Monday, December 19, 2016

Diatom of the Month: December 2016 - Tabellaria fenestrata

           by Kristen Dominguez*
          As an undergraduate student in Evelyn Gaiser’s Lab at Florida International University (FIU), I was
          provided the opportunity to visit and study the algae of the pristine and gorgeous Lake Annie.
          Located at the Archbold Biological Station (halfway from Miami to Orlando), this sinkhole lake fed
          by rainfall and groundwater is home to a wide variety of organisms, including many planktonic
          algae. In 2006, this tiny lake became part of the Global Lakes Ecological Observatory Network that
          examines global trends in lake ecosystems.

Fig. 1. Kristen taking Secchi depth measurements of water transparency at Lake Annie.

Fig. 2. Kristen Dominguez (left), Dr. Evelyn Gaiser (middle) and Dr. Emily Nodine (right) collecting samples at Lake Annie.

          In monomictic lakes such as Lake Annie, little mixing takes place between the warmer surface
          waters and the deeper colder waters during the hotter months; but, as fall and winter come, the
          water on top gets cooler and thus mixes with the cold water below. These temperature fluctuations
          occur each year with some variations between different lakes. Our key research questions are:
          what species would be affected by these changes in thermal structure, and how would water
          column stability affect phytoplankton diversity?  For several months, I worked on a microscope to
          identify and count the algae found in 72 samples from a period covering the transition from
          winter mixing to summer stratification in Lake Annie.      
         The same work is being done by students at GLEON lakes all over the world! Now that I am
         analyzing the data, I realize the significance of our work. We observed a strong positive
         relationship between water column stability and the number of dominant species (comprising 95% of
         the total biovolume). Among these was Tabellaria fenestrata, our new diatom of the month. This
         diatom is adapted to oligotrophy in Florida (Whitmore 1989), neutral pH of 7, and lives either in the
         plankton (Krammer and Lange-Bertalot 1991) or attached to vegetation or other hard substrates
         (Koppen 1975). It can form long straight chains1Other key features of the frustule of T.
         fenestrata are illustrated in Fig. 3.

Fig. 3. Tabellaria fenestrata: 1. Central inflation wide; 2. Central striae reach axial line; 3.
Girdle bands open; 4. Septa present (scalebar = 10 µm; source: DeColibus, 2013).

          In Lake Annie, various diatoms, including T. fenestrata was more dominant in later dates after the
          lake mixing events, and so they seem to prefer more stratified conditions. Here climatic oscillations
          have led to marked changes in transparency and thus stratification via heat budget variations; and
          even small rainfall changes may lead to significant consequences on the biota (Gaiser et al. 2009).
          Diatom communities changed due to acidification caused by atmospheric pollution during
          industrialization, and consequent recovery from around 1970, as well as hydrological, phosphorus
          loading and alkalization (Quillen 2009). We are fine-tuning our hypotheses in order to enhance our
          understanding of the relationships between water column stability and diatom abundance,
          dominance, and diversity patterns in this subtropical ecosystem.

*        *Undergraduate student in the Gaiser Lab at the FIU Southeast Environmental Research Center.
           This post was written in collaboration with Dr. Evelyn Gaiser and Dr. Luca Marazzi.


1.                DeColibus, D. (2013). Tabellaria fenestrata. In Diatoms of the United States. Retrieved December
2.               Gaiser E.E., N.D. Deyrup, R.W. Bachmann, L.E. Battoe, H.M. Swain. (2009). Effects of climate variability on
           transparency and thermal structure in subtropical, monomictic Lake Annie, Florida. Fundamental and Applied
           Limnology 175: 217–230.

3.               Koppen, J.D. (1975). A morphological and taxonomic consideration of Tabellaria (Bacillariophyceae)
          from the northcentral United States.Journal of Phycology 11: 236-244.

4.              Krammer, K. and Lange-Bertalot, H. (1991). Bacillariophyceae. 3. Teil: Centrales, Fragilariaceae,
          Eunotiaceae. In Ettl, H., Gerloff, J., Heynig, H. & Mollenhauer, D. (Eds.). Süsswasserflora von
          Mitteleuropa. 2(3): 1-576. Gustav Fisher Verlag, Stuttgart, Germany.

5.              Quillen A.K. (2009) Diatom-based Paleolimnological Reconstruction of Quaternary Environments in a
          Florida Sinkhole Lake, PhD- Dissertation. Florida International University, Miami, 131 pp.
6.               Whitmore, Thomas J. (1989). Florida diatom assemblage as indicators of trophic assemblage and pH. 
          Limnology and Oceanography 34(5): 882-895. American Society of Limnology and Oceanography, Inc.


Monday, November 21, 2016

Diatom of the Month: November 2016 - Medlinella amphoroidea

by Tom Frankovich*

I would like to introduce you all to Medlinella amphoroidea, a new taxon that was observed on loggerhead sea turtles, as the November diatom-of-the month. But, before I get to discussing the morphology and ecology of this new genus and species, I will tell you all a personal story of serendipity and professional relationships. It was early 2013, and I had received an email from Dr. Brian Stacy, a marine veterinarian at the National Marine Fisheries Service, and a friend from when we worked together investigating parasites in marine gastropods. Brian told me that his wife, Dr. Nicole Stacy, also a marine veterinarian, was interested in identifying organisms that she suspected were diatoms that were on skin smear slides and contaminants in blood, urine and teat fluid samples from Florida sea turtles and manatees.

Fig. 1. Dr. Brian Stacy performing a necropsy on a loggerhead turtle, Caretta caretta (Photo courtesy Brian Stacy, unknown photographer).

I subsequently found out that pathologists were frequently misidentifying diatoms and reporting them as “parasite eggs”! Obviously, it is important to distinguish likely benign diatoms from harmful parasites, and so I told Nicole that I would gladly examine photomicrographs of her samples and that it would be no problem to identify these suspected diatoms using descriptions of the local diatom flora. After all, the sea turtle and manatees probably picked up these diatoms from the surrounding environments, right? Wrong! Nicole had immediately sent me images of various samples collected from manatees and sea turtles. The samples were uncleaned and were stained with a dye to reveal cytological characteristics of interest to a pathologist. These are not the best samples for a diatomist to examine, so most diatoms could only be identified in the broadest of terms (e.g., radial centric, raphid pennate). I asked Nicole if she had material to clean, mount, and examine using standard diatom methodologies. She told me that she only receives prepared slides from the field. End of story? Not yet. About a week had passed when an Everglades Park Ranger knocked on my office door at our Florida Bay research station and asked if I could help him move a dead manatee that was reported in the bay. I suppose most people would say no to moving a dead smelly manatee, but for me this was a gift from the heavens. I finally got my hands on an adequate sample for my planned examinations, but I was in for a rapid deflation of my presumed diatom identification abilities, and for a big surprise.

Fig. 2. A manatee captured for a health assessment (left) and a close –up of the manatee skin (right) with a film of epibionts, including diatoms (Photos by Tom Frankovich).

If you are a fellow diatomist in the blogosphere, you may agree with me that the most exciting part of our work is looking at a sample for the first time. Like a child waiting for Christmas morning, I anxiously awaited for the cleaning and rinsing of the new diatom sample to be complete. What I saw through the microscope was an assemblage unlike anything I had seen previously. First, instead of seeing a very diverse collection of tens of diatom taxa, I saw an assemblage comprised of very few taxa. 95% of the valves appeared to belong to 2 or 3 taxa. Second, I could not identify the dominant taxa, not even to a genus!  Even after scouring 58 reference books, and a file cabinet of reprints of benthic diatom taxonomy, I was still lost! Time to call for help. I emailed photomicrographs to Dr. Mike Sullivan, the former 20+ year editor of Diatom Research, and the person who first sparked my interest in diatoms. I told him of my challenges. He immediately replied back saying that he was not surprised that I was unable to identify the genus in those references. He indicated that the diatoms belonged to one of two genera – Tursiocola or Epiphalaina. These genera were exclusively epizoic, and up until 2012, were known only from the skin of whales and therefore, we were very unlikely to find these in benthic diatom literature.
The small number of species within these genera and the relatively recent descriptions with SEM images of these taxa made it relatively easy to compare our specimens against the described species and determine if they were new to science. Subsequent SEM analyses revealed that there were 3 new species of Tursiocola in our sample (check out last year’s blog on T. ziemanii). This discovery of a new diatom world on the skin of a dead manatee, and opportunistically working with marine veterinarians, have opened up a whole bunch of new opportunities and investigations and brings our blog conversation to the present diatom-of-the-month Medlinella amphoroidea. This diatom was described from sea turtles captured in Florida Bay. After seeing the new diatoms on the manatee, we wanted to know if the same or similar diatoms occurred on sea turtles as we suspected from some of Nicole’s cytologic specimens. We found a similar low diversity species assemblage with some of the same genera; the species composition was different, but we also described another new Tursiocola species (T. denysii) along with M. amphoroidea.
So here is the profile of Medlinella amphoroidea. This species is very abundant on the neck of loggerhead sea turtles, accounting for up to 50% of diatom valves observed in skin samples. It is a very small diatom, only 7-13 microns (µm) in length. Using light microscopy, its valves are likely to be misidentified as a Catenula or small Amphora species because of its shape and eccentric raphe-sternum, but careful focusing through valves with attached valvocopulae1 or through intact frustules will reveal septa2 present on the girdle bands, differentiating Medlinella from these other genera. M. amphoroidea is most similar to species in the epizoic genera Tripterion, Chelonicola, and Poulinea and other “marine gomphonemoid (Gomphonema-like) diatoms”. The amphoroid shape of the valves and the unique volate pore occlusions3 of the areolae distinguish Medlinella from these genera. The genus name honors Dr. Linda Medlin in recognition of her work describing marine gomphonemoid diatoms.       

Fig. 3. Microscope images of Medlinella amphoroidea; a) girdle view; b), c), d) valve / face view (Photos: a), c), d) Matt Ashworth; b) Frankovich et al., 2016; scale bar = 2 μm).

I hope my story will encourage some of you out there to share your passion for diatoms with other scientists and to pursue any opportunities that may present themselves. The seeds of future exciting discoveries start with a conversation. Thanks again Luca and readers, for our continuing conversations on the diatom-of-the-month blog.

* Research Faculty at the Southeast Environmental Research Center, Florida International University.
1. Valvocopulae: the first girdle bands that attach to the valve
2. Septa: inward projections of silica that partially separate areas within the cell.

3. Volate pore occlusions: flap-like outgrowths from the sides of the pores with narrow points of attachment and irregular branching, as opposed to cribrate or rotate occlusions.

Tuesday, November 8, 2016

Drain the Swamp

“I know more about ISIS than the generals do” Donald Trump advocates “draining the swamp” in Washington.  This statement is personal to me.  After spending the past 6 years studying swamps, I can say in no uncertain terms that draining swamps is bad. Swamps and other wetlands provide habitat to over half of the species deemed threatened or endangered in the US, filter our water, store more carbon than any other ecosystem, protect us from flooding and much more, making wetlands our most valuable ecosystems, thus their protection under the Clean Water Act.

FCE researchers wading through the swamp 
Suggesting that draining swamps is a way to fix America’s problems is to reject science.  We have destroyed over half of our wetlands in this country to devastating effect.  The Everglades provides a great example.  The largest ecological restoration effort in the history of the world revolves around undraining the swamp.  We reduced the Everglades to half of its historical extent for development, but now realize that we made a mistake. We have lost water quality, fisheries productivity, bird usage, carbon storage and seagrass health all because of draining the swamp.  Each of these things is important to the ecosystem, but also to our economy, as The Everglades fill our drinking water aquifers, provide nursery for economically important fisheries, bring tourists from across the world and protect us from storm surge.  Wetlands  also take  CO2  from the atmosphere and store it more efficiently than any other ecosystem (this seems particularly important adjacent Miami, the city at the highest economic risk from sea level rise in the world).  Moreover, swamps can be destroyed in hours, but take centuries to restore.   If the Donald would have looked this phrase up, he would realize that it is now currently illegal without mitigation under the Clean Water Act, that it is widely criticized and is in direct opposition to our national environmental and economic interest… Sound familiar?

I just heard a discussion on the radio that demands comment.  A caller on a radio program called in to suggest that climate change is a false liberal construct aimed at ushering in a new world order.  The idea that every university across the world is conspiring to keep dissenting views of climate change out of publication is absurd to anyone that has ever stepped foot in academia.  First, we argue about everything, that is how universities work.  Second, we overemphasize novelty in research.  If someone could publish a paper disproving climate change their career would be made.  However, the drumbeat of climate change science is accelerating while nothing has comprehensively disproved it.

Sean Charles exploring the Everglades
Truth has come to the fore in this election.  Science is our most systematic way to help understand truth.  In the political realm, politicians that support action on science are pitted against politicians bankrolled by fossil fuels, yet public opinion is still strongly polarized.  Scientists and one of our largest industries would benefit if they could disprove climate change, yet no one has published dissent in a respected journal.

By constantly denying scientific understanding and taking a catch phrase “drain the swamp” that metaphorically praises the act of destroying some of our most valuable ecosystems, Trump has shown that he is uniquely unfit to preserve our environment.  I hope my students, regardless of their political views can see past this ridiculous discussion.  Climate change is real.  Swamps are great.  Vote swamp!

*These views are attributed to the author, and while FCE supports the science, they don’t necessarily reflect his political opinions  

Sean Charles
PhD Candidate
Florida International University

Sunday, October 30, 2016

Diatom of the month – October 2016: Brachysira brebissonii

by Charlotte Briddon* 

Brachysira brebissonii (formerly known as Anomoeoneis brachysira) is a freshwater, benthic diatom. It is widespread in lakes and rivers from the Arctic to tropical and temperate regions. In 1981 the Anomoeoneis and Brachysira genera were separated, as two sets of longitudinal ribs were observed in Brachysira specimens, one surrounding the valve (marginally at the junction of valve face and mantle), and another composed of two straight ribs, discontinuous in the central area that border the raphe, which the genus Anomoeoneis lacks.

              Brachysira brebissonii (photo taken by Paul Hamilton at Egg Harbour Lakes, New Jersey, United States; see Hamilton, 2010).

Case study of Tasik Chini
I have chosen this diatom because it has played a meaningful role in aiding our understanding of past and current environmental conditions/water quality at Tasik Chini, (a flood pulse wetland in Malaysia). Tasik Chini, a natural freshwater flood pulse wetland, consists of a series of 12 interconnected basins in central Pahang and is hugely important from a conservation viewpoint in that it is has been awarded protected status by UNESCO's Man and Biosphere Programme. This program’s goals are to establish a scientific basis for the improvement of relations between people and their environments. It uses a combination of sciences to improve human livelihoods and to safeguard natural and managed ecosystems. Understanding how this lake has been impacted by an array of anthropogenic activities such as deforestation, mining and agriculture over the last 100 years or so is crucial in formulating conservation efforts to retain ecological integrity at this site.
 Oil Palm Plantation from the Tasik Chini lake catchment (photo: C. Briddon).
Brachysira brebissonii is acidophilous, it has an affinity for environments with pH < 7, with an optima of ~ 5.9 (Stevenson et al. 1991). Changes in abundance of this diatom in a sediment core can, therefore indicate pH variations in the lake over time. An abundance increase of this diatom over time may be due the onset of lake acidification from either natural (e.g. catchment geology or vegetation) and/or anthropogenic influences (such as atmospheric deposition of sulphates) (Wolfe and Kling, 2000).
   Nucifera Nelumbo, the famous water louts from Tasik Chini (photo: C. Briddon).

Analyzing a 90 cm sediment core taken from Basin 12 at Tasik Chini, we found this diatom to be most abundant in younger sediments deposited when anthropogenic impacts were largest at this site. The increasing relative abundance of Brachysira brebissonii provides important evidence of acidification and eutrophication of Tasik Chini over the latter half of the 20th century, most likely caused by increases in human activities such as mining, agriculture (palm oil and rubber plantations), hydrological manipulation and deforestation.
In addition, Brachysira brebissonii was found to be the most abundant diatom (~36 % maximum) in contemporary diatom habitats sampled in April 2016. It was observed in high numbers on leaves and stem of the iconic water lotus (Nelumbo nucifera), a key species for eco-tourism at Tasik Chini). Thus, this diatom may also be an indicator species for the presence of this floating-leaved plant.

*Charlotte is a first year Ph.D. student at the University of Nottingham, under Suzanne McGowan's supervision. She conducted her work on Brachysira brebissonii during her MRes studies at Keele University during a placement at the University of Nottingham Malaysia Campus.


Hamilton, P. (2010). Brachysira brebissonii. In Diatoms of the United States. Retrieved October 18, 2016, from
Stevenson, R. J., Peterson, C.G., Kirschtel, D.B., King, C.C.,  Tuchman, N.C. (1991) Density-dependent growth, ecological strategies, and effects of nutrients and shading on benthic diatom succession in streams. Journal of Phycology 27, 59–69
Wolfe, A.P., Kling, H.J. (2001). A consideration of some North American soft-water Brachysira Taxa and description of Barctoborealis sp. nov. Lange-Bertalot –Festschrift

Thursday, September 29, 2016

Diatom of the month – September 2016: Aulacoseira granulata

by Luca Marazzi*

Last week about 800 ecologists from 72 countries, including myself, attended and presented their research at the 10th INTECOL Wetlands conference in the beautiful city of Changshu (2 hrs west of Shanghai). Before this event that takes place every four years (in 2012 we were in Orlando for INTECOL 9), I was honored to give a long seminar on my work on the algal communities of the Okavango Delta and Everglades at the Nanjing Institute of Geography and Limnology (NIGLAS) of the Chinese Academy of Sciences. I was invited to do that by my friend Xuhui Dong (we studied together for our PhD at the UCL Environmental Change Research Center in the UK). Xuhui and his colleagues recently conducted a paleolimnology study of several floodplain lakes along the mighty Yangtze River (Dong et al., 2016), where they found large numbers of Aulacoseira granulata [(Ehrenberg) Simonsen 1979], which is therefore our September diatom (a belated post).



           Fig. 1. Diatoms of the genus Aulacoseira are characterized by point symmetry around their center                   ( above: filament with live cells; below (left): frustule with spine
                                                below (right): cell with spines. LM scalebar = 10 µm.

This is a centric, planktonic, non-motile, filament-forming species that needs medium nutrient levels (mesotrophic), and prefers turbulent conditions. In Liangzi Lake Taibai Lake, and Shitang Lake (Fig. 2), A. granulata reached relative abundances of 78% in reference communities from sediment cores dating 1800-1950. This is due to the fact that, before the 1950s, the lake was subject to strong mixing2 and free exchanges of mass and energy with the Yangtze River through its connection with the lakes, which seem to have created good conditions for large populations of this diatom3.

Fig. 2. Geographical distribution of 10 diatom-based palaeolimnological sites along the Yangtze River in Eastern China (Source: Dong et al., 2016).

Given the impressive number and extent of lakes and wetlands near the conference venue (369 wetlands, totaling 32,037 hectares, paddy fields excluded, or ~ 25% of Changshu city's total area5), many types of diatoms and other algae must very happy around here! And no wonder that Changshu may well become the first Wetland City under the Ramsar Convention on Wetlands of International Importance. Among these wetlands, I and another ~50 attendees or so visited the Shanghu Lake, Nanhu Urban Wetland Park, and Shajiabang National Wetland Park (see Fig. 3); these are human-made aquatic ecosystems, and very peaceful and nature-and-culture-rich oases in an extremely densely populated region of China. Definitely worth a visit, if you happen to be around.

Fig. 3. Boating in a beautiful spot of the Shanghu Lake site during the conference excursion.


“The 10th INTECOL Wetlands conference logo includes water, bird, fish and plant four wetland elements which combine into an integrity. The shapes of flying crane, green aquatic plant, and swimming fish link into a colorful ribbon, expressing the 10th INTECOL International Wetlands Conference would be a linkage of international communication, exchange and cooperation for wetlands professionals and workers over the world” (

Analyzing the abundance patterns of Aulacoseira granulata and other planktonic and benthic diatoms, paleolimnologists are able to reconstruct past environmental conditions, such as nutrients, pH, salinity, plant cover, and land use so that gradual and abrupt environmental changes can be better understood and predicted. Wetlands are under severe threats (the Wetland Extent Index has declined 30% in the 1970-2008 period4), understudied, and not too clearly defined yet, therefore, if we want to deeply inform their conservation and sustainable management, international collaborations stemming from high-profile conferences such as INTECOL Wetlands are crucial. I am happy to report from Changshu that this community is very motivated and vibrant. And diatoms, beyond being stunning living organisms, are essential to better understand aquatic ecosystems, so let’s conserve them and their habitats, shall we?

* Postdoctoral Associate in Dr. Evelyn Gaiser's lab at Florida International University.

1. Dong X., Yang X., Chen X., Liu Q., Yao M., Wang R. and Xu M. Using sedimentary diatoms to identify reference conditions and historical variability in shallow lake ecosystems in the Yangtze floodplain. Marine and Freshwater Research 67, 803–815.
2. Owen R., and Crossley R. (1992). Spatial and temporal distribution of diatoms in sediments of Lake Malawi, central Africa, and ecological implications. Journal of Paleolimnology, 7, 55–71.
3. Yang G.S., Ma R.H., Zhang L., Jiang J.H., Yao S.C., Zhang M., and Zeng H. (2010). Lake status, major problems and protection strategy in China. Journal of Lake Sciences, 22, 799–810.
4. Dixon MJR, Loh J, Davidson NC, Beltrame C, Freeman R, Walpole MJ. (2016). Tracking global change in ecosystem area: The Wetland Extent Trends Index. Biological Conservation, 193, 2735.
5. Source: