Thursday, February 16, 2017

Researching Algae, the Unsung Heroes of Aquatic Food Webs

by Luca Marazzi*

Why is it important to study algae? To start with, algae produce ~ 50% of the oxygen on planet Earth, they are food for small and large animals that in turn are eaten by people, but they also recycle nutrients and absorb CO2 from the air; by existing and doing their own thing, these microorganisms provide these so called ecosystem services to human beings (Fig. 1). Moreover, as algae reproduce fast and are often adapted to specific environmental conditions, understanding how many species of algae, and which ones, live where and why give us cues as to the health of aquatic ecosystems, such as rivers, lakes, and wetlands. 

Fig. 1. Simplified scheme of the role of algae in food webs (from my Ph.D. Thesis).

* Dr. Luca Marazzi is a freshwater ecologist working in Dr. Evelyn Gaiser’s research group in the School of Environment, Arts and Society at Florida International University. His main interest is how biodiversity, ecology, and distribution of algae in subtropical wetlands change with hydrology, nutrient concentrations and habitat. He curates the “Diatom of the month” blog series aimed to raise awareness on these algae, key primary producers and indicators of environmental change.

How did I get to do research on algae? For my Environmental Science MSc dissertation project, I worked in the northern Italy’s Alps studying Passerine bird migration, then my career path took me to office-based research on air quality and climate change. Wanting to go back to field research, I got a Ph.D. opportunity at University College London to study the biodiversity and biomass of microscopic algae in the Okavango Delta, a subject and a place I didn’t know much about, apart from biology courses and natural science readings. Between 2009 and 2010, I spent ~3 months in Maun (NW Botswana), to carry out the necessary sampling in this incredible, remote, and near pristine wetland in the middle of the Kalahari; another ~ 70 months were needed to master and apply taxonomy and microscope skills, conduct statistical analyses, read, think, and write my Thesis, as well as working to support my graduate studies.
Fast-forward 8+ years, here I am in sunny Miami, some 8,000 km away from the cold and misty mountain pass where I did my MSc research and 12,200 km from the Okavango, to work on another amazing wetland, the Everglades, as part of a Postdoctoral Associate contract in Dr. Evelyn’s Gaiser laboratory at Florida International University (FIU). After a few months at FIU putting together a database for the Comprehensive Everglades Research Plan Monitoring and Assessment Plan (CERP-MAP) and planning my publications, I decided, with my postdoc and Ph.D. advisors, to undertake an ambitious comparative study of patterns and drivers of species richness and life-history strategies in the Okavango and Everglades. We estimated that, the Okavango hosts, on average, ~80 species of algae in each sampling site, the Everglades have ‘only’ ~ 20 (Fig. 2). This is likely due to phosphorus scarcity, habitat fragmentation due to water diversion schemes, and nutrient pollution in the Everglades whereas the Okavango is still a near pristine wetland. Moreover, Florida is a long peninsula, while the Zambezi ecoregion in Africa has been historically well connected so that organisms may be able to better disperse to and from this wetland than in the Everglades. For more information, our paper “Algal richness and life-history strategies are influenced by hydrology and phosphorus in two major subtropical wetlands” is published in this month's issue of Freshwater Biology.

Fig. 2. Map of estimated algal richness and photos from the air: Okavango (above) and Everglades (below). Okavango (site averages); UPH= Upper Panhandle; LPH=Lower Panhandle; XAK=Xakanaxa; BOR=Boro; SAN=Santantadibe. Everglades; LKO=Lake Okeechobee; LOX=Loxahatchee; Out_ENP=Outside of Everglades National Park (including the Water Conservation Areas, WCA 2 and 3); ENP=Everglades National Park.

Although, in the Okavango, the flooding cycles have a stronger influence on species richness, as compared to phosphorus in the Everglades, maintaining and restoring the natural hydrology in these wetlands is critical for the preservation of algal communities, and thus for the health of food webs. Due to their outstanding geographic features and biodiversity, both these wetlands are protected as World Heritage sites, and are included in the Ramsar Convention on Wetlands of International Importance, and so it is critical to keep monitoring these ecosystems

What’s next?
I am currently researching how algal dominance changes with nutrients and hydrology in the Everglades, which is relevant for freshwater flow and water quality restoration scenarios. I am also trying to create opportunities for comparative research in other subtropical wetlands. Last September, I visited the Nanjing Institute of Geography and Limnology of the Chinese Academy of Sciences and, with other 800 experts, attended the excellent 10th INTECOL Wetlands conference in Changshu. I presented my comparative work and co-organized a workshop on future directions in wetlands studies, strengthened previous connections and made new ones with various colleagues working in Asia, South America and Australia. In June, other FIU scholars and I are planning to present our work at the next Society of Wetland Scientists’ meeting in Puerto Rico (“Celebrating Wetland Diversity Across the Landscape: Mountains to Mangroves”), where we aim to foster new collaborations with ecologists conducting research on wetland ecosystems and food webs in Central and South America, and beyond. Moreover, Dr. Gaiser, Dr. Barry H. Rosen (USGS) and I co-organized a special session on how algae / periphyton mats may respond to different nutrient and hydrology scenarios in the Everglades for the Greater Everglades Ecosystem Restoration (GEER 2017) conference. As wetlands are facing unprecedented anthropogenic impacts due to, for example, land use change, water diversion, and global warming, such collaborations among scientists, and between us and policy makers, are crucial to foster and inform sustainable management practices and strong conservation and restoration activities.

Fig. 3. (from top to bottom) In front of the conference venue with Drs. Wolfgang Junk (Federal University of Mato Grosso, Brazil), Max Finlayson (Charles Sturt University, Australia) and Xuhui Dong (Aarhus Institute of Advanced Studies, Denmark and Chinese Academy of Sciences); our International Network for Next Generation Ecologists workshop; two pictures from one of the conference fieldtrips to Shanghu Lake.

Friday, January 20, 2017

Diatom of the Month: January 2017 – Amphora coffeaeformis

By Keely Mills*

I am a fan of hot temperatures and sunny climates. This may sound strange coming from someone who lives in a wet and grey part of the UK (Nottingham). However, hot weather is one of the main reasons I love researching tropical lakes, and a trait I share with the January 2017 ‘Diatom of the Month’. I would like to introduce you to my favourite diatom: Amphora coffeaeformis (Fig. 1) [now renamed Halamphora coffeaeformis] – a salt-tolerant species, indicating a shallow, slightly saline environment (Gasse, 1986).

Fig. 1. A specimen of Amphora coffeaeformis found in the sediments of Lake Nyamogusingiri, Uganda (photo: K. Mills).

So, how did I come to ‘discover’ this diatom, and how did it come to be my favourite? My story starts as a new Ph.D. student at Loughborough University in 2005. I was working with Dr David Ryves on a project focussed on the Ugandan Crater Lakes, where I would use a palaeolimnological approach to infer past climate and environmental changes that took place over the last 1,000 years or so (Mills, 2009; Mills & Ryves, 2012). Back in 2005 there was much debate surrounding the spatial extent of wet and dry periods in East Africa, and one of my aims was to feed in to this debate, assessing whether past changes in rainfall in Uganda were similar (or different) to existing records from large and small lakes in Kenya, Ethiopia, and Malawi. Understanding the regional complexity of long-term changes in rainfall is crucial for modelling the Earth’s climate system, and I hoped my research would go some way to help.

Now, the region of western Uganda is as unique as it is beautiful as it is home to more than 80 crater lakes, associated with the tectonic activity related to the western arm of the East African Rift Valley System (Fig. 2).

Fig. 2. The four crater lake clusters (FP=Fort Portal, Ka=Kasenda, KK=Katwe-Kikorongo, Bu=Bunyaruguru) of western Uganda (as described by Melack, 1978), and images of some of the crater lakes (clockwise from upper left): Kako, Kamunzuka, Kifuruka, and Nyungu.

As part of my doctoral research, I obtained a sediment core from Lake Nyamogusingiri (12.5 m deep, conductivity of 554 μS cm-1). I analysed the diatom stratigraphy of this systems to allow me to infer changes in lake level that might result from rainfall variations during key time periods, such as the Little Ice Age (LIA) and the Mediaeval Climate Anomaly (MCA). In many lake sediment records from East Africa, the impact of the LIA is quite chaotic, resulting in dry periods interspersed with extremely wet periods (see CO2 Science for an overview). However, the MCA was quite a dry period in this region. I hoped to identify these ‘wet’ and ‘dry’ periods using known ecological preferences of the different diatom species, and a quantitative modelling approach.

After counting seemingly hundreds of samples from Lake Nyamogusingiri, I was beginning to get a little disheartened. My sediment samples were extremely diatom rich, but appeared to be full of Aulacoseira species (including the ‘Diatom of the Month – September 2016’)! Whilst their relative abundances fluctuated, their presence (along with other species, such as Nitzschia lancettula) suggested that there was deep(ish) freshwater in this lake all the way back to c. AD 1250…Devastated was not the word. Was I ever destined to find some indication of regional drying in these lake systems? I pressed on, knowing I had to finish counting the entire core.

But then Eureka!  At 110 cm down. Around AD 1225. I spied my very first Amphora coffeaeformis (Table 1). I knew I had it in the bag - my lakes were sensitive to the MCA (Fig. 3; Mills et al., 2014). I have honestly never felt so much joy, nor so much love for microscopic photosynthetic algae! That is how Amphora coffeaeformis became my favourite diatom, holding great memories for my research. I still get excited when I periodically cross this species in diatom preps.

Table 1: Amphora coffeaeformis – vital statistics (Gasse, 1986)
Sodium-chloride; stagnant and running
1000 – >10,000 μS cm-1
- <8.5
- <50 meq. l-1
10 - >35°C
Length: 15-40 μS
Width: 5-7 μS 
Striae in 10 μm: 17-21 (centre)
Well developed in hot springs, or spring-fed rivers (Afar region).
Eurythermal, high temperatures (44°C) does not inhibit development

Fig. 3. Diatom stratigraphy from Lake Nyamogusingiri showing selected taxa (> 8% in any one sample), ordered by weighted-averaging optimum (ascending). The appearance of Amphora coffeaeformis is highlighted in the red box (from Mills et al., 2014).

Palaeolimnology, particularly the use of diatoms, is an important tool in helping scientists to understand the response of lake systems and their biota to past environmental perturbations (both natural and human-induced). We can only understand the future impacts of a changing climate and increased human pressures on freshwater resources by having some idea of how these systems have responded in the past. Such data can allow us to implement long-term management strategies of freshwater, especially in regions such as East Africa that are water stressed, yet whose human populations rely heavily on the ecosystem services that freshwater lakes provide.

*Environmental Geoscientist at the British Geological Survey, Keyworth, UK.


Melack, J.M. (1978) Morphometric, physical and chemical features of the volcanic crater lakes of western Uganda. Archiv für Hydrobiologie 84: 430-453.

Gasse, F. (1986) East African diatoms: Taxonomy, ecological distribution. Biblioteca Diatomologica 11, Crammer, Berlin/Stuttgart, 201 pp.

Mills, K. (2009) Ugandan crater lakes: limnology, paleolimnology and palaeoenvironmental history. PhD Thesis, Loughborough University.

Mills, K., Ryves, D.B. (2012) Diatom-based models for inferring past water chemistry in western Ugandan crater lakes. Journal of Paleolimnology 48: 383-399.

Mills, K., Ryves, D.B., Anderson, N.J., Bryant, C.L., Tyler, J.J. (2014) Expressions of climate perturbations in western Ugandan crater lake sediment records during the last 1000 years.

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.