The Use of Diatoms for Water Quality Determination and Biomonitoring in South Africa

A WRC funded project


Assemblages of diatoms provide a recognized and valuable aid in determining water quality and, importantly, undertaking paleoenvironmental assessments of environmental change. Phycological approaches, in particular those examining the ecological associations of phyto- and epiplanktonic communities, are powerful descriptors of physico-chemical and biological cause and effect pathways. In many cases it has been shown that the use of diatoms for predictive or forensic assessments provides a more sensitive, robust and seasonally-durable methodology when compared with similar approaches based on invertebrate populations. The value of diatom material retained in sediment layers provides an historical perspective that can be retrieved through the expedient of careful sediment coring. Such analyses provide a fingerprint of change that can extend back over centuries. While sediment coring is commonly applied to pollen studies, its use for studying diatoms and molluscs is virtually unknown in South Africa.

The use of diatoms in particular, and phytoplankton in general, in South African water quality studies has, until recently, been virtually non-existent. The results emanating from Phases 1 and 2 of this project have awakened a wider recognition of the value of this technique such that it is already being applied across entire river systems, in urban environments and in wetland assessments.

Phase 1: Diatoms in South African Waters: The South African Diatom Collection

The Phase 1 report (WRC TT242/04) is available from the Water Research Commission (


The South African Diatom Collection

The South African Diatom Collection ('the Cholnoky Collection') is of international significance, but is not sorted or collated. Formal curatorship of the Collection remains an issue of crucial importance. The collection comprises the following elements stored in as documents, bottles of dried material and permanent glass slide mounts:

  1. A number of special slide series donated to the CSIR by the British Museum. These series comprise 'type' specimens against which the validity of the specimens are identified and validated.
  2. SA Reference Slides. These pertain to the diatoms documented in the unfinished Diatom Flora of Southern Africa publication.
  3. The Giffen Collection - a series of slides from Kidds Beach and the Amatola Mountains (Eastern Province), and the west coast of South Africa.
  4. The Cholnoky Collection - covering many parts of South Africa and surrounding southern African states - this component comprises in itself some 14 000 slides of which only 500 have been processed.
  5. The REM Archibald and F Schoeman Collection - covering many ecological studies around South Africa.
  6. Various slides from overseas diatomologists.
  7. Approximately 15 000 (fifteen thousand) publication reprints and 350 reference texts.

Objectives of the First Phase

This first-phase of this project (WRC k5/508) reviewed and collated the material contained in the Collection, and transferred the South African information to a database where it can be overlaid with water quality information. One of the central aims of the project is to determine whether or not the information may be used to determine reference water quality conditions for various types of surface waters. The material in the Collection represents studies on many Southern African surface waters, many of which have since been significantly altered by human activity.

Phase 2: Development of a Diatom Assessment Protocol (DAP) for South African Rivers and Streams

Objectives of the Second Phase

The second phase of the diatom project (WRC K5/1588), completed in March 2006, developed a suite of tools necessary for the practical use and application of diatoms in South Africa. The DAP Toolkit comprises sample collection and processing manuals, training videos covering all aspects of sampling and sample processing, and software and printed taxonomic keys. All of these products will become available from the WRC during the third-quarter of 2006. In addition to the Toolkit the project team presented a series of workshops in the Western Cape, Pretoria and KwaZulu Natal.

Diatoms Diatoms

Planning for Phase 3

Emanating from Phase 2 has been the wider recognition amongst SA water quality managers and practitioners that diatoms can play a central role in water quality and biomonitoring in this country. Use of the application was successfully employed in the State of the Rivers assessment for the Crocodile-Marico West river system. Accordingly the third phase of the project aims to collect regional data and provide a calibrated index for South African systems that is aligned with the six classes (A-F) used in the RDM and Ecostatus methodologies. This phase will also encompass training of diatomologists at three regional centres, additional training workshops and further refinement of the DAP Toolkit, as well as testing of the application for use in urban canals and waterways and the launch of a web-based interactive diatom identification program.

About the researchers

The project was undertaken by Bill Harding, Colin Archibald - brother of the late Richard Archibald who was largely responsible for compiling the Collection into its present form, and Jonathan Taylor. Bill Harding, a phytoplankton ecologist who for many years has used algal assemblages as indicators of environmental condition and change, campaigned for over a decade for this project to go ahead. Colin Archibald, formerly of the CSIR (Durban) is one of less than a handful of diatom taxonomists in South Africa, and the only person with an intimate understanding of the Collection. Jonathan Taylor of the North West University is responsible for the technical and taxonomic elements of the project.

Contact Us

The researchers welcome interest in this project. Please feel free to contact us.