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The paramo

15 Jan 2017


Raul Trejos of the Universidad of Caldas sinks into the peat with a smile. The water temperature was about 9 degrees C (~50 degrees F).

After breakfast at the hotel, which included fresh fruit, eggs, rice, and soup, we loaded up into two cars and drove up the winding road from Manizales toward the paramo to a site located just below Nevado del Ruiz National Park. Several other scientists, including Natalia Hoyos of the Universidad del Norte, and Felipe Vallejo, Raul Trejos, and Andres Pardo of the Universidad of Caldas, joined us. We ascended over 1000 meters in about an hour, and the driving experience was just as thrilling as it was in Bogota. Cars and motorcycles would pass other vehicles even on the very windy sections of this road. Even a public bus passed around a blind curve! The double yellow line on the road is clearly just a suggestion, and taken no more seriously than the posted speed limit is in much of the US.

As we ascended, the views of the rainforest and mountains were breathtaking, with the forest vegetation clearly changing as we progressed higher. Somewhere over about 3000 meters the trees disappeared and were replaced with tussock grasses and frailejón (pronounced fry-lay-hon-nez), which are some of the most characteristic plants of the paramo. Frailejón (Espeletia sp.) is in the Asteraceae family, which includes species with composite flowers like sunflowers, daises, and dandelions. However, other than the recognizable composite flower on the plant it is quite unique, with a thick trunk, hairy leaves, and old dead leaves that remain attached to the plant, presumably to protect it from the cold. The roots don’t apparently penetrate very deep in the soil, because it was not uncommon to see individuals toppled over.


Frailejon (Espeletia sp.) growing in the paramo near Nevada del Ruiz National Park.


Triunfo peatland.

Our goal for the day was to visit and collect surface samples from a peatland that was previously cored by Jaime and others.  At Lehigh University we are currently analyzing testate amoebae in this core. Testate amoebae are a subgroup of amoeba that produce a decay-resistant and morphologically distinct shell. These organisms have been used estimate past changes in the hydrology of peatlands, because different species are found in dry versus wet habitats. A major goal of this new collaboration will be to assess the potential of using testate amoebae along with other indicators to reconstruct past hydrological and ecological changes within the paramo. However, currently nothing is known about the ecology of testate amoebae in peatlands of the paramo, so we are collecting surface samples to better understand the distribution of testate amoebae today, and we will use this  information to interpret the changes that we are document in the peat core.


Ash cloud from Nevada del Ruiz volcano.

On our short hike to the peatland we were lucky enough to observe the Nevado del Ruiz volcano venting gas and ash. Although I have seen lava flows in Hawaii, an eruption like this was a first for me. The Nevada del Ruiz has been experiencing small eruptions like this over the past several years. However, the last major eruption was in 1985 and it caused the deadliest mud and debris flows in recorded history, killing over 25,000 people and burying an entire town.

The peatland was spectacular, and we spent a productive day collecting surface samples. Jaime almost didn’t make it out, but with a little effort he managed to avoid becoming the first known bog body of the paramo.


Jaime Escobar of the Universidad del Norte sinks into the peatland during our hike out.

Tropical testate amoebae as hydrological indicators? (reblog)

From inside the shell

Sampling testate amoebae in a tropical peatland. A recent paper in Microbial Ecology by Swindles et al. suggests that testate amoebae have potential as hydrological indicators in tropical peatlands. Sampling testate amoebae in a tropical peatland. A recent paper in Microbial Ecology by Swindles et al. suggests that testate amoebae have good potential as hydrological indicators in tropical peatlands.

Testate amoebae have been successfully used as indicators of past changes in peatland hydrology, particularly ombrotrophic (i.e., nutrients derived exclusively from precipitation) peatlands of north-temperate and boreal regions.  Over the past couple decades, many ecological studies of testate amoebae have been performed in these northern bogs, allowing empirical relationships between community composition and surface moisture to be described. Because the shells of testate amoebae preserve well in the acidic and anaerobic environment of bogs, these modern relationships have been used to infer past changes in the relative wetness of the bog surface from the composition of subfossil communities.  Much recent work has focused on the validation and interpretation of testate amoeba paleohydrological records from bogs, and their application to pressing global change questions.

Surveying along a transect across the peatland. Surveying along…

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New blog on testate amoebae

Announcing a new collaborative blog focused on testate amoebae. The coverage will include any research on or utilizing these interesting organisms – including their evolution, taxonomy, biology, ecology, paleoecology, and their applied use as bioindicators. Link to first blog post below…


50 million-year-old testate amoebae.

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.””



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…

Blast From the Past: Raised History Video

Chris Fastie making the Raised History video in 2004.

Chris Fastie saw the video of our recent Wisconsin field work and kindly uploaded a video he made back in 2004. The video features a group of us collecting a core from Bloomingdale Bog in the Adirondacks of New York. Perhaps it is a bit dated, but it is very professionally done and quite funny!  I sometimes use this video to introduce paleoecology in my classes.

Raised History from Chris Fastie on Vimeo.

From Chris: “Extracting a three meter peat core from Bloomingdale Bog near Saranac Lake, New York on September 17, 2004. This video lived on DVDs until July, 2012 when it was encoded as mp4.”

Amoebae trapped in amber… (link)

Some really old amoebae…

Worth Pitching? Fossil amoebae discovered in amber | Assignment: Impossible, Scientific American Blog Network

Worth Pitching? Fossil amoebae discovered in amber | Assignment: Impossible, Scientific American Blog Network.

The answer is blowin’ in the wind

Peat mining at Minden Bog in Michigan. Minden Bog is probably the last true raised bog left in the state, and more than half of it has been mined. This picture was taken looking north from about the center of the bog, where peat mining was actively underway (Photo: R.K. Booth)

They are bug-infested wastelands. Wet and soggy places unfit for agricultural crops. Areas that should be made “useful” by drainage. Or at least those were the prevailing attitudes before the value of wetlands became widely recognized. In fact, government policies actively promoted the drainage of wetlands in the 1800s and much of the 1900s, with various incentive-based programs aimed at “reclaiming” swamps and other “overflowed” lands. Public funding was also provided for drainage activities. However, wetlands are now universally recognized as valuable providers of ecosystem services, playing critical roles in water purification, flood control, storm protection, nutrient removal from agricultural runoff, carbon storage, fishery support, and providing habitat for rare plants and animals. Thus, today many conservation agencies are actively working to identify, manage, protect, and restore wetlands. Many of these efforts are focused on the protection of systems that have been little impacted by human activities, or restoring degraded wetlands to a more natural state. Therefore, knowledge of how humans have impacted our remaining wetlands is critical to successful protection and restoration.

Drainage. Ditching. Filling. Extracting peat. These are some of the more obvious activities that damage or destroy these ecosystems. However, human activities also have indirect effects, such as ecological changes brought on by invasive species, changes in the acidity or chemistry of surface waters, changes in water levels due to groundwater use, and climate change. However, for some wetlands, there may be another indirect effect that has not been fully considered. Dust. Microscopic dust. Could something so small really have a big impact? We recently addressed this question by studying a bog in western Pennsylvania.

Sundew (Drosera sp.) is a carnivorous plant common to bogs and other nutrient-poor wetlands. A sticky substance, resembling dew in appearance, is released at the tip of each tentacle and traps small insects. The carnivorous habit allows the plant to supplement its nutrient intake. (Photo: R.K. Booth)

Dust, deforestation, and bogs

European settlers logged the vast majority of eastern North America about 100 to 150 years ago, substantially altering terrestrial ecosystems and the regional landscape. In many regions, widespread agriculture was established shortly after logging. Collectively, these activities increased soil-dust movement. Mobilization of dust would have occurred as cultivated fields replaced forests, and the treeless landscape would have allowed dust to move greater distances. This dust landed on adjacent ecosystems, including “wastelands” where agriculture was not possible…those soggy, bug-infested wetlands.

Bogs – a unique type of wetland characterized by very low nutrients – would be expected to be more sensitive to dust deposition than other wetland types. Why? Because the organisms that occur in bogs are adapted to low-nutrient availability. Carnivorous plants, which supplement their nutrient uptake by capturing small insects, are commonly found in bogs, and virtually all plants in bogs have some adaptation that allows them to survive in the nutrient-limited environment. Soil dust contains nitrogen, phosphorus, and other elements, so increasing dust deposition might actually fertilize the bog. You might think that this would be a good thing, as more fertilizer on your garden clearly makes for happier plants. However, on a bog it has the potential to change the outcome of competition among plants, alter microbial communities, and change the rates of important processes like decomposition and primary production.  Changes in the relative rates of these processes would alter rates of peat accumulation – a fundamental property of these wetland ecosystems. But is the fertilization effect of dust enough to do these things? Can increased dust deposition cause the composition of bog plant communities to change?  How about microbial communities?  Is the impact of dust fertilization large enough to alter the relative rates of decomposition and primary production? Can enhanced dust deposition fundamentally change the bog ecosystem, including the ecosystem services it provides?

Titus Bog is surrounded by a nearly impenetrable shrub swamp, which made hauling the sediment-coring equipment to the site a bit of a challenge. (Photo: M.E. Sullivan)

The ecology of dust?

Alex Ireland carefully wraps up a portion of a peat core from Titus Bog, and prepares it for transport back to laboratory. (Photo: RK Booth)

Of course, in most regions of eastern North America, widespread deforestation occurred over a century ago, so to address our questions a retrospective approach was needed. Luckily, bogs preserve a record of past dust deposition and environmental conditions in the form of peat, which gradually accumulates in these environments. The acidic and oxygen-depleted environment within the peat is well-suited for the long-term preservation of plants and other organisms that occurred within and around the bog in the past. We carefully examined the paleoecological record from Titus Bog, a protected wetland in western Pennsylvania, to assess whether dust deposition increased at the time of deforestation, and if so, how this affected the bog. We collected a series of peat cores from the wetland, and used the information contained in these cores to reconstruct how the ecology of the bog has changed over the past several hundred years (Ireland & Booth 2012).

Conceptual model summarizing the ecological dynamics that likely resulted from the indirect effects of deforestation of the uplands surrounding Titus Bog in the late 1800s and early 1900s. From Ireland & Booth (2012).

Our results revealed that before European settlement, Titus Bog was a typical acidic bog, dominated by mosses that thrive in low-nutrient conditions. However, a layer of mineral dust marks the onset of big ecological changes in the peat cores. This mineral-rich layer contains pollen from agricultural weeds that expanded rapidly as Europeans converted forests to fields, allowing us to confidently link the increased dust deposition with human land clearance. Measurements of nutrient content of the peat revealed that the dust fertilized the surface of Titus Bog, and the increased nutrient availability led to changes in plant communities. In particular, it allowed woody plants to out-compete the mosses, shifting the relative abundance of these plant groups.  As the plant communities were changing in response to increased nutrients, the microscopic organisms living on the wetland surface also changed, indicating that the dust deposition led to changes in multiple trophic levels. These changes in plant and microbial communities were also associated with increases in rates of decomposition, which may have altered the rate that the system performed one important ecosystem service – the sequestration of carbon dioxide from the atmosphere.

Today, much of the land south and east of Titus Bog is still used for agriculture, although a thin forest buffer exists between the agricultural fields and the wetland. (Photo: RK Booth)

Interestingly, the wetland that exists today is fundamentally different from the one that was present just a few hundred years ago, although the reestablishment of a thin forest buffer may be helping the system slowly recover.  Our results highlight the importance of forest buffers, particularly upwind of bog environments, in the management of these systems. Things that are small and easy to overlook, like dust, can have big impacts. In the case bogs, successfully protection really may need to consider what is blowin’ in the wind.

See a post on the paper at the Journal of Ecology Blog, or read the full paper here.

White pines (Pinus strobus) growing on Titus Bog. The paleoecological record and tree-ring collections suggest that white pine became much more abundant on the bog after European deforestation of the upland (Ireland & Booth, 2012).

-rkb & awi-

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