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The microbes are in charge (Pymatuning Wetlands 2015, Day 4)

A student clearly trying to closely examine the obligate anaerobic bacteria.  Or he fell in a hole.

A student clearly trying to closely examine the obligate anaerobic bacteria. Or he fell in a hole. (Photo: AS)

After a breakfast of energy-rich waffles, the Pymatuning wetlanders slowly descended the rungs of the redox ladder into the world of wetland biogeochemistry. The microbes rule this world, and we examined the ways they make living by examining nitrogen, iron, manganese, sulfur, and carbon cycling in wetlands.  Electron acceptors, photosynthesis, oxidation, reduction, aerobic respiration, diffusion, mineralization, nitrification, denitrification, sulfur bacteria, photosynthetic sulfur bacteria, redox potential, ferric iron, ferrous iron, nitrogen fixation, sulfer-reducing bacteria, extended glycolysis, heterotrophs, chemoautotrophs, facultative anaerobes, obligate anaerobes, methanogenic bacteria, cation exchange capacity,  and other trophic-genic-ifications until our brains were full and it was time to cool off in the marsh.

Collecting vegetation cover data at Pymatuning Creek Marsh.

Collecting vegetation cover data at Pymatuning Creek Marsh.

We spent much of the afternoon at Pymatuning Creek Marsh, where the students established transects along the moisture gradient from the edge of the wetland to the interior, and quantified the distribution of vegetation, water-table depth, and pH. While the students collected data I had a little time to quietly explore the marsh a bit, and I took a few pictures…

My least favorite organism in the marsh today. (Deer fly, Chrysops sp.)

My least favorite organism in the marsh today. (Deer fly, Chrysops sp.)

It was hotter than yesterday and the deer flies (Chrysops sp.) were relentless. Much blood was lost. But we obtained the necessary data and managed to collect a few more plant specimens.  This group of students has a fantastic attitude and they are all quite a lot of fun. We returned to the lab to press plants and sort out the unknown plant species that they encountered along the transects.

Tomorrow we will explore the lacustrine wetlands of Pymatuning reservoir, and visit a swamp and some shallow water environments to round out our “must-know” plant list for the first week of class.

And a few more students are now contributing to the twitter feed: #PLEwetlands

"I'll carry this because it looks cool"

“I’ll carry this because it looks cool”

Down the redox ladder and into the marsh (PLE day 4)

A happy and muddy wetlander.

A happy and muddy wetlander.

The Pymatuning wetlanders started day four of wetland ecology by fearlessly clutching the rungs of the redox ladder and descending into the wetland biogeochemical environment.   They learned about the landlords of these ecosystems – the microbes, and how the activities of these organisms control the way that these ecosystems function.  For many students, this material is the most challenging part of the class.  However, this group of students is full of questions, which keeps things lively and a lot of fun  – not to mention that it keeps the instructor on his toes 🙂

After their brains were swamped with biogeochemical cycles (the students also have started complaining about my bad puns), we headed off to Pymatuning Creek Marsh to collect plant community data as part of a comparative study of marsh and swamp vegetation. The students laid transects from the edge to the interior of the marsh, and used their recently acquired plant identification skills to estimate changes in the abundance of plant species along this environmental gradient.  It was a beautiful afternoon, and the students seemed to enjoy practicing their marsh-plant identification skills.

Collecting vegetation abundance data at Pymatuning Creek Marsh.

Collecting vegetation abundance data at Pymatuning Creek Marsh.

Red-winged blackbird (Agelaius phoeniceus) nesting in cattails (Typha latifolia) at Pymatuning Creek Marsh.

Red-winged blackbird (Agelaius phoeniceus) nest in the cattails (Typha latifolia) at Pymatuning Creek Marsh.

Marsh, swamp, bog, fen, peatland, mire, shallow pond, billabong, and prairie? (PLE Day 1)

“A wetland is an ecosystem that arises when inundation by water produces soils dominated by anaerobic processes and forces the biota, particularly rooted plants, to exhibit adaptations to tolerate flooding.” (Keddy, 2010)

Nine students hailing from five Pennsylvania schools – Clarion University, Indiana University of Pennsylvania, University of Pittsburgh, Slippery Rock University, and Lehigh University – all began a journey today to become “wetlanders.”  The course is a three-week, field-intensive  investigation of wetland ecology offered at the University of Pittsburgh’s Pymatuning Laboratory of Ecology (PLE), located on the shore of Pymatuning Reservoir in western Pennsylvania.  In this course, we cover the content of a semester-long course in fifteen days… which represents about a week’s worth of material each day. The students (and instructor) are physically and mentally immersed in these unique and valuable ecosystems for the duration of the course.  Strap on your waders and prepare to get wet!

Using the FWS wetland mapper in preparation for tomorrow's discussion of wetland classification.

Using the FWS wetland mapper in preparation for tomorrow’s discussion of wetland classification.

Students observing the carp at the spillway on Pymatuning Lake.

Students observing the carp at the spillway on Pymatuning Lake.

This morning we began by visiting some local wetlands and adjacent uplands, and discussing the defining characteristics of wetlands. We compared soil and vegetation along a wetland-upland gradient, observed and discussed gas bubbles rising from wetland soils, and talked about anaerobic conditions and how rooted plants deal with the challenges of these environments. We then stopped for lunch at the (in)famous Linesville spillway, and observed the continual influx of phosphorus into the lake (in the form of hand-tossed stale bread). We spent the afternoon discussing wetland definitions, the various names used for wetlands (e.g., marshes, swamps, peatlands) including some particularly strange/confusing ones (e.g., reed swamp, prairie, billabong), and wetland ecosystem services. The students then gained some familiarity with the FWS wetland mapper in preparation for tomorrow’s discussion of wetland classification systems. I’m looking forward to visiting Morgan Swamp preserve tomorrow!  A few student tweets from the first day:

 

 

The end of week two! (PLE day 10)

Yay for wetlands!

Yay for wetlands!

The Pymatuning wetlanders went to Pymatuning marsh and Hartstown swamp this morning to collect the wells that we installed during the first week of class. We also made measurements of redox potential at different depths within the marsh, and used the measurements to make some predictions about composition of the gases that this marsh is currently producing. In anticipation of the busy, final week of class, the students then had the afternoon to catchup on their plant collections and work on their macroinvertebrate project.

Have the students’ marsh-walking abilities improved during the first two weeks?  I’ll let you be the judge after viewing the video below…

Measuring redox potential.

Measuring redox potential in Pyamtuning marsh.

Collecting water from within the sediments for measurement of redox potential.

Collecting water from within the sediments for measurement of redox potential.

Microbes making a living (PLE day 5)

A northern leopard frog (Lithobates pipiens).

A northern leopard frog (Lithobates pipiens).

The Pymatuning wetlanders finished discussing wetland biogeochemistry this morning by examining the phosphorus cycle in wetlands and then broadly discussing primary production, decomposition, nutrient cycling, and nutrient limitation in wetlands. The microbes are really the landlords of these ecosystems, and their activities dramatically influence the wetland environment.

We then finished data collection for our comparative vegetation project, and collected a few common submerged aquatic plants for our plant collections. Pressing plants and data entry filled out the afternoon.

We are five weeks into the semester…err, five days into the “semester.” In this 15-day field course, each day we cover approximately one week’s worth of the material that would typically be covered in a semester-long course. In fact, the students should must begin studying for the mid-term exam this weekend. So many plants, so little time.

Smelling your way down the redox ladder: wetland ecology in a bottle

“The act of smelling something, anything, is remarkably like the act of thinking. Immediately at the moment of perception, you can feel the mind going to work, sending the odor around from place to place, setting off complex repertories through the brain, polling one center after another for signs of recognition, for old memories and old connection.” – Lewis Thomas

Students experiencing olfactory "thrills" while measuring dissolved oxygen and redox potential of soil microcosms after flooding. The rotten-egg odor was intense in several of these samples.

Students experiencing olfactory “thrills” while measuring dissolved oxygen and redox potential of soil microcosms after flooding. The rotten-egg odor was intense in several of these samples.

Incorporating multiple senses into the learning process is a hallmark of experiential learning, and has long been viewed as a successful education strategy.  In a classroom setting, combining activities like observing, listening, speaking, writing, and drawing can help students to acquire, synthesize, and reinforce their knowledge of the world.  In a field course, the senses of smell and even taste can also inform and enrich the educational experience. Smelling the twig of a black birch, the leaves of spicebush, the flowers of skunk cabbage, or the wonderful rotten-egg aroma of a salt marsh are ecological observations that lead to questions of “why?” and “how?”  Furthermore, the sense of smell seems to be strongly linked to memory, albeit in poorly understood ways (i.e., the Proust effect).  Incorporating these sorts of sensory experiences into laboratory and lecture-based courses is challenging. However, I recently discovered a laboratory activity that was developed to explicitly appeal to the students’ sense of smell.  Well, perhaps “appeal” is the wrong word here.  The activity nicely demonstrates some important aspects of wetland biogeochemistry, a topic that my wetland ecology students often struggle with, and it does this while providing some considerable olfactory “thrills.”

Setup of two experiments. Each experiment included six microcosms, flooded for different lengths of time. Six experiments were done in total, allowing us to assess the influence of sulfate and organic matter quality and quantity on biogeochemical changes induced by flooding.

Setup of two experiments. Each experiment included six microcosms, flooded for different lengths of time. Six experiments were done in total, allowing us to assess the influence of sulfate and organic matter quality and quantity on biogeochemical changes induced by flooding.

The lab was developed for a soil science class by R.S. Dungan, B.D. Lee, and C. Amrhein. It can be downloaded here.  A set of microcosms are created by the students, each containing a soil which is flooded for a different length of time. A simple gaslock is used to prevent oxygen from entering the microcosms. We used six microcosms, representing flooding durations of 20 minutes, 1 day, 7 days, 14 days, 21 days, and 35 days.  In the original activity, the soils were amended with a small amount of gypsum (for a source of sulfate) and nitrogen-rich organic matter (alfalfa).  Students then measure changes in dissolved oxygen, iron, nitrate, and the presence of hydrogen sulfide.

We modified and expanded the lab for an upper-level wetland science course.  For example, we ran experiments with and without an added sulfate source, approximating the chemical environments of a salt marsh versus a freshwater wetland.  Within each of these environments, we also tested the effect that organic matter quality and quantity had on the biogeochemical changes induced by flooding.  To do this, one set of microcosms contained no added carbon (i.e., only the carbon that was present in the soil), one was amended with alfalfa (low carbon:nitrogen ratio), and one was amended with Sphagnum moss (high carbon:nitrogen ratio). In addition to measuring dissolved oxygen, iron, and nitrate, we also measured sulfate, redox potential, and pH.  Changes in concentrations were plotted against time and redox potential.

Photographs of the microcosms, after 35 days, for the different experimental setups.

Photographs of the microcosms, after 35 days, for the different experimental setups.

The results were fantastic, and some are summarized in the video and figures below.  I learned a few things by doing this lab; in particular, I think that with a little practice I could estimate redox potential using only my nose.  Certainly that would be a great skill for a wetland delineator to have!

The short video includes repeat photographs of a single flask, and provides a nice visual summary of the observed changes. Too bad you can’t send smells through the internet…

Figure showing all the data collected by the class, with concentrations plotted against redox potential measurements. Below are student comments along the redox potential gradient.

Figure showing all the data collected by the class, with concentrations plotted against redox potential measurements. Below are student comments along the redox potential gradient.

Biogeochemical changes with soil flooding, showing selected data from the class. Soils included a small amount of gypsum as a sulfate source, and the three lines indicate the results with organic matter of varying quality and quantity.

Biogeochemical changes with soil flooding, showing selected data from the class. Soils included a small amount of gypsum as a sulfate source, and the three lines indicate the results with organic matter of varying quality and quantity.

Biogeochemical changes with soil flooding, showing selected data from the class. No sulfate source was added, and the three lines indicate the results with organic matter of varying quality and quantity.

Biogeochemical changes with soil flooding, showing selected data from the class. No sulfate source was added, and the three lines indicate the results with organic matter of varying quality and quantity.

Questions for the students

A. Write a paragraph for each of the following questions, citing the appropriate figures:

  1. Describe the sequence of biogeochemical changes that occured after soil flooding. What chemical transformations take place?  Why do these changes occur?
  2. Explain the observed differences between the experiments with and without the added sulfate source. Why did these differences occur? What implications do these results have for understanding energy flow in salt marshes and freshwater wetlands?
  3. What is the likely effect of organic matter quality and quantity on the pattern and rate of biogeochemical changes after flooding? Why?

B. Write a sentence (or  equations) for each of the following questions:

  1. Hydrogen sulfide was produced in the experiment that reached a highly negative redox potential. What other gases were likely produced first?
  2. What visual changes occurred in the experiment (added sulfate, low C:N) between day 15 and 20 (see video)? What caused these changes?
  3. Why does nitrate increase in the first few days? What process is taking place?
  4. If we allowed these experiments to continue longer, what gas might be released eventually?
  5. Write the chemical equations for the redox transformations involving oxygen, nitrate, iron, and sulfate.

Literature Cited

Dungan, R.S., B.D. Lee, and C. Amrhein. 1999. Stinking Mud: An Introductory Soil Science Laboratory Exercise Demonstrating Redox Reactions in Flooded Soils. J. Nat. Resour. Life Sci. Educ. 28:89–-92.

Leaping the hedges with a butterfly amoeba

At the Milwaukee Public Museum with the butterflies.

I recently went to the Milwaukee Public Museum with my family.  This destination was carefully chosen because they have a butterfly exhibit, and my 5-year old daughter has developed a butterfly obsession.  In my experience, obsession of this sort is a good thing; in fact, it is the kind of thing that got me into science in the first place.  After I proudly watched her carefully hold and observe the different species of butterflies, and even have a few pleasant conversations with them, I wandered the exhibit and observed the diversity of colors and shapes myself.  There were some really spectacular species.

A butterfly amoeba

Perhaps because I recently had reason to open up Joseph Leidy’s incredibly beautiful 1879 foundational work describing North American testate amoebae (a group of amoebae that construct and live inside tests, or shells), my mind drifted to a statement Leidy made comparing a particular species of testate amoeba to a butterfly.  Apparently the simple beauty and elegance of this particular testate amoeba caused him to radically change his research focus.  He became obsessive about testate amoebae, or rhizopods as he called them. As with his previous research activities (e.g., paleontology, parisitology), his contributions to this new research area were enormous.

The testate amoeba in question was Hyalosphenia papilio.  In Leidy’s words:

“No other lobose rhizopod has more impressed me with its beauty than this one.  From its delicacy and transparency, its bright colors and form, as it moves among the leaves of sphagnum, desmids, and diatoms, I have associated it with the idea of a butterfly hovering among flowers.

A portion of a plate from Joseph Leidy’s 1879 monograph showing some of his drawings of Hyalosphenia papilio….the butterfly amoeba.

Leidy notes that he first observed the species thirty years prior to the publication of his seminal work, and seeing the species brought him fond memories of his explorations in the New Jersey pine barrens:

“Upward of thirty years ago, while examining the structure of sphagnum, my attention was distracted by the movements of a singular animal, whose character and affinities I did not then recognize.”

“This interesting Rhizopod, together with a profusion of other remarkable microscopic forms of both animal and vegetal life, of which many are novel and yet undescribed, recalls pleasing recollections of excursions into the sphagnous bogs, cedar swamps, and pine barrens in the southern region of New Jersey.

His fondness for the species is particularly evident in the next quote.  I can’t help to laugh a bit at the image of  him breaking out the microscope at a holiday dinner party, in order to display his “pets” to his friends.  Perhaps I should try this the next time I host a lab get together!

“I have collected it from early spring to late autumn, and have retained it alive in sphagnum, in a glass case, through the winter.  During the Christmas holidays, I have repeatedly exhibited it, in the living condition, to the admiration of friends.

A portion of a plate from Leidy’s 1865 Cretaceous Reptiles of the United States, showing some vertebrae from Hadrosaurus. (Image source)

What I find most interesting about this, is that Leidy was 50 years old when he decided to pursue this new line research.  He apparently dropped all of his other research endeavors, and focused solely on investigating these simple organisms for four or five years.  This shift in research focus was made by an already famous man who described the first complete dinosaur fossil, as well as many other North American fossils, and was widely recognized as the leading expert in parasitology.

A drawing of Trichina spiralis (now Trichinella spiralis), the  nematode parasite responsible for the disease trichinosis, done in 1887 by Joseph Leidy. Leidy first discovered that trichinosis was caused by a parasite that survived in undercooked meat (Chapman, 1891).  Image source: Collection 532. Joseph Leidy Teaching Diagrams. Academy of Natural Sciences of Philadelphia.

His obituary in the Proceedings of the National Academy of Arts and Sciences suggests that he left his paleontological research because of the extreme rivalries and unfriendly arguments that were shaping the field at the time – rather than get involved in these controversies Leidy may have just moved on.  He certainly would not be the only scientist to do such a thing.  However, according to his own words, it was the beauty of Hyalosphenia papilio that led him to study testate amoebae:

 “September 9th, 1873, the fiftieth anniversary of my birth, a friend, Clarence S. Bement, presented me with a Hartnack microscope, which, from its convenient size and form, I kept on my study table.  From time to time I was led to make observations on Fresh-water Rhizopods detected in sediments collected in the vicinity of Philadelphia.  A year later, in examining water squeezed from sphagnum obtained at Absecom, I observed many individuals of the same singular animal above indicated, but now, understanding its nature, I described it as Difflugia (Hyalosphenia) papilio.  It was the rediscovery of this beautiful form which impelled me to pursue the investigations which constitute the material of the present work.”

Published in 1897, his “Freshwater Rhizopods of North America” is a stunning combination of science and art, and still the most exhaustive description of North American testate amoebae.  For an interesting read on Leidy and the culture of science in mid-1800s North America, pick up a copy of Leonard Warren’s “Joseph Leidy: The last man who knew everything.”  For more on Leidy and a wonderful online version of the drawings included in the 1879 masterpiece, go here and here.

Joseph Leidy with his microscope circa 1870.

Leaping the hedges

The idea of following one’s interests, wherever they take you, is very attractive to me.  Of course, the culture of science has changed dramatically since the 1800s and scientists are generally narrower in focus and constrained by institutional expectations of tenure and promotion.  However, Leidy’s path of scientific exploration still seems a natural one, and I suspect that if more scientists followed his model instead of obsessively chasing promotion or the next big grant, we would collectively learn more about the natural world.

When I interviewed for a faculty position one of the questions that I was asked was to describe my 5-year research plan.  I was prepared for such a question, as it seemed like the sort of thing that I would be asked.  In fact, I carefully designed my research talk (candidates in academia usually “interview” for several days, typically giving one or two public lectures) to incorporate aspects of my long-term research plan.  Seven years later, perhaps not surprisingly, the most interesting science that I have done had little to do with my “plan.”  The projects that have excited me the most have been the things that I or my students have stumbled upon…things that I never could have planned.

I sincerely doubt that Joesph Leidy had a plan.  Sometimes something as simple as a beautiful amoeba, or a colorful butterfly, or perhaps an amoeba reminiscent of a butterfly…. can lead a scientist to wonderful new places.  Hopefully they will lead a certain 5-year old girl to some interesting places too.  The trick is identifying and following your passions (and obsessions), and knowing when it is time to move on to something new.  Leidy knew both…and he said so in the concluding statements of his great work:

“”I may perhaps continue in the same field of research and give to the reader further results, but I cannot promise to do so; for though the subject has proved to me an unceasing source of pleasure, I see before me so many wonderful things in other fields that a strong impulse disposes me to leap the hedges to examine them.””

-rkb

Addendum:

After posting I ran into this great piece.  A nice example of testate amoebae as inspiration for art.

Testate amoeba versus the diatom

What happens when a testate amoeba and a diatom get into a brawl?  The testate amoeba wins of course.  Below is a fun video of a testate amoeba spitting out a diatom – it has been up on youtube for quite a few years, but I happened to stumble across it today.  The diatom is expelled at the very end…

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