Algal and testate amoebae communities of urban ponds and green roofs


A major challenge facing biodiversity is conflicts for space with a growing global human population. Green roofs, whereby the roof of a building is planted with vegetation on a waterproof membrane, present a potential solution within urban settings. These are becoming increasingly popular (1-3) as they provide multiple benefits associated with the increase in biodiversity value and a range of ecosystem services (3-5). In addition to providing terrestrial habitats for pollinators and stopover points for birds, green roofs regularly contain ephemeral and occasionally semi-permanent puddles which are likely to provide habitat for aquatic communities. However, these habitats, the biological communities they support and their roles in the ecosystem have not yet been characterised.
This PhD project aims to address this research gap. It will focus on diatoms and testate amoeba which play an important role in biogeochemical cycling and are used as indicator species to address water quality problems. The project will provide a novel insight into the composition of these communities on green roofs, and determine how these communities differ from those in urban ponds. Algal communities in urban ponds have a long history of investigation (6-8) but there are still substantial research gaps and our knowledge about them is far from complete. For example, several diatom species that were new to science were discovered in a single pond in Edinburgh (9), but their distribution and ecological relationships remain unexplored. Testate amoeba, are even more understudied, although our knowledge of their ecological interactions in urban ponds is growing (10-12). This PhD project thus presents an exciting opportunity to provide new information to close these research gaps and to contribute to the management of urban habitats; it may even have a potential to discover new species.

The successful applicant will have an opportunity to design testable hypothesis and structure their research around the following questions:
– how does species richness and abundance of green roof aquatic communities contribute to the overall biodiversity and ecosystem services provided by green roofs, and how do these compare to urban ponds?;
– how do diatoms and testate amoebae interact with other biota (especially macroinvertebrates) and with each other?
– how does the ephemerality of these non-permanent habitats influence species composition and life history?
– how effective are components of the green roof community as indicators of water quality?;
– what are the preferences of the specific taxa for epipelic (i.e. living on sediments), planktonic or epiphytic ((i.e. living on plant surfaces) habitats?;
– is there variation in chemical composition of amoebae and diatoms, and how does this affect biogeochemical cycling?;

The project will benefit from co-location with other ongoing ecological research currently underway at the prospective studies sites. The successful PhD candidate will be based at Heriot Watt University in Edinburgh and benefit from collaboration with the established research team at Heriot Watt, University of Glasgow (Institute of Biodiversity, Animal Health and Comparative Medicine, and the Scottish Universities Environmental Research Centre), Royal Botanic Gardens Edinburgh (RBGE), NatureScot, and the Institute for Food and Agricultural Research and Technology (IRTA – SantCarles de la Rapita, Catalunya, Spain).
It is expected that the PhD student (supported by the supervisors and SAG, and in cooperation with the collaborative network) will lead a number of interdisciplinary publications, including peer-reviewed journal articles and presentations at conferences and workshops. Emphasis will be put on the dissemination of the resulting recommendations via internet forums and newsletters and other information outlets of RBGE, The Wildlife Information Centre, NatureScot, Scottish Wildlife Trust, Edinburgh Natural History Society, and Edinburgh City Council.

Click on an image to expand

Image Captions

Examples of freshwater diatom and selected testate amoebae.



Regular samples of epipelic, epiphytic and planktonic communities will be taken at the selected research sites. Monitoring of auxiliary physical and chemical parameters (pH, oxygen, conductivity, water quality) will be carried out using standard field and lab methods. In ponds, water quality will also be assessed using macroinvertebrate indices obtained through sweep net sampling.

Analysis of samples

Scanning microscopy will be used to investigate fine details of the diatoms shells and amoebae tests (thus aiding their identification), and to assess their chemical composition. Metabarcoding will be used to characterise the microbiological communities at the study sites, to confirm identification, and to assess contribution of selected species to the overall biodiversity. Light microscopy will be used to estimate the abundance and distribution of the target species in the collected samples. Data on vegetation will be available from the parallel ongoing projects.

Project Timeline

Year 1

Months 1- 6: literature review, designing hypotheses and selection of the sampling sites; training in microscopy techniques, sampling methods and algal identification
Months 3 – 10: trials of sampling and analysis techniques and preliminary studies; training in macroinvertebrate identification
Months 8 – 12: start of the sampling and preliminary statistical analysis (following training in statistics/R);

Year 2

Months 13 – 24: continue sampling and analysis, write up of conference and journal papers; training in communication and presentation skills

Year 3

Months 25-32: Analysis of the results and write-up of data for the thesis; conference presentations and submission of journal papers
Months 32-36: Complete analysis and write-up of data, prepare and submit manuscripts.

Year 3.5

Months 37-41: Finalise the write up of thesis and manuscripts
Month 42: Thesis submission

& Skills

Training in light and scanning electron microscopy will be provided at Heriot-Watt by Dr. Jim Buckman and Dr Alex Poulton
Training in algal identification will be provided both in house (expertise available at Heriot Watt, Dr Alex Poulton), and by attending a specialised training course (e.g. Freshwater Biological Association or British Ecological Society), as well as through placement in RBGE or IRTA (with Professor David Mann).
The student will also receive training in statistical and ecological modeling in R (SCENE Field Station, University of Glasgow).
In addition the student will be trained in preparing manuscripts and presenting results at conferences, and have access to a range of further postgraduate training courses offered by Heriot-Watt University.

References & further reading

Selected Internet Links:

1. Ascione F, Bianco N, Rossi F, Turni G, Vanoli G. Green roofs in European climates. Are effective solutions for the energy savings in air-conditioning? Applied Energy. 2013;104:845-59.
2. Castleton HF, Stovin V, Beck SBM, Davison JB. Green roofs; building energy savings and the potential for retrofit. Energy and Buildings. 2010;42(10):1582-91.
3. Grant G, Engleback L, Nicholson B, Gedge D, Frith M, Harvey P. Green roofs: their existing status and potential for conserving biodiversity in urban areas. English Nature; 2003.
4. Kadas G. Green roofs and biodiversity: can green roofs provide habitat for invertebrates in an urban environment?: Lap Lambert Academic; 2010.
5. Oberndorfer E, Lundholm J, Bass B, Coffman RR, Doshi H, Dunnett N, et al. Green Roofs as Urban Ecosystems: Ecological Structures, Functions, and Services. BioScience. 2007;57(10):823-33.
6. Mann DG. The species concept in diatoms. Phycologia. 1999;38(6):437-95.
7. Mann DG, Droop S. Biodiversity, biogeography and conservation of diatoms. Biogeography of freshwater algae: Springer; 1996. p. 19-32.
8. Mann DG, McDonald SM, Bayer MM, Droop SJM, Chepurnov VA, Loke RE, et al. The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species. Phycologia. 2004;43(4):459-82.
9. Mann DG, McDonald SM, Bayer MM, Droop SJ, Chepurnov VA, Loke RE, et al. The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species. Phycologia. 2004;43(4):459-82.
10. Krivtsov V, Birkinshaw S, Arthur S, Knott D, Monfries R, Wilson K, et al. Flood resilience, amenity and biodiversity benefits of an historic urban pond. Philosophical Transactions of the Royal Society A. 2020;378(2168):20190389.
11. Krivtsov V, Arthur S, Buckman J, Bischoff J, Christie D, Birkinshaw S, et al. Monitoring and modelling SUDS retention ponds: case studies from Scotland. ICONHIC2019.
12. Krivtsov V, Arthur S, Buckman J, Kraiphet A, Needham T, Gu W, et al. Characterisation of suspended and sedimented particulate matter in blue-green infrastructure ponds. Blue-Green Systems. 2020;2(1):214-36.

Further Information

Jim Buckman,

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