ORIGINAL RESEARCH

 

Preliminary checklist for freshwater diatom species of the Karoo, South Africa

 

 

M. Holmes^{I, II}; E.E. Campbell^I; M. de Wit^II; J.C. Taylor^{III, IV}

^IDepartment of Botany, Nelson Mandela University, Nelson Mandela Bay, South Africa
^IIAfrica Earth Observatory Network (AEON) - Earth Stewardship Science Research Institute (ESSRI), Nelson Mandela University, Nelson Mandela Bay, South Africa
^IIIUnit for Environmental Science and Management, North-West University, Potchefstroom, South Africa
^IVSouth African Institute for Aquatic Biodiversity (SAIAB), P/Bag 1015, Makhanda 6140, South Africa

Correspondence

 

 

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ABSTRACT

BACKGROUND: Species checklists are a way in which local biodiversity can be monitored. There is no readily accessible database or checklist of diatom flora of South Africa. This publication gives an account of the diatom taxa encountered during two survey projects (2010-2012 and 2015-2017) within the Eastern Karoo.
OBJECTIVES: This list has been compiled to allow for: (1) comparisons with future research in the geographical area; (2) comparison with ecological data from other countries; (3) monitoring the occurrence of new species; and (4) documentation of the disappearance of 'clean water' indicator species.
METHODS: Sampling took place in the area known as the Eastern Karoo during the two projects. Samples were scrubbed, cleaned and checked for live cells. Permanent slides were made and diatoms identified using light and electron microscopy. Each species was assigned a four-letter code from the software Omnidia version 6.
RESULTS: A total of 474 taxa were encountered, some of which are, as yet, un-described. This list contains taxonomic rank currently assigned as well as the Omnidia codes as this software is commonly used throughout the world and in South Africa for diatom assessment protocols.
CONCLUSION: The National Environmental Management: Biodiversity Act does not cover the protection of diatom species, which can only realistically be conserved if the habitats in which they are found are also conserved. This species checklist can serve as a catalyst for a move towards legislation accepting the use of diatoms as bioindicators for freshwater within South Africa.

Keywords: diatoms, freshwater, bioindicator, Karoo.

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Introduction

Species lists cover the occurrence of taxa in a geographical area and provides an overview of biodiversity in an area as well as a benchmark for environmental decision-making. Information of species occurring on such a list needs to be traceable (Garnett et al. 2020). Occurring in every aquatic and moist habitat, diatoms are living representatives of the environmental conditions of the habitat in which they are found. These single-celled organisms (Bacillariophyceae) are found together in associations that can be considered indicators of a particular type of water body (Schoeman 1976).

In South Africa, diatoms have been tested as bioindicators of water quality (Taylor 2004; De la Rey 2008; Matlala et al. 2008; Holmes & Taylor 2015; Pelser 2015; Musa & Greenfield 2018; Cameron 2019; Mangadze et al. 2019; Joubert 2021; Holmes et al. 2022). Diatoms, with their robust silica cell walls, have been successfully used in forensic analysis (Scott et al. 2014; Piegari et al. 2019) and historical assessments of water quality (Barker 1992; Dixit et al. 1992; Otu et al. 2011; Gordon et al. 2012; Schmidt et al. 2017). Successful application of bioindicators requires that they be correctly identified. It is for this reason that a checklist of species recorded during two projects within the Eastern Karoo area has been compiled.

The correct identification of diatoms is often perceived to be difficult (Taylor et al. 2007a). While the processing of samples as well as the identification thereof requires light microscopy, it is not impossible for this to be done by trained observers. The datasets from which this article is produced were processed on a farm in the Karoo where a laboratory was set up with a limited budget. Identification and enumeration for both data-sets were done using an entry level phase contrast light microscope. Confirmation of the identification of those cells with uncertain identification was done with high resolution microscopes at either North-West University (Potchefstroom) or Nelson Mandela University (South Campus). This demonstrates that the use of diatoms as bioindicators is not limited to only those with access to university or research institution facilities.

In 2009, diatoms were included as biomonitoring organisms in the Rapid Habitat Assessment Method Manual (Department of Water Affairs and Forestry) and in 2012 they were included in the draft Rapid Ecological Reserve Assessment. The River Eco-status Monitoring Programme (REMP) replaced the River Health Programme (RHP) in 2016 and currently forms part of the National Aquatic Ecosystem Health Monitoring Programme (Department of Water and Sanitation 2016). This programme, as did its predecessor, uses only fish, invertebrates and riparian conditions to assess ecosystem health. However, in 2017, diatoms were included in the report pertaining to the development of operational procedures for the monitoring of rivers (Department of Water and Sanitation).

Although diatoms are not routinely included, they were included in several Determination of Water Resource reports (Department of Water and Sanitation 2022a, 2022b). Unfortunately, in the Karoo, fish are rarely found and, due to the extreme cold in the Karoo, insects often only occur in the summer months. It would therefore be beneficial if diatoms (occurring all year round) become part of the monitoring programme.

Red Data Species Lists classify species according to their risk of extinction and highlight areas that require conservation. While Red Data Species Lists exist for fauna and terrestrial flora in South Africa, there is no such list for diatoms. The diatom Red Data List currently in use was developed for European conditions (Cantonati et al. 2022).

The objective of this paper was to compile a preliminary checklist of diatom species from the Eastern Karoo and to highlight species found on the Red Data List.

An attempt was made to include older species lists (Archibald 1983; Bate et al. 2004; Janse van Vuuren & Taylor 2015; Roussouw et al. 2018) but none of these documents have been digitised and given that there was no uniform method of reporting the species lists within the Karoo, it will be a mammoth undertaking to collate a complete list. The species list from Bate et al. (2004) has not yet been found but the permanent slides are available for perusal.

 

Materials and methods

Sampling took place in the area known as the Eastern Karoo (Figure 1) during the two projects. The first project included the upper reaches of the Great Fish River (spring-fed, Holmes & Taylor 2015) while the second project took place within the whole area shown in Figure 1 covering both stream and reservoir sites during the period 2015 to 2017 (Holmes et al. 2022, 2023). This semi-arid area is reliant on underground water (often stored in reservoirs above ground) and, mostly intermittent, springs. The area has extremes in weather between the winter (down to -8°C) and summer months (> 40°C) (pers. obs., M. Holmes).

Reservoirs are filled with underground water either by windmill or solar pumps. The water in these reservoirs is stored for future use and water turnover rates vary depending on water use. In the case of the reservoirs, samples were taken from the reservoir wall (usually cement substrate), unglazed ceramic tiles (placed in the reservoir after the first sampling and used as a comparison substrate for subsequent samples) and then at random sites from the plastic floatation devices from which the tiles were suspended.

Springs have a shallow water environment (1 cm to 30 cm depth) that relies completely on rain and underground water sources for recharge. Samples were scrubbed from cobbles and pebbles within riffles, using a well-cleaned toothbrush (Taylor et al. 2007b). One toothbrush per sample was used and upon returning to the laboratory, was well cleaned with detergent and water. Random samples of aquatic plants having epiphytic diatoms were taken for comparison. Samples were checked (using light microscopy) for the percentage of live cells, with chloroplasts in the cells.

Diatom samples were processed using acid digestion with the hot KMnO₄ and HCl method (Taylor et al. 2007b). Permanent slides were mounted using Pleurax. All wet material and permanent slides are held on the farm Clifton.

Identification was done using a Nikon E100 phase contrast microscope with an Olympus 100x/1.30 N.A. phase contrast objective and a Nikon 100x/1.25 N.A. phase objective. Photomicrographs were taken with a 1/2.5-Inch 5Mp CMOS Digital Image Sensor using the software IC Measure (The Imaging Software Company). At Nelson Mandela University an Olympus BX51 microscope with differential interference contrast (100x 13 N.A.) was used. Photographs and measurements of cells were taken with the mounted camera and analySIS image processing software. Scanning electron microscopy was done at the Centre for High Resolution Transmission Electron Microscopy (CHRTEM) at the Nelson Mandela University using a JEOL JSM7001F scanning electron microscope. Cleaned samples were placed on an isopore 0.2 μm pore-size membrane (Millipore™) filter precoated with gold. Once dried, the samples were attached to an aluminium stub with carbon conductive double-sided tape and sputter coated with gold at 25 mA for 30 seconds. Imaging was done at an accelerating voltage of 3 kV.

Each species was assigned a four-letter code from the software Omnidia version 6 (Lecointe et al. 1993, 1999, 2016). Omnidia (v6) was used to compile the species lists from the projects. For species that could only be identified to genus level, a unique code was assigned to each species while for those that could not be identified to a genus level, the code ZZZZ was assigned. Although environmental preferences for cosmopolitan diatoms can vary, there are some species that are always considered pollution sensitive. As pristine conditions decline, some of these diatom species have been placed on Red Data Lists. Species occurring on the two most recent Red Data Lists for diatoms in Europe were accessed (Rote Liste Zentrum 2018; Täuscher 2020).

 

Results

A table with an alphabetical list - including the four-letter Omnidia codes - of the diatoms identified in the Eastern Karoo is given in Table 1. The list of species only identified to genus-level or above can be requested from the corresponding author (with images, file size >50 MB).

A total of 474 taxa were recorded from 607 samples (n = 101 from 2010 to 2012 and n = 506 from 2015 to 2017). Several species that could not be identified to genus level were given the code ZZZZ. The species in this grouping (ZZZZ) that were of the same morphological 'taxa' were grouped together (n = 48 'taxa'). Several species previously misidentified are now placed in different groupings and listed in Table 2. Amphora sp0 was found to have a range of morphological variation within the same sample (Figure 2, Table 2).

There were six species groupings within the genus Brachysira. Although the cell in Figure 3A is similar in shape to B. neoexilis, under SEM it is shown not to be that species. Brachysira sp. 2 (Figure 3B) occurred in many samples and both sometimes in large numbers but did not occur together in the same sample.

The dominant species (from flowing water) from Holmes and Taylor (2015, n = 101) was Nitzschia frustulum (15.8 %) followed by Rhopalodiagibba [= Epithemia gibba] (9.6 %). The most prolific species for the Karoo Shale Gas Project, (both standing and running waters, n = 506), were Achnanthidium minutissimum (17.4 %), Denticula kuetzingii (10.1 %) and Encyonopsis krammeri (5.8 %).

 

Discussion

This species list shows the diversity in the diatom flora of the Karoo. It can be used to assist with and update freshwater diatom identification in South Africa. The list provides a basis from which to improve species occurrence information and identification.

The waters of the Karoo are alkaline (pH >6.1) with large differences in electrical conductivity (158-8400 μS/ cm), as well as wide ranges of calcium, chloride, oxidised nitrogen and sulphate (Janse van Vuuren & Taylor 2015; Holmes et al. 2023, and in progress).

The list covers species that were recorded in standing water (water reservoirs containing borehole water) and fountains (slow running water). This list excludes the information from Archibald (1983 for upper Sundays and Great Fish rivers) and upper Sundays River (Bate et al. 2004; Janse van Vuuren & Taylor 2015; Roussouw et al. 2018). No other studies on diatoms within the Karoo could be found.

As the species list is based on diatom counts from various projects that had a set number of cells counted, it must be noted that there may be species present in the Karoo that were not enumerated within that limit and are not accounted for on this preliminary species list.

Species within the Nitzschia frustulum group are often identified as N. frustulum when they are actually N. inconspicua or N. soratensis. While N. frustulum is known to withstand changes in osmotic pressure (and thereby fluctuating water levels, Taylor et al. 2007c), N. inconspicua indicates brackish-marine conditions with N. soratensis found in freshwater only (Trobajo et al. 2013).

Another common species complex prone to have species lumped together is Achnanthidium minutissimum complex. As was found during the Karoo Shale Gas Project, there were at least 24 Achnanthidium taxa that could not be placed in a species with certainty. The A. minutissimum grouping is constantly evolving as information on new species is published. Misunderstanding surrounds the identification of Ulnaria biceps and Ulnaria monodii (and similar species, Cantonati et al. 2018) in South Africa (Table 2). These species have different ecological requirements, which could lead to incorrect ecological inference. It is therefore imperative that the identification of these species be revisited.

Limitations

Although the diatom Red Lists are based on species found in Germany, it is widely known that these sensitive species occur in unimpacted habitats and may disappear in disturbed habitats. It is suggested that nitrates (and therefore human activities) could pose a threat to these species (Cantonati et al. 2022). Autecological information for diatoms in South Africa is often taken from the literature based on surveys from different regions around the world. As was shown by Holmes (2022), this information cannot be broadly superimposed on to South African conditions. Local conditions do have an effect on diatom community composition. The lack of an accessible database for the identification of South African diatoms, together with the lack of standardised data for South African ecological conditions, hampers the inclusion of these organisms as a biomonitoring tool.

This review of the Karoo diatom samples (2010 to 2012 and 2015 to 2017) with the preliminary species list presented here highlights the shortcomings for diatom identification in South Africa. A revised diatom identification guide for South African diatoms is overdue with current literature being outdated both in terms of nomenclature and taxonomy.

Several species in the Karoo are possibly, as yet, un-described. Of the issues that came to light during the compilation of this list was the difficulty of access to historical records. The question surrounding identification of certain species, some of which are mentioned in Table 2, is an area which requires further investigation. This work may be considered as only a preliminary list of diatom species found in two projects within the Eastern Karoo.

Recommendations

For ecological studies to be effective, validated and updated checklists are essential. Checklists of an area allow for changes in community structure to be detected. As with any checklist, there is a constant need for it to be updated to remain useful. Human activities have the potential to pose great risk to biodiversity and as diatoms are good indicators of environmental change, it is important to know about any changes in species composition.

In view of the climate change crisis issues around the world, diatom records are important to infer changes in environmental conditions (past and present day). Many of the historical records in South Africa are not easily accessible to researchers. It would be highly beneficial for the scientific community if these records could be catalogued (in a central database) together with geo-location and, where possible, water chemistry before they are lost.

 

Acknowledgements

Mr R.C. Holmes is thanked for his financial and logistical support during these projects. Thank you to all the landowners on which the study sites are situated for allowing unlimited access as well as SANParks for access to the Mountain Zebra National Park and Kamdeboo National Park (Permit reference HOLM1332). The 2016/7 project was funded by Iphakade (reference UID 9475) and formed part of the AEON Karoo Shale Gas Project baseline study. AEON publication number is 215 and the Iphakade publication number is 288.

Authors' contributions

M. Holmes (Nelson Mandela University and AEON-ES-SRI) was responsible for both the MSc and PhD project designs used for the compilation of this species list in addition to conducting all field work (including field work costs), all diatom identification (with the assistance of J.C Taylor) and enumeration. She performed all the statistical analysis for the projects with input from both E.E. Campbell and J.C. Taylor. E.E. Campbell (Nelson Mandela University) was the supervisor of the PhD for M. Holmes for the Karoo Shale Gas Project, which included a preliminary diatom baseline of Karoo waters (2015-2017). J.C. Taylor (North-West University) was the supervisor for the MSc project for M. Holmes (2010-2012) based on the diatoms of the upper Great Fish River. He was instrumental in assisting with the setup of the laboratory on Clifton and was co-supervisor on the above-mentioned PhD. He continues to collaborate on diatom identification. M. de Wit, as head of AEON-ESSRI (Nelson Mandela University), was responsible for all researchers under the Karoo Shale Gas Project. He unfortunately passed away during the PhD project and his contribution was therefore limited. He was, however, instrumental in the concept of the PhD project being accepted and implemented.

 

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Correspondence:
M. Holmes
e-mail:karoocats007@gmail.com

Submitted: 18 March 2024
Accepted: 30 October 2024
Published: 13 May 2025