JCU Aquatic Resources
Friday, November 15, 2013
Thursday, November 14, 2013
Diatom slides from core sample
This week in lab we extruded sediment from the core we
collected at Beach City on October 10th and learned how to prepare
and examine diatom slides. The process of preparing diatom slides from a
sediment core occurs in five steps: extruding the core from the collection
tube, cleaning the sediment in nitric acid, rinsing and centrifuging the
sediment, drying cleaned sample onto coverslips, and fixing dried material onto
microscope slides.
Step 1: Extruding the core
extruding a core |
For the sake of time, we only collected 4 samples from our
core, but ordinarily an entire sediment core would be extruded and collected in
1-cm or 1/2-cm intervals. To extrude the core, the sediment must be pushed from
the bottom up through the top of the collection tube. To prevent loss of sample,
a plastic “stage” is attached to the top of the collection tube (fig. 1). This
stage also allows for the sediment to be scraped into Whirl-Paks at desired
intervals. Each Whirl-Pak was labeled with its corresponding measurement in the
core (i.e. the top centimeter of sediment is labeled “0-1”).
Step 2: ‘Cleaning’ the sediment
plastic "stage" attached to collection tube |
Approximately 0.5 grams of each sediment sample was mixed
with 20 mL of DI water and 10 mL of nitric acid in a beaker and boiled on a hot
plate until the solution reached a volume of ~10 mL. This step is necessary to
remove organic matter from the sample. Because the inorganic sediment and
diatoms cannot be separated in core samples, removing organic material makes
diatom identification and count data easier to collect. At the end of this
step, we are left with inorganic material (sediment + diatoms) and nitric acid.
samples boiled in nitric acid |
Step 3: Rinsing the sediment
We did not complete this step in class, but the samples must
be rinsed with DI water in order to remove the nitric acid. To do this, the
sample is transferred to a Falcon tube and centrifuged at 2000 rpm for 10
minutes. The supernatant nitric acid is decanted and the tube is refilled with
DI water. Next, the tube must be shaken to resuspend the sediment pellet. This
process is repeated 6 times to completely remove the acid.
Steps 4 and 5: Preparing permanent mount slides
A solution of ~0.1 mL of cleaned sample + ~0.9 mL DI water
was pipetted onto a coverslip and allowed to dry for 24 hours. Three dilutions
of each sample were made and prepared slides were examined for concentration of
diatoms. Dry coverslips were fixed to microscope slides using Naphrax permanent
mountant. For the remainder of class, we looked at previously made permanent
mount diatom slides and identified different genera based on morphology.
Some of the common genera found were also known indicator organisms. Acidophiles: Eunotia, Frustulia, and Actinella, as well as Pleurosira, an indicator of elevated conductivity. Below are examples of each morphological group of diatoms: Centrics, with radial symmetry (most often seen in valve view); Araphids, without a raphe and often found in chains or star-shaped colonies; Eunotioids, acidophiles with an abbreviated (short) raphe along the valve mantle; Monoraphids (not pictured), with a raphe on only one of the two valve faces, Biraphids, with raphes on both valve faces (pictured: a "Naviculoid" biraphid with symmetry to both the apical and transapical axes); Gomphocymbelloids, with asymmetry to one or both axes (or symmetrical to both!), Epithemioid, with its raphe in a canal, Nitzschoid, with its raphe in a keel along one side of the valve, and Surirelloid, with a single raphe in a keel around the entire periphery of the valve face.
Asterionella, an araphid, and two (separated) centric Stephanodiscus valves |
Pinnularia, a biraphid |
Eunotia, with an abbreviated raphe along the valve mantle |
Cymbella, a biraphid with asymmetry to both apical and transapical axes |
Epithemia, with a raphe in a canal |
Surirella, with a single raphe around the periphery |
Nitzschia, with its raphe in a keel |
Wednesday, November 13, 2013
Diatoms from Soil Cores
Background:
Diatoms
are single celled organisms that have shells composed of silica. These
incredibly diverse tiny organisms can be found in both freshwater and marine
ecosystems. They are often studied as important indicators of past ecological
conditions, because when the diatom dies, the silica shells remain in the
sediment. Because they remain in
the sediment for long periods of time, the composition of diatoms found at a
specific location in a soil core can tell researchers what conditions were like
when that layer was deposited. Diatoms can indicate water salinity,
temperature, and pH, as well as show nutrient and pollution levels in a system.
For example, imagine a system that experienced no pollution until humans
developed the surrounding area. The diatom composition before and after human
development would differ. You would expect to see more pollution tolerant
diatoms in the soil after development, and fewer pollution sensitive diatom
species.
Extracting a Core
Sediment core extraction required several
pieces of equipment. Two boats were used to navigate the body of water (lake)
in order to find a desired location for an extraction. Once a desired location
was found, the boat remained stationary for a minute to ensure no sediment
agitation occurred before taking a sample. Then, the core tube was slowly
lowered into the water and forcefully pushed into the sediment, reaching a
desired depth. The extraction of the core was performed by careful lifting of
the sediment core tube, followed by a quick placement of a rubber stopper at
the end of the tube. Finally, both ends of the core tube were plugged and taped
to insure preservation of the sample. While, performing a sediment core
extraction, it was observed that the bottom of the core was fairly dark due to
anoxic conditions that are associated with deeper sediment layers. The top
however, observed a brown-dark greenish color, indicating higher levels of
oxygen. While extruding the sediment core, the pH of water was tested using a
pH meter, which indicated a fairly neutral and acceptable value within the
range of 6.5 to 8.
Removing the Bottom Stopper and Inserting Plunger |
Creating Samples
Samples from a sediment core are important in studying the history of a desired body of water. They are great indicator of historical biodiversity which can be used to recreate past environments conditions. This information can be compared to the present biodiversity and further analyzed in order to grasp a better understanding of the changing environmental conditions such as the pH, as well as nutrient and pollution concentrations within the body of water.
Samples from a sediment core are important in studying the history of a desired body of water. They are great indicator of historical biodiversity which can be used to recreate past environments conditions. This information can be compared to the present biodiversity and further analyzed in order to grasp a better understanding of the changing environmental conditions such as the pH, as well as nutrient and pollution concentrations within the body of water.
Extruding the Soil Core |
In
order to create samples from the extruded core, whirlpac bags were obtained and
labeled to ensure accurate tracking of samples. Then, the water layer present
inside the sediment core tube was expelled using a plunger- like tool that
pushed the sediment from the bottom to the top. A specially designed tray was
fitted on top of the sediment core which was used to concentrate the sediment
samples into 1 cm intervals. The intervals were collected (by scraping the top)
and stored inside designated whirlpac bags. All of the samples collected were
then further analyzed by preparing microscopic slides in order to observe
diatom biodiversity.
This Plate Helps Measure Out 1cm of soil |
Samples are Scraped into Whirlpak Bags for Sampling |
Preparing Slides
To
analyze the diatoms in the sample, they must be spread out onto microscope
slides. The first step in slide preparation is to remove as much of the organic
matter and soil from your samples. This can be done by boiling a small about of
sample in nitric acid, to break down organic compounds. After the samples are
boiled, they are rinsed with water several times to remove traces of acid. The
finished diatom mixture is cloudy and will need to be diluted farther before it
can be made into slides. It is recommended that you make three separate
dilutions of each sample while making slides.
Boiling Samples to Purify Them |
A Purified Sample: Ready for Dilution and Slides |
The
slides themselves are made by placing the sample onto a clean cover slip. The sample should cover the entire
cover slip and form a mound in the middle. These will need to sit for at least
twenty-four hours, as they dry.
Once dry, the cover slips can be permanently mounted to a clean
microscope slide. Attaching the
cover slips permanently allows researchers to preserve samples for later
analysis.
Alison Demonstrates How to Correctly Make A Slide |
Make sure to get a mound of water in the middle of your cover slip. It shouldn't spill onto other cover slips. |
Wednesday, November 6, 2013
A Visit to Triangle Lake Bog and Herrick Fen
Triangle Lake Bog - November 2013 |
Herrick Fen - November 2013 |
Located an hour south of Cleveland, there are two beautiful wetlands: Triangle Lake Bog and Herrick Fen. Both of these properties are examples of endangered habitats. Most of Ohio’s wetlands have been destroyed by development, while the wetlands that are left are continually threatened by eutrophication and suburbanization. Eutrophication threatens wetlands with large increases in nutrients from fertilizer run offs. The large inflow of nutrients disrupts the delicate balance of these systems.
Triangle Lake Bog - Early September 2013 |
Triangle Lake Bog was formed when glaciers moved across Northern Ohio approximately 25,000 years ago. As the glacier retreated it left behind heavy ice blocks that broke off and settled into the soil. After the ice melted, the depression filled in forming a kettle lake. The remnants of this kettle lake can be seen in the middle of Triangle Lake Bog. Bogs are a unique type of wetland because they lack water inflow and outflow; they are fed only through precipitation. The lack of water flow causes bogs to be acidic and low in oxygen. Nutrient levels are low in bogs because decomposition is slowed by the acidity and anoxic conditions. These traits that are characteristic of bogs make them the home of a number of unique species.
Herrick Fen - Early September 2013 |
Herrick Fen was formed at approximately the same time as Triangle Lake Bog on top of a large gravel deposit left behind by the glacier. Fens are continuously fed by groundwater and water drainage from the surrounding areas. Because the fen has constant water influx, the soil is considered hydria (saturated and sometimes anoxic). Nutrient levels in fens are higher than in bogs because the mixing water has higher oxygen content and encourages more decomposition. Fens are also home to some of the special species found in bogs.
Tamarack is a common tree found in bogs and fens |
Grass of Parnassus: a rare plant found at Herrick Fen |
Close-up of the digestive juices in the pitcher plant |
Pitcher plants at Triangle Lake Bog |
Sundews (Family: Droseraceae) are carnivorous plants that are characterized by having specialized tentacles. The tentacles contain a gel like substance that will attract prey such as fruit flies, gnats and ants. After a prey insect gets stuck on the tentacles, the tentacles will wrap around the insect to prevent escape. The trapped animals will be dissolved by the enticing mucus and then absorbed as nutrients.
Sundews grow in beds of Sphagnum moss |
Close-up of Sundew: Red tentacles are visible |
Another type of carnivorous plants that can be found in Ohio are bladderworts (Family: Utricularia). These plants are aquatic and are characterized by having a unique trap mechanism, which involves actively pumping water in order to initiate the trap. During contact with prey, a trap mechanism is initiated which will cause the plant to swell up due to active intake of water from the environment and at the same time suck in the prey. Once the prey has been engulfed by the bladderwort, they will be dissolved by the digestive secretions produced by the plant.
Bladderworts (photo credit: plants.usda.gov) |
These wetland habitats are home to so many unique plants that this blog is only able to highlight a few of them. There are more beautiful things to be seen at these nature preserves. It is well worth the drive from Cleveland to visit them. It is important that people visit these wetlands and appreciate their biodiversity. The general public needs to continue to educate themselves about the importance of these habitats and why they should be protected.
For more information on these locations, visit:
Herrick Fen
Triangle Lake Bog
For more information on the plants species above, visit:
http://plants.usda.gov/java/
Wednesday, October 30, 2013
Catch of the Day: The Fish Families of Ohio
Professors and students work together to identify a "mystery" fish. |
This
week’s lab involved taking a tour through the fish families of Ohio, guided by
Dr. Sheil. We began by covering the
basics of fish morphology. The first thing emphasized was the arrangement of
fins and their proper titles, which included: the dorsal fin, caudal fin, anal
fin, pelvic fin and pectoral fin. The bony supports within fins are fin rays,
which are softer and more flexible, and spines, which are stiffer processes. The
bony plate that covers the gills is called the operculum. The line running the
length of the fish’s body is known as the lateral line, and it is a sensory
organ used to detect pressure changes in water.
Basic external anatomy. (Photo credit) |
Our
lecture also covered the three basic scale types: ganoid, cycloid and ctenoid
scales. Ganoid scales are the basal, or ancestral, scale type that has an upper
surface covered in ganoine, which is a mineralized tissue comparable to enamel.
Cycloid scales are a rounded type of scale, whereas ctenoid scales have more of
an irregular shape.
Basal (heterocercal) and derived (homocercal) tail conditions. (Photo credit) |
Another of the basic morphological characteristics discussed were the two types of
tails. The ancestral condition is a heterocercal tail, which is asymmetrical,
with the vertebral column extending into the larger lobe. Alternately, the
symmetrical homocercal tail type is derived and seen much more commonly in the
fish of Ohio.
After
learning the basics we were ready to take a plunge through the different
families of fish found in Ohio. We traveled to each of the different tables throughout
the lab and sketched the preserved representatives of the families, taking note
of particular morphological features that will aid in identification.
Petromyzontidae: Lampreys
Lamprey specimens. Note the buccal funnel (right), which these parasites use to attach to fish hosts, as shown in the center photo. (Photo credit) |
Lampreys
are parasites of other fish. They use their buccal funnel (mouth), which is
lined with cornified “teeth,” and rasping tongue to feed of host fish. Although
lampreys have a mouth, they are jawless, so they lack an operculum. The
lamprey’s overall morphology resembles an eel in the sense it lacks pelvic and
pectoral fins. The dorsal fin is posteriorly displaced and is fused with the
caudal and anal fin. The dorsal fin can be undivided, have a wide notch between
the dorsal and caudal fins, or have a deep notch between the two fins. The
condition of the dorsal fin and the anatomy of the mouth are often used to
characterize species belonging to this family.
Acipenseridae: Sturgeons
Representatives from Acipenseridae. These fish have conspicuous bony plates on their dorsum, four conspicuous barbels on the ventral snout, and heterocercal tails. (Photo credit) |
The
sturgeon is a large, prehistoric-looking fish that has an ancestral, heterocercal
tail. This fish has bony plates, or scutes, that are arranged in rows running the
length of the body. Under the snout, one can see four distinct barbels and a
tubular mouth used for sucking food items off the substrate. There are two
species in Ohio, Acipenser fluvescens and
Scaphirhynchus platorynchus. Scaphirhynchus platorynchus can be
differentiated due to its long, slender tail and large, bony plates on the
caudal peduncle.
Lepisosteidae: Gars
Members of Lepisosteidae. Note the slender snout and abbreviated heterocercal tail. (Photo credit) |
Gars
have a long snout that is filled with long, fang-like teeth, making them look
fierce in appearance. Typically found in slow-moving and turbid tributaries,
these fish turn right or left to grab prey as they swim through the water
column. This fish has an elongated body that is covered with rhomboid, ganoid
scales, which function as “armor-plated” protection. The dorsal fin is
posteriorly displaced, which is often associated with “sprinter” fish or fish
that swim near the surface. The operculum of members of this family has many
bones on the “cheek” rather than just a singular opercular shield. It should
also be noted the gars have an abbreviated heterocercal tail. The genus that we have
in Ohio is Lepisosteus.
Clupeidae: Herrings and Herring allies
Alewife specimens. The vertical eyelid and the ventral row of keeled scales that help distinguish this fish. (Photo credit) |
This
“cute” family of fish has a few unique morphological characteristics that can
help in identification. First, the dorsal fin is situated almost directly over
the pelvic fin. Secondly, this family of fish has no lateral line system. Also,
on the underside of the fish there is a row of keeled scales that resemble saw
teeth. Furthermore, the anal fin is so broad and long it almost appears to
interact with the caudal fin. A particularly interesting member of this group
is the alewife (Alosa pseudoharengus),
which has a “bizarre” eyelid that opens and closes vertically as opposed to
horizontally, and is a dead giveaway for identification.
Salmonidae: Salmons, Trouts, and Whitefish
Examples of fish belonging to Salmonidae. In the photo on the left, the pelvic axillary process is highlighted. In the photo on the right, the adipose fin can be seen. (Photo credit) |
These
fish have small cycloid scales which give them a smooth appearance. Both male
and female fish of this family possess a bilateral axillary process located
above the pelvic fin. Cameron shared that he recently completed work for a research
project that utilized this fleshy process for genetic testing. Researchers
remove the process without significant negative impact on the fish by clipping
it with a pet nail trimmer. Another feature of this group is presence of an adipose fin, which is a small, fleshy fin, composed of fat and located between the dorsal and caudal fin. The
brook trout (Salvelinus frontinalis) and
the lake trout (S. namaycush) are two
examples of fish from this family that can be found in Ohio.
Esocidae: Pikes
Fish belonging to Esocidae are distinguished by their "duck bill" shaped mouths. (Photo credit) |
These
fish look distinct because their snouts resemble duck bills and are filled with
large canine teeth. Similar to gars, the pike’s dorsal fin is displaced
posteriorly because this fish swims near the surface and is a “sprinter.” These
voracious predators rest in the grass, wait for prey, and then shoot out to
grab them with their sharp teeth. Esox is
the genus found in Ohio. Muskellunge and pike are typically found in
large lakes, while pickerels live in small streams.
Catastomidae: Suckers, Redhorses and Buffalo fish
The
most obvious feature of fish in this family is the subterminal mouth. The large
and striated, sucker-like lips are used to adhere to substrate and suck up food,
such as periphyton from rocks and logs. In Ohio, we can find the red horse (Moxostoma), the buffalo fish (Carpoides),
and the common white sucker (Catastoma
commersoni). We were cautioned
not to confuse Carpoides with the
common carp, which belongs to Cyprinidae. Carpoides
superficially resembles a carp, but is distinguished by a nipple-like process
on the bottom lip and a lack of barbels.
Ictaluridae: Catfishes, Madtoms
Madtom (left) and catfish (right) specimens. Note the small size of the madtom, as well as the unforked, rounded caudal fin. Alternately, the larger catfish displays the characteristic forked caudal fin. (Photo credit) |
Members
of this family usually have more than eight barbels around their mouth. An
interesting feature lies within the fins, with both the dorsal and pectoral
fins having a large spine. The spines are defensive weapons, which prevent fish from being swallowed by impaling predators. Dr. Sheil mentioned that people walking in lakes will sometimes accidentally step on skeletons of these fish and receive a painful puncture wound from the dorsal spine. These fish lack scales, but an adipose fin is
present. Catfish (Ictalurus) and madtoms
(Noturus) can be easily confused if
one does not know what specific morphological features to compare. However, adult
madtoms do not get much larger in length than the distance between your extended
thumb and pinky finger, while catfish can grow to be quite large. Looking at the
tail can also help one decipher between the two. Madtoms have an unforked,
rounded caudal fin, whereas the caudal fin of the catfish is forked.
Cyprinids
have a more terminal mouth and in some species, the upper jaw has fleshy barbels
that hang from it. Sometimes these barbels can be cryptic. One example of a familiar Ohio cyprinid is the common carp (Cyprinus
carpio). The goldfish (Carassius
auratus) is distinguished from the common carp due to a lack of barbels on its
upper jaw. Another group within Cyprinidae is the minnows (Campostoma), which can be characterized by a large “C" shaped upper lip that causes a
heavy overbite. Fathead minnows (Pimephales)
have only a slight overbite, but very crowded scales on the dorsum.
Anguillidae: Freshwater Eels
American eel specimens. Note the continuous dorsal, caudal and anal fin. (Photo credit) |
The
freshwater eel has almost a serpent-like appearance, with pelvic fins absent
and a fused dorsal, caudal and anal fin. This fish has scales so small it
appears to be scaleless. On each side of the fish we find a single opercular
opening. A freshwater eel species found in Ohio is the American eel (Anguilla rostrata).
Atherinidae: Sliversides
Sliversides
resemble a miniature freshwater barracuda. These fish have a very flat head and
back, along with a “bird–beak” shaped mouth. Sliversides also have very large
eyes. Running down the length of the body is row of serrated scales that stand
out against the conspicuous cycloid scales of the rest of the body. Sliversides
also have two dorsal fins, the first of which is shorter and has six spines. In
Ohio, we find the brook silverside (Labidesthes
sicculus). When captured in a seine net, these fish are easily recognized
by the silver flash on their side that reflects light.
Moronidae: White Basses
Specimens from Moronidae. Note the spine on the opercular flap. (Photo credit) |
The
fish in this group have two dorsal fins, the first of which has spines that are
sharp and the second just has flexible rays. The key feature for this family is
a spine that is located on the opercular flap. Members of this family commonly
seen in Ohio are white bass (Morone
chrysops), striped bass (M.
saxatilis) and white perch (M.
americana). Moronids can be distinguished from members of Centrarchidae by
the condition of the dorsal fins, which as discussed below, are fused in
centrarchids.
Centrarchidae: Blackbass, Crappies and Sunfishes
Fused dorsal fins are characteristic of many members of the Centrarchidae family. (Photo credits: 1, 2) |
When
it comes to members of this family, attention to detail is critical for identification.
Counting the number of dorsal and anal fin spines as well as examining the size
of the scales is very important. In Ohio, members of this family include blackbass
(Micropterus), which have fused
dorsal fins and small scales. The sunfishes also have fused dorsal fins, but
larger scales than the blackbass. Finally, Ohio is home to crappies (Pomoxis), which have 5-8 dorsal spines and
5-7 anal spines.
Percidae: Walleyes, Perch and Darters
Morphological features such as obvious paired dorsal fins, a torpedo-like body, and spines associated with the anterior of the anal fin distinguish fish belonging to Percidae. (Photo credits: 1, 2) |
Fish
in this family generally have large, blocky heads and the body depth tends to
be less than the head length. The overall shape of the body resembles a
torpedo. These fish also have conspicuously paired dorsal fins and a spine
associated with the anterior end of the anal fin. In Ohio, we find walleye (Stizostedion), which have a very flat
belly and two dorsal fins. We also have darters (Etheostoma), which have very blunt faces and huge pectoral fins. Finally,
we have the roughbelly darters and logperches (Percina) that have a more tapered face compared to darters in the
genus Etheostoma, as well as
significantly smaller pectoral fins.
Gobiidae: Gobies
The cup-shaped pelvic fin of the goby acts a suction cup and allows the fish to hold onto rocks. |
This
invasive group of fish is distinguished by its cup-shaped pelvic fin, which
acts as a suction cup to allow them to withstand the current and sit in place
on the benthos. As we learned in a previous lab, these voracious gobies will
eat the eggs of other fish species in the time that it takes a fisherman to
pose with the captured fish for a photo. There are strict restrictions on fishing
activity due to the threat of goby predation on the eggs of native fish
species.
We
concluded the lab by helping improve the JCU Biology Department’s fish
collection by identifying and sorting "unknown" fish specimens. Using a
dichotomous key specific to families of Ohio fishes, we were able to organize
mixed collections of unknown fish into fresh and properly labeled preservation
jars.
In addition to basic morphological features such as fin condition,
presence or absence of barbels, tail type and snout shape, it was necessary to
count scales to determine finer classifications of unknown specimens.
Fish Family List
A figure detailing different types of scale counts that can be performed to achieve more specific taxonomic classification. (Photo credit) |
Fish Family List
Petromyzontidae: Lampreys
Acipenseridae: Sturgeons
Lepisosteidae: Gars
Clupeidae: Herrings and Herring allies
Salmonidae: Salmons, Trouts, and
Whitefish
Esocidae: Pikes
Catastomidae: Suckers, Redhorses and
Buffalo fish
Ictaluridae: Catfishes, Madtoms
Cyprinidae: Carp, Minnows, Daces,
Shiners and Goldfish
Anguillidae: Freshwater Eels
Atherinidae: Sliversides
Moronidae: White Basses
Centrarchidae: Blackbass, Crappies and
Sunfishes
Percidae: Walleyes, Perch and Darters
Gobiidae: Gobies
Subscribe to:
Posts (Atom)