Month: September 2016

Sponges and Spicules

Jennifer Gonzales

We've dabbled a bit with invertebrates thus far, talking about house flies and various planktonic organisms, but now we're going to work our way into some more "visible" representatives, even if they often get overlooked. That group, the phylum Porifera, represents the 8,755 valid species of sponge, most all of which are marine. While some sponges are very colorful (such as the Caribbean Blue Sponge) or very large (Giant Barrel Sponge), most sponges are small or cryptic and require very fine-scale analysis for proper species identification. Seems like a perfect application for SEM technology! Continue reading below for an introduction to spicules (the "bricks" of sponge architecture) and how they can be used to identify individual species.

Some terminology, to begin, because sponge taxonomy is a whole other language in itself even by science standards. The exoskeleton of sponges (so, the parts that you see) are composed of a mixture of  spongin and/or spicules. Spongin is a modified type of collagen protein, and forms the "fibers" or "mortar" that hold spicules together.  Generally, species are identified based on the presence or absence of spongin in a sample. Spicules are the structural components of a sponge, or the "bricks," and the shapes, sizes, and composition are unique for each species. Together, you can look at these features under a microscope to make a positive identification.

 

Spicules are composed of either Calcium or Silica. Looking at composition is another way to narrow down possible sponge groupings. The "brightness" of the sample under the SEM is one way to guess at content. Calcium has a higher atomic number than Silica and is a better conductor, so it appears brighter. However, we recently learned how to use the Energy-Dispersive X-ray (EDX) function of our SEM. EDX detects and measures X-rays generated by a sample, the specifics of which are determined by elemental composition. With this tool, we were able to determine the elemental makeup of several geographically diverse samples.

Left: a siliceous deep-sea sponge whose spicules form discrete hexagonal patterns, the bottom of which you can see. Right: a calcareous semi-tropical sponge with a loosely-formed spicule matrix.

This is a very basic description of sponge identification, but there are loads of resources available on the internet, and spicules themselves can be quite beautiful. For more information, please feel free to visit:

  1. Shape of Life for short videos about sponges and their spicules
  2. The World Porifera Database for recent publications, photos, and information
  3. Southern California Association of Marine Invertebrate Taxonomists for the aforemetioned "dictionary" of spicule morphological terms

The Workings of a Scanning Electron Microscope

Jennifer Gonzales

Now that you have been exposed to what types of images a Scanning Electron Microscope or SEM, can produce, it might be time to understand a little bit about what the SEM is and how it works.

A SEM is essentially an extremely well magnified with high resolution microscope. At some point in all our lives we have been exposed to microscopy. It doesn’t matter whether it was to manipulate sunlight on a hot day to burn a bug or in a high school biology class. The point is, microscopy essentially takes something you are interested in and lets you look at it from a new newer but smaller perspective.

 

In the science world, there are a variety of different microscopes that use a handful of mechanisms. The compound microscope and the dissection microscope are two of the most common. These microscopes use visible light to look at the specimen. Although the resolution is not great, the magnification allows a scientist to see down to the cell level. The confocal microscope uses a laser light that scans across the specimen. The image that is created from the scan is then transferred to a computer where the scientist can do further analysis. The SEM and the Transmission Electron Microscope or TEM both use electrons, or negatively charged particles, to create an image. When using the SEM, the pedestal with the sample is coated with conductive material such as gold or graphite. The electrons from the beam of the SEM bounce off the sample creating backscatter electrons that are used to make an image in 3D. The TEM allows for some electrons to pass through the sample so that the scientist can look at different layers within the sample. Both the SEM and the TEM have very high magnification and resolution, as I am sure you have seen in some of our previous posts. This technology along with add on tools such as the Energy Dispersive X-Ray Analysis tool, or EDX, allows scientists to look at specimens at the atomic level, making species identification and elemental composition of a specimen precise.

 

 

The best part of the SEM is getting to see relatively anything at its structural level. We can experiment with just about anything and explore its inner workings within minutes. Even though our field of study lies with the ocean, our curiosity and excitement over the use of the SEM has encouraged us to explore all realms around us including the fly on the windowsill. Who knows what we will look at next!

Biogenic Ooze

Jennifer Gonzales

Biogenic sediments extracted from deep-sea sediment cores enable scientists to piece together a story about Earth’s early marine environments and past climate. This particular sample was collected off the coast of Papua New Guinea in the western Pacific Ocean by the International Ocean Discovery Program’s expedition RR1313. Microfossil-rich sediments, such as the one pictured above is termed a biogenic ooze and is characterized by containing greater than 30 percent skeletal debris.

 

The disk-shaped organism featured above is a well-preserved concentric diatom surrounded by a type of phytoplankton, known as a coccolithophore. In terms of shape and size, coccolithophores are a highly diverse group of phytoplankton that produce calcareous skeletons composed of calcium carbonate (CaCO3) called coccoliths. Whereas diatoms are encased by a hard-shelled silica (SiO2) body, often referred to as opal. The siliceous shells of diatoms allow them to endure turbulent mixing in the upper layers of the ocean. As diatoms bloom and die, they sink to the bottom of the ocean and become exceptionally useful in paleoceanographic research. Microfossils are used to infer rates of sedimentation, biological productivity, nutrient availability and oxygenation events which are imperative to understanding past, present, and future climate.

 

Foraminifera and Coccolithophores

Jennifer Gonzales

Chances are you'll be seeing a fair bit of discussion regarding plankton as we go forward, because (1) they show up in many of our samples, and (2) there's a lot we can learn by studying them! SEM is especially useful for the study of plankton, as their small size makes traditional compound microscopes somewhat ineffective. This photograph, taken during our first run-through with the SEM, shows an image at 1,200X magnification, as compared to the 100X magnification you might hope to get with a standard scope!

 

In the above photo we can see examples of both zooplankton (microscopic animals) and phytoplankton (microscopic plants). The first is the obvious, bulbous species in the middle of the image. This is the test, or shell, of a Foraminifera. Forams represent an ancient and speciose group of zooplankton which live mostly in sediment (as is the case here), but also in the water column. Within the red squares you will see a second, smaller phytoplankton species known as a Coccolithophore. The round plates are known individually as placoliths, and bundle together around the algal species to form a coccosphere. I've included the photo below to give you an idea of how they appear when alive in nature. Similarly, coccolithophores inhabit both benthic and open-water habitats.

 

Plankton species such as these can provide a surprising amount of information not only about themselves, but also about the environment in which they grow.  The tests you see here are made of calcium carbonate (CaCO3) which the organisms "pull" out of the water and use to build their hard parts. As such, isotopic analysis of these tests can tell you about the atmospheric and oceanic conditions at the time of their formation, since the two systems are linked in the carbon cycle. When the organism dies, calcium carbonate sinks to the bottom of the ocean in the form of coccoliths and other tests and become a part of the sediment record, which can be studied later by scientists as part of a sediment core.

There are many other applications in the study of plankton, some of which we will likely cover in future installations. Stay tuned, and remember: It's the little things.

Common Housefly

Jennifer Gonzales

This SEM image of a housefly at 47x magnification highlights the intricacies possessed by even the most common lifeforms. One may be intrigued by the stark contrast between the fine hairs and the thousands of hexagonal structures making up the eyes. Together the eyes create a mosaic-like image, giving flies spectacular peripheral vision. This may seem like a huge visual advantage. However, flies are unable to focus; they can see motion and form, but are unable to clearly see objects. This is why flies are so quick to flee. They see something headed their way, but have no clue what it may be.

 

The hexagonal shape making up a fly’s vision is not unique in the natural environment. This structure is found in numerous natural features such as honeycombs, columnar basalt, turtle shells, snakeskin, etc. This structure is so commonly found due to its geometry. Triangles, squares, and hexagons are the only three shapes with equal sides and angles that fill a flat plane. Of these, hexagons require the least total length of wall, making it the more efficient shape.