetic heritage, this is only inherited from your mother, as the mtDNA from sperm is destroyed during fertilization of the egg.

Chloroplasts: This is the region in a plant cell where photosynthesis occurs.  As with mitochondria, these exist outside of the nucleus, but contain their own DNA.

Structure of a plant cell. The mitochondria and chloroplast can be seen outside of the nucleus

Endosymbiosis: When one organism lives within another without damaging the host, and becomes incorporated into it.  The most well-known type of endosymbiosis for most people is the algae which live inside corals, where they provide through photosynthesis, the energy required for the coral.  They become surrounded by a membrane, and thus become part of the coral itself.

The modern theory of endosymbiosis suggests that mitochondria and chloroplasts originated by the joining of two individual organisms. This is similar to the way that coral and zooxanthellae have a symbiotic relationship, although zooanxthelles are able to be ejected from their host if the conditions become unfavourable. (As an aside, zooxanthellae are a form of algae known as Dinoflagellates…and are totally awesome in their own right, their shapes are almost as amazing as diatoms)

This modern theory was put forward by Lynn Margulis in 1967, and is based on the structure of eukaryotic cells, as well as genetic studies of chloroplasts and mitochondria.

It is thought that the original endosymbionts for the chloroplast were cyanobacteria, and the host was a protist.  The cyanobacteria provided sugar to the host from photosynthesis, and the host provided carbon dioxide and nutrients for the cyanobacteria to perform photosynthesis.  As part of this union, chloroplasts (and mitochondria) lost some of their own genetic material, and proteins known as chaperone proteins transport material from the nucleus across to the chloroplast.  This made some of the genetic material in the chloroplast redundant, and it became more dependent on the hosts own genetic material. Chloroplasts today have less than 10% of the genetic material of free-living cyanobacteria.

The exact origin of endosymbiosis to form eukaryotes is still debated (This does not mean scientists do not agree whether it happened, they are discussing the HOW), some think that it was predation that led to the first endosymbiont.  This does happen in nature today, there is a species of comb jelly which preys on jellyfish and incorporates their stings into its own body for defenses, and there is one organism which “eats” photosynthetic green algae, but does not digest them, but uses their photosynthesis to form sugars. (Paramecium bursaria)

For more information on the origins of eukaryotes, this site has good descriptions
http://evolution.berkeley.edu/evolibrary/article/_0_0/endosymbiosis_03

There is further evidence for this endosymbiosis in the way that mitochondria reproduce.  Mitochondria reproduce in the same way as bacteria, by a process of binary fission. This differs from the way eukaryote cells usually divide, which is a process called mitosis (This process in itself is fascinating, especially now we have microscopes to show it)

Mitochondria, and chloroplasts both exist outside of the nucleus, in membranes of their own.  Chloroplasts have two membranes surrounding them, reflecting the inner and outer membrane of prokaryotes, some chloroplasts have 3 or 4 membranes surrounding them, suggesting a secondary endosymbiosis of an organism which already contained a chloroplast.

Which happened first? Mitochondria or Chloroplasts? All eukaryotes have mitochondria, but only plants have chloroplasts, so the incorporation of the mitochondria must have happened before the divergence into plants, fungi and animals.

How many times did this occur? phylogenetics suggests that this occurred at least 6 separate times (phylogenetics is the study of relationships between organisms based on molecular data and physical similarities) for chloroplasts.  The initial cyanobacteria endosymbiosis was then repeated with chloroplasts from later organisms, such as red algae.

So, once again, we have those little microscopic organisms we spend so much time trying to eradicate to thank for me sitting here rambling, and you being patient and reading this.

Suggested sites: There are numerous websites which go into detail on this, as well as a large number of scientific papers. If you want to read about the early life on earth, I recommend “Life on a Young Planet” by Andrew Knoll, it covers the first 3 billion years of life on the planet in an easy to read format. For websites, the ones I have linked (including Wikipedia) are good places to start, but also see:

http://www.fossilmuseum.net/Evolution/Endosymbiosis.htm

http://learn.genetics.utah.edu/content/begin/cells/organelles/

Oxygenation of the atmosphere – or why we love bacteria, part I

One of the critical steps in the development of life as we know it today was the evolution of cyanobacteria (also called blue-green algae).  These single-celled organisms are responsible for adding oxygen to the atmosphere, and paving the way for the higher life forms that we have today.

They were not the first autotrophs (organisms that generate their food directly from sunlight, or inorganic chemicals, as opposed to heterotrophs (like us), who get their carbohydrates second-hand by consuming other organisms),  one view is that organisms similar to purple sulfur bacteria existed first, and it is the transition from these to cyanobacteria that today’s post is about.

Purple sulfur bacteria are only able to grow under anaerobic conditions (that is, conditions without oxygen present), because the synthesis of pigments in the cell is suppressed if oxygen is present. The early atmosphere of the earth was not oxygenated as it is today (as evidenced by sulfur isotopes in rocks over 2.45 billion years old, among other indicators), although there is some debate about the exact timing of the first atmospheric oxygen (NB: This does not mean I am saying “Science does not know what happened”….the time period in discussion is a few million years, and the discussions are about whether any atmospheric oxygen was immediately reacted with iron or other chemicals in the oceans).

Ok, so about these cute little purple sulfur bacteria, they are photosynthetic, so this means they use sunlight to obtain their carbohydrates.  Unlike plants today which use chlorophyll (the reason they have a green colour, but more on that later), these purple bacteria use a compound called bacteriochlorophyll, which uses different wavelengths of light, and does not produce oxygen as a waste product – This is kind of handy, since, as we saw in the previous paragraph, sulfur bacteria do not function so well in the presence of oxygen.

So, I have just mentioned photosynthesis, which is the method that plants use to obtain sugars from sunlight.  The equation for this in sulfur bacteria is as follows (Simplified version).

CO₂ + 2H₂S → CH₂O + H₂O + 2S, (or carbon dioxide + 2 lots of hydrogen sulfide is converted using light to carbohydrate + water + 2 sulfur molecules.)

Hydrogen sulfide is the rotten egg smell, and is emitted by volcanos.  The early earth was very geologically active, and volcanic activity was much higher than it is today, providing plenty of hydrogen sulfur for these bacteria to use.

This equation is important, because it was the discovery of this method of photosynthesis which demonstrated that it is water, and not carbon dioxide which is used for producing oxygen.  Prior to that, it was thought that the carbon dioxide was split to produce the waste product of oxygen.

So, back on the early earth, there were these bacteria pumping out sulfur, and using up the CO2 and H2S from volcanos.  Because they were purple, they used light in a different wavelength to the  plants of today, which reflect back the green portion of the incoming light, and thus we see them as various shades of green.  These purple sulfur bacteria reflected light back at both the higher end of the spectrum (red) and the lower end (blue), giving them their colour.

Absorption of light for purple and green chlorophyll pigments.

(Image from
http://www.sidthomas.net/SenEssence/Genes/chlinsen.htm
)

So, now we have oceans filled with reddish purple bacteria! I always try imagining how our planet would have looked back then, not so much a pale blue dot with green patches, but more likely a vivid colour like we see today when we get blooms of purple sulfur bacteria in places like Yellowstone park and other oxygen low, sulfur rich hot springs.

The next development was for some bacteria to evolve to use the light that was not being used by these organisms.

As you can see from the image, the purple bacteria would have used the light at in the centre of the spectrum, leaving light at the ends available for use, so any organisms which evolved to utilise this would have had a competitive advantage. If you want to know more about the evolution of cyanobacteria, without getting overly heavy on technical stuff, there are two systems within plants which do the conversion of light, these are called Photosystem I and Photosystem II. Green sulfur bacteria have Photosystem I only, and purple bacteria have Photosystem II only, so it is currently thought that the evolution of an organism which had both, either by endosymbiosis, or by sexual reproduction (yes, bacteria get it on too!) led to the cyanobacteria. (This is not my main area of interest, so please feel free to correct me if I got that wrong).

Ok, so now we have bacteria that reflect light in the green region, and use it from the ends of the spectrum, and have two photosystems…so what?

Well, it so happens that chlorophyll (the pigment involved), when using electrons to generate energy, gets electrons by splitting water, instead of hydrogen sulfide.  (This happens in photosystem II, in case you were wondering) So, now we have a new equation for photosynthesis, which is more familiar:

CO₂ + 2H₂O → CH₂O + H₂O + O₂

By using water (which was in abundance), and producing oxygen (which the sulfur bacteria could not tolerate), the cyanobacteria gained a large evolutionary advantage.  In addition, due to the release of oxygen into the atmosphere, ozone was formed by the reaction of sunlight with oxygen to form O₃

Ozone is what is primarily responsible for filtering out the UV from the sun, so once atmospheric oxygen, and ozone were in place, the stage was set for the long evolutionary road which would eventually lead to me sitting here typing, and you sitting somewhere else in the world reading these words.