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.


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