Tt281 07

A Methods Manual for the
Collection, Preparation and
Analysis of Diatom Samples
Version 1.0
JC Taylor, WR Harding
& CGM Archibald
TT 281/07
Water
Research
Commission

A Methods Manual for the Collection,
Preparation and
Analysis of Diatom Samples
Version 1.0
Report to the
Water Research Commission
by
JC Taylor*, WR Harding**
and CGM Archibald***
* School of Environmental Sciences and Development
North-West University (Potchefstroom Campus)
** DH Environmental Consulting [DHEC]
*** KZN Aquatic Ecosystems [KZNAE]
WRC Report TT 281/07
January 2007

ii
This report is part of a set on Diatoms. The other report is:
WRC report TT 282/07: An Illustrated Guide to Some Common Diatom Species
from South Africa
Each report is provided with a DVD of
1. Training Videos for Diatom Field Sampling and Laboratory Practice
2. An electronic Diatom Taxonomic Key. Also, see plates in TT 287/07
These are obtainable from:
Private Bag X03
Gezina, Pretoria
0031 South Africa
The Methods Manual emanates from a Water Research Commission research project
entitled: Development of a Diatom Assessment Protocol (DAP) for River Health
Assessment (WRC project no K5/1588), for which DH Environmental Consulting was
the Lead Consultant.
ISBN 1-77005-483-9
SET No 1-77005-482-0
Printed in the Republic of South Africa
DISCLAIMER
This report has been reviewed by the Water Research Commission (WRC) and
approved for publication. Approval does not signify that the contents necessarily
reflect the views and policies of the WRC, nor does mention of trade names or
commercial products constitute endorsement or recommendation for use.

iii
TO THE USER:
This is a beta version manual for trial use in river biomonitoring programmes. As such the
authors welcome any comments or suggestions regarding the content and usability.
Please note that subsequent versions of the manual will contain additional training and
decision support aids, as well as image support for certain of the terms contained in
the glossary.
Please forward comments or suggestions, or address queries to:
DH Environmental Consulting
PO Box 5429
HELDERBERG
7135
Fax: 021-8552528
E-mail: diatoms@dhec.co.za
DH Environmental
Consulting
KZN Aquatic Ecosystems

iv
FOREWORD
This method manual is intended for those who wish to become familiar with the methods of
collecting diatom samples in a meaningful and repeatable manner, whether the outputs from
these samples will be used for taxonomy or biodiversity studies or to infer water quality. The
latter aim will be dealt with more extensively in this guide.
The application of diatom-based water quality monitoring has become a reality with the
recent development of expertise in the fields of diatom taxonomy and ecology in South
Africa. This, coupled with the support from government initiatives (e.g. the River Health
Programme) as well as from the Water Research Commission, together with a growing
interest amongst the scientific community of South Africa has sparked a new awareness of
this particular field of study. Links with a number of international diatomists has also aided in
the growth of knowledge and the verification of ecological and taxonomic data.
In addition, software packages are now available for index calculation, sample data archiving,
capture of digital images, as well as simple and complex electronic diatom keys. The
production of simple taxonomic guides, both in South Africa and around the world, has also
lessened literature costs and allowed a more rapid and accurate approach for the assessment of
water quality using diatoms. However, diatom-based monitoring is not a rapid field-based
assessment technique and always includes a component which has to be completed in a
laboratory. A sound taxonomic knowledge of the diatoms is required as well as the relevant
set of microscopy skills.

v
BACKGROUND
There is a long and proud history of diatom research in South Africa, mainly as a
result of the work of the late Dr Bela Cholnoky, a the pioneer diatom specialist. This
is described in the WRC Report TT 242/04 – “The South African Diatom Collection:
An Appraisal and Overview of Needs and Opportunities”.
The WRC research project K5/1588, envisaged and planned by DH Environmental
Consulting, and undertaken in collaboration with KZN Consulting and North West
University, has resulted in a series of practical tools for the collection, processing and
examination of diatom samples from South African Rivers.
Diatoms provide a valuable and well-understood means of biomonitoring – one which
is focused at the base of the aquatic foodweb and highly representative of water
quality. Although the need for careful microscopic examination and taxonomic
identification of species is somewhat demanding, the technique is intended to provide
a ‘fourth leg’ to the River Health Programme suite of monitoring tools (currently
invertebrates, vegetation and fish).
Project K5/1588 has produced the following tools:
A Methods Manual which details sampling procedures and the laboratory
processing of samplings for slide mounting and microscopic examination. The
content of the manual also provides general information pertaining to the
occurrence of diatoms in aquatic systems. (WRC Report TT 281/07)
An Illustrated Guide to some common diatom species from South Africa
(WRC Report TT 282/07)
Two DVD-quality videos that demonstrate the field and laboratory procedures
described in the manual. These training videos will also be available on CD.
A stand-alone software-based taxonomic key to the diatom species most
commonly encountered in South African rivers and streams. This is an
hierarchical, interactive tool that assists the user in learning more about
diatoms and diatom taxonomy while seeking an identification for an observed
species. The taxonomic key allows the user to undo incorrect entries, and
includes photomicrographs in various formats that assist with confirming the
final result.
The results of this project are dedicated to the memory of South African diatom
specialist “Archie” Archibald.

vi
TABLE OF CONTENTS
NOTE TO THE USER............................................................................................................. iii
FOREWORD............................................................................................................................ iv
BACKGROUND....................................................................................................................... v
GLOSSARY........................................................................................................................... viii
SECTION 1: INTRODUCTION............................................................................................... 1
1. History of diatom research in South Africa.............................................................1
2. How do you recognise diatoms in natural environments?.........................................4
3. Diatoms – Living cells with a role in aquatic food webs ..........................................5
4. Diatoms – Colony formation and attachment ..........................................................6
5. Diatom frustules – What do diatoms look like?.......................................................7
5.1 Pennate and Centric diatoms .........................................................................8
6. What can you expect to see when viewing a prepared diatom slide?.........................9
SECTION 2: FIELD PROCEDURES.................................................................................... 11
1. Habitats for diatom-based water quality monitoring ..............................................11
1.1 Preferred substratum...................................................................................12
1.2 Alternative substrata (in order of preference)................................................12
1.3 Introduced substrata....................................................................................12
2. Sampling for aquatic bio-diversity studies............................................................13
2.1 Cobbles and small boulders (rocks) ........................................................13
2.2 Phytobenthos (“Floatation method” for epipsammon and epipelon)................13
2.3 Qualitative sampling of sediments ...............................................................13
2.4 Phytoplankton ............................................................................................15
2.5 Terrestrial or soil diatoms............................................................................16
3. Toolkit for Fieldwork (field apparatus).................................................................17
4. Decision ‘tree’ for sampling for water quality monitoring......................................18
5. Site selection for water quality monitoring - Principles..........................................19
6. Sampling locality details and field notes/forms.....................................................21
7. Useful water quality variables and information to collect concurrently with diatom
samples for diatom index validation. ...................................................................22
8. Choice of substrata (detail)..................................................................................23
9. Sampling ...........................................................................................................24
9.1 Solid substrata............................................................................................24
9.2 Sampling from emergent aquatic macrophytes..............................................24
9.3 Sampling from submerged aquatic macrophytes ...........................................24
10 Preservation of diatom material and labelling samples...........................................25
SECTION 3: LABORATORY PROCEDURES..................................................................... 26
1. Preparation.........................................................................................................26
1.1 Toolkit.......................................................................................................26
1.2 Pre-preparation examination of freshly sampled material...............................29
1.3 Cleaning techniques with rationale...............................................................29
1.4 Other methods (Incineration).......................................................................34
2 Preparation of diatom slides ................................................................................35
2.1 Preparation.................................................................................................36
3 Preparation for Electron Microscopy (EM)...........................................................38
3.1 Preparation for SEM...................................................................................38
3.2 Preparation for TEM...................................................................................38

vii
4a Archiving...........................................................................................................39
4. Enumeration and simple biometrics .....................................................................40
5. Counting records (electronic and manual methods) ...............................................43
6. Microscopy........................................................................................................43
7. Image capture, analysis and archiving..................................................................43
8. Sources of error in diatom community analysis.....................................................44
9. Recommended software packages........................................................................45
10. Key reference works...........................................................................................47
REFERENCES........................................................................................................................ 48

viii
GLOSSARY
Aerophilic - Depending on free oxygen or air.
Areolae. - Perforation through valve with internal or external sieve membrane.
Autecology - The ecology of individual organisms or species.
Autotrophic - Capable of self-nourishment; said of all organisms in which photosynthetic
activity takes place, in which inorganic constituents are transformed to cell material via
photosynthetic activity, as opposed to parasitism or saprophytism.
Bio-film - A surface accumulation, which is not necessarily uniform in time or space, that
comprises cells immobilised at a substratum and frequently embedded in an organic polymer
matrix.
Centric diatom - Radially symmetric diatom; compare to pennate diatom.
Chlorophyll a - Chlorophyll a is quite often used as a surrogate measure of the amount of
phytoplankton in a water sample. Comparing water bodies on the basis of chlorophyll a
content implicitly assumes the algae are composed of equivalent amounts of chlorophyll
though. The chlorophyll content of algae is usually about 0.5-1.5% of the dry wt. But
increased amounts, up to 6% have been recorded in algae culture in weak light. Chlorophylls
are "tetrapyrrolic molecules with a central magnesium atom and two ester groups", hence the
need for micronutrients by plants and animals.
Chlorophyll a is the "master pigment" in bluegreen algae and higher plant photosynthesis
(apparently some photosynthesizing bacteria can do it without chlorophyll a). It is chlorophyll
a that ultimately captures energy from light (photons) and packages it as energy in chemical
bonds for use by plants and eventually animals. There are other "accessory pigments" (such as
chlorophylls b, c, and d, carotenoids, phycoerythrins, phycocyanins, and xanthophylls) which
can trap light energy at shorter wave lengths and pass it along to chlorophyll a which absorbs
at longer wavelengths. It is the unique combination of accessory pigments with chlorophyll a
that help to distinguish certain groups of algae and higher plants from one another. For
example, Euglenophyta are characterized by the presence of chlorophyll a and the accessory
pigments b-carotene and the xanthophyll, lutein.
Chloroplasts - In eukaryotic organisms, the cellular organelle in which photosynthesis takes
place.
Chrysolaminarin - (a glucose-mannitol polymer) carbohydrate food reserve.
Detritus - Living organisms constitute only a very small portion of the total organic matter of
ecosystems. Most organic matter is nonliving and is collectively called detritus. Detritus
consists of all dead particulate and dissolved organic matter. Dissolved organic matter is
about 10 times more abundant than particulate organic matter. Much of the newly synthesized
organic matter of photosynthesis is not consumed by animals, but instead enters the detrital
pool and is decomposed.
Euphotic zone - The surface waters of rivers or lakes where enough light penetrates for
photosynthesis to occur. The depth of the euphotic zone varies with the water's extinction
coefficient, the angle of incidence of the sunlight, length of day and cloudiness.
Frustule - The valves and their associated girdle elements.

ix
Girdle – The collective term for all structural elements between two valves.
Girdle bands - The elements of the girdle.
Girdle view - "side" view of a diatom.
Glides - Stream areas with low velocities and with a smooth surface. Water depth generally is
less than half a meter.
Heterotrophic - Organisms that derive their nourishment from existing organic substances.
Heterotrophs can be herbivores, carnivores, omnivores or detritivores.
Littoral zone - An interface zone between the land of the drainage basin and the open water
of lakes. Most lakes of the world are relatively small in area and shallow. In such lakes, the
littoral flora contributes significantly to the productivity, and may regulate metabolism of the
entire lake ecosystem.
Wetland and littoral regions of freshwater ecosystems are commonly intensely metabolically
active owing to the presence of aquatic macrophytes. Phytoplankton productivity is generally
lower in the littoral zones, containing stands of aquatic macrophytes, largely because of
competition for nutrients (including carbon) by submersed macrophytes, and by a reduction of
light by macrophyte foliage. (Also see Macrophytes).
Macrophytes - The term aquatic macrophyte generally refers to the macroscopic forms of
aquatic vegetation, and encompasses macroalgae (e.g. the alga Cladophora, the stoneworts
such as Chara), the few species of mosses and ferns adapted to the aquatic habitat, as well as
true angiosperms. Four groups of aquatic macrophytes can be distinguished as follows:
Emergent macrophytes grow on water-saturated or submersed soils from where the water
table is about 0.5m below the soil surface (supralittoral) to where the sediment is covered
with approximately 1.5m of water (upper littoral).
Floating-leaved macrophytes are rooted in submersed sediments in the middle littoral
zone (water depths of approximately 0.5m to 3m), and possess either floating or slightly
aerial leaves.
Submersed macrophytes occur at all depths within the photic zone. Vascular angiosperms
occur only to about 10m (1 atm hydrostatic pressure) within the lower littoral
(infralittoral), and nonvascular macrophytes (e.g. macroalgae) occur to the lower limit of
the photic zone (littoriprofundal).
Freely floating macrophytes are not rooted to the substratum; they float freely on or in
the water and are usually restricted to nonturbulent, protected areas.
Mucilage - A general term for complex substances composed of various types of
polysaccharides, becoming viscous and slimy when wet.
Pennate diatom - Bilaterally symmetric diatom.
Periphyton -Refers to microfloral growth upon substrata in fresh waters. A much more
explicit manner of expression is to refer to the organisms with appropriate modifiers
descriptive of the substrata upon which they grow in natural habitats. These algal
communities can be classified into,
Epipelic algae as flora growing on sediments (fine, organic),
Epilithic algae growing on rock or stone surfaces,
Epiphytic algae growing on macrophytic surfaces,
Epizooic algae growing on surfaces of animals, and
Epipsammic algae as the specific organisms growing on or moving through sand.
(See also Phytoplankton).

x
Phytoplankton - The phytoplankton consists of the assemblage of small plants having no or
very limited powers of locomotion; they are therefore more or less subject to distribution by
water movements. Certain planktonic algae move by means of flagella, or possess various
mechanisms that alter their buoyancy. However, most algae are slightly denser than water,
and sink, or sediment from, the water. Phytoplankton are largely restricted to lentic
("standing") waters and large rivers with relatively low current velocities. (See also
Periphyton).
Puncta - General term for pore/perforation through valve when substructure (i.e. sieve
membrane) is unknown or lacking.
Raphe - Slit through valve along apical axis. Composed of (usually) two branches per valve.
Refractive index - The ratio of the speed of light in a vacuum to the speed of light in a
medium under consideration.
Relative abundance - A measure of the ratio between different species in a population or
community.
Riffle - Fast-flowing, shallow segment of a stream where the surface of the water is broken
over rocks or debris.
Runs - Transitional segments of streams, between a riffle and a pool, with moderate current
and depth.
Spines - Conical or forked solid external projection.
Striae - Rows of puncta/areolae, usually oriented along transapical axis, separated by
unornamented ribs. Striae appear as dark lines under lower magnifications and as a series of
dots (punctae) at higher magnification.
Valve - Siliceous part of the frustule containing most of the morphological features used to
describe diatoms (taxonmically, morphologically, etc.). Each valve has two surfaces, the face
and the mantle.
Valve face - Portion of the valve apparent in valve view (oriented to the valvar plane).
Valve mantle - Portion of the valve, differentiated by slope, that is apparent in girdle view
(oriented to the apical plane).

1
SECTION 1: INTRODUCTION
1. History of diatom research in South Africa
Diatom research in South Africa can be divided into five distinct periods. The first period
covers a span of some seventy years, beginning with Shadbolt’s (1854) account of the
diatoms from Port Natal, and continuing with brief reports and notes on odd specimens found
in various samples sent to the leading diatomists of the day (e.g. Cleve 1894 and 1895; Grove,
1894).
The second period spanned the time between the two world wars and is characterised by
accounts of diatoms found in the more general algological surveys made by a number of
algologists, notably Felix Eugen Fritsch, Florence Rich and Edith Stevens (e.g. Fritsch and
Rich, 1924, 1930).
The third period involved the most comprehensive study of diatoms in South Africa, and
commenced after the arrival of Dr Bela Jeurno Cholnoky in South Africa in 1952. Cholnoky
was a Hungarian refugee whose chief interest in life was the diatoms. Through his intensive
and extensive taxonomic and ecological studies he built up the diatom collection of the then
National Institute for Water Research (CSIR) in Pretoria, making it the centre for diatom
research in this country. Cholnoky placed little faith in only the chemical analysis of water
quality, arguing forcefully that the chemical and physical characteristics of a water body
could be determined more reliably and easily through a study of the diatom associations
found living in it (Cholnoky, 1968). His diatom investigations focussed, therefore, on two
aspects – the taxonomy of the diatoms and their species specific autecology.
During this third period he also trained his successors, Dr R. E. M. ‘Archie’ Archibald who
became his assistant in 1964; Dr Ferdi Schoeman who joined the institute in 1968; and Prof
Malcolm Giffen of the University of Fort Hare. Dr Archibald and Dr Schoeman were trained
in the ecology and taxonomy of freshwater diatoms while Prof Giffen was encouraged to
study marine littoral and estuarine diatom taxa.
Following the death of Cholnoky in 1972, the fourth period saw a very fruitful partnership
between Dr Archibald and Dr Schoeman in which new approaches to the taxonomy of
diatoms were made, culminating in the production of “The Diatom Flora of Southern
Africa”(Schoeman and Archibald, 1976- 1981). For each species included in this flora,
samples of the type material were obtained and examined using traditional light microscopy
techniques as well as electron microscopy. In this way the authors were able to check their
identifications and fix the concepts of species according to their own observations of the type
material. The resulting detailed descriptions and commentaries on each species, together with
the first attempts to produce a diatom atlas correlating drawings, and both light and EM

2
photomicrographs earned high praise for the first six parts of this Flora. Unfortunately, the
thorough treatment of each species was considered to be excessively costly and time
consuming, resulting in the Flora being discontinued.
After the curtailment of the Flora there was a shift in the direction of diatom studies at the
NIWR, and two lines of research were followed. The first of these adopted a purely
taxonomic direction of study in which selected species were individually examined and
thoroughly revised in the light of both type material and local material. Special attention was
focussed on the genus Amphora, but other species in other genera were treated when and if
material became available. The second line of research returned more to the style of
investigation used by Cholnoky in his surveys from different regions but incorporated the new
developments in electron microscopy and photomicroscopy.
At the end of 1986 Dr Schoeman left the NIWR, bringing to an end a fruitful partnership, in
which he was the co-architect of so much that was achieved for over a decade. Continuing on
the foundation laid by Cholnoky, the NIWR group had developed into the largest diatom
research centre in the Southern Hemisphere at that time. Details of this collection have been
discussed in Harding et al. (2004).
The third and fourth period of diatom research at the NIWR(CSIR) saw the strength of human
resources engaged in diatom work rise from one to four full-time researchers as well as
several for whom diatoms were a secondary interest, then decline again to one person, Archie
Archibald, occupied full time with the help of an assistant. Following the untimely death of
Dr Archibald in December, 1999 meaningful diatom research ceased at the CSIR. The Diatom
collection was subsequently transferred to the CSIR in Durban under the care of Colin
Archibald before his retirement in 2002.
The fifth or current period of diatom research in South Africa includes research undertaken
under the leadership Prof Guy Bate (University of Port Elizabeth now Nelson Mandela
Metropolitan University) which commenced with a study of diatoms in South Africa in the
late 1990’s. The research focussed on the ecological aspects of diatom assemblages for
determining water quality and attempted to apply a descriptive European diatom index for
South African conditions (Bate et al, 2002). This research continued with the publication of a
Water Research Commission report relating freshwater, brackish and estuarine species to key
water quality variables (Bate et al., 2004).
Also during this same period Dr Bill Harding commenced with an evaluation of the ex NIWR
(now CSIR-Environmentek) diatom collection, as well as initiating further diatom studies by
producing a set of protocols (of which this volume forms a part) by which diatom samples can
be collected, prepared and the species in the samples identified – and by the use of which
diatoms can form a valuable component of biomonitoring in South Africa. Diatom studies
have also been undertaken in the last five years at the North-West University (Potchefstroom

3
Campus) where the application of numerical diatom indices to South African rivers was tested
(Taylor, 2004). Other students are now engaged in both diatom ecological and taxonomic
studies at M.Sc. and Ph.D. level. This revival of interest in the diatoms together with the
production of standard protocols and the rigorous testing of numerical diatom-based indices,
should culminate in the realisation of Cholnoky’s prediction that diatom associations can be
used to give a reliable and accurate indication of the chemical and physical characteristics of a
water body.

4
2. How do you recognise diatoms in natural environments?
A common source of error in inferring ecological conditions using diatom communities arises
from sampling from un-colonised substrata. Diatom communities may be detected on
substrata by feel (slimy or mucilaginous) or may be seen as a thin golden-brown film
covering substrata. In some conditions or at certain times of the year this film may become
thicker and much more noticeable. The essential natural microhabitats are solid substrata,
exposed damp sediments and the stems of rooted vegetation. Diatoms are also present in the
seston or suspended component of the phytoplankton. Man-made and other objects (paper or
plastic bags, pieces of wood) are also frequently colonised by diatoms.
Fig. 1 and Fig. 2 show a thick layer of diatom cells attached to boulders. Fig. 3 shows a layer of
diatom cells growing both on sediment and on pebbles. Fig. 4 shows diatoms growing thickly around
submerged tree branches. Fig. 5 shows the film of diatoms to be found on the submerged stems of
Phragmites australis. Fig. 6 shows diatoms inhabiting sediments.
1 2
3 4
5 6

5
3. Diatoms – Living cells with a role in aquatic food webs
Diatoms are a key component of aquatic ecosystems and constitute a fundamental link
between primary (autotrophic) and secondary (heterotrophic) production. Many micro-
organisms feed on diatoms and in this way they are integrated into aquatic food webs.
Diatoms are frequently used as bio-indicators, and if they are not investigated live they may
be perceived simply as “glass boxes” used to give information about water quality. It is worth
the time to study the living communities and to note the other algae and the interactions
between the algae and other micro-organisms.
Fig. 1 a diatom community completely dominated by Diatoma vulgaris Fig. 2 a sediment diatom
community with Navicula spp. and Pinnularia viridis. Fig. 3 mixed diatom community with large
cells of Gyrosigma sp. Fig. 4 shows cells of Cymbella sp. living in association with the blue-green
algae Oscillatoria. Fig. 5 shows the filamentous diatom Aulacosiera granulata being grazed by a
protozoan. Fig. 6 shows diatoms being grazed by Amoeba sp.
1 2
3 4
5 6
1 2
3 4
5 6

6
4. Diatoms – Colony formation and attachment
Diatoms release mucilage through various structures in the cell wall to facilitate locomotion
or attachment of the cells to various substrata. Mucilage secretions can also be used to form
colonies of various patterns. This material must be eliminated for microscopic detailed
examination of the cell wall. After a diatom sample has undergone the necessary steps to
prepare it for light microscopy at high magnifications all that can be seen is a silica structure.
This skeleton or cell wall is typically referred to as the frustule. Chemical treatment
eliminates all organic material from both inside as well as outside the cell walls.
Fig. 1 shows the attachment of Cymbella sp. to a substratum with a mucilage stalks. Fig. 2 shows
Encyonema caespitosum inhabiting a mucilage tube. Fig. 3 shows the dichotomously branching
mucilage stalks to which cells of Gomphonema sp. are attached. Fig. 4 Melosira varians with cells
attached both to the substratum and each other by mucilage pads. Fig. 5 stellar colonies of the
diatom Asterionella formosa. Fig. 6 Achnanthidium minutissimum attached by means of mucilage
stalks to Lyngbya sp.
1 2
3 4
5 6

7
5. Diatom frustules – What do diatoms look like?
Diatoms are unicellular algae that occur mostly as single cells but some species form
colonies. They have certain features which make them unique amongst the algae. The
particular features include the siliceous cell wall (frustule) the possession of unique
photosynthetic pigments and specific storage products (oil and chrysolaminarin). There are
two groups of diatom common in freshwaters namely the centric diatom species which are in
general circular in shape and adapted to live in the water column as part of the phytoplankton
and the pennate diatoms that live in benthic habitats but are often temporarily re-suspended
in the water column.

8
5.1 Pennate and Centric diatoms
Pennate diatom
Centric diatom

9
6. What can you expect to see when viewing a prepared diatom slide?
A series of neatly aligned pictures that have been cropped and graphically enhanced are
normally displayed to illustrate diatom taxa in books, manuals and guides. Whole cells are
usually illustrated in valve view in such guides and most of the morphological characteristics
are visible. Fragments or broken pieces are not normally shown. However, your slides will
have diatom cells that are orientated at different angles, often lying obliquely or in girdle view
and some may be damaged or fractured fragments. Different types of microscope illumination
may also provide slightly different images to those found in routine identification guides.
Fig. 1 shows a scattered slide mount of diatoms under low magnification. Fig. 2 shows the same
mount under high magnification (x1000) using incident light. Fig. 3 shows the same as Fig 2 but a
green filter is used to increase contrast. Fig. 4 shows the use of differential interference (DIC) optics.
Fig. 5 shows the use of Phase contrast optics and Fig 6a shows Fig. 4 correctly orientated, cropped
and converted to greyscale, while 6b shows digital enhancement and contrast correction.
1 2
3 4
5 6a 6b

11
SECTION 2: FIELD PROCEDURES
To facilitate the reading of this document references have been kept to a minimum. However
it should be mentioned that the methods described below have been based on several key
documents including: Kelly et al. (1998), CEN (2003), DARES (2004) and Taylor et al.
(2005).
1. Habitats for diatom-based water quality monitoring
The four distinct diatom assemblages that occur closely associated with particular
microhabitats are generally recognised as the:
Epipelon that frequents the surface of the sediments
Epipsammon that occurs on and between the sand particles
Epilithon that inhabit gravel, stone and bedrock
Epiphyton that is attached to macrophytic plants
Diatom community structure is governed to some extent by substrata associations but there
are other important influences on community composition, namely:
Chemical constituents in the water
Water turbulence and disturbance (mainly from floods)
Resource supply (mainly from inorganic nutrients)
Grazing by micro-organisms
Light regime within microhabitats
Health and safety of field operators (practical advice)
Diatom sampling should be both enjoyable and informative, however, there are
attendant risks involved with these activities. The following points should be noted:
1. Always wear thigh waders or some other form of protection for your feet.
2. Always wear a life jacket while sampling.
3. Never sample in parts of the river which are out of your depth.
4. When sampling rivers which may be heavily polluted or polluted with faecal matter,
be sure to always wear gloves.
5. When sampling in regions such as KwaZulu Natal, Limpopo and Mpumalanga care
should be taken to avoid crocodiles and hippopotami. Great care should be
exercised when sampling. These animals pose a very real threat to people and are
attracted to activities at the sides of rivers and lakes.
6. In some rivers leeches may also be abundant.

12
1.1 Preferred substratum
Cobbles and small boulders (rocks) are the preferred substratum for monitoring diatoms in
the riverine environment, and almost all diatom indices throughout the world can be applied
to the community (i.e. the epilithon) that is found on this substratum.
The most important reasons for this choice of substratum can be summarised as follows:
Cobbles and small boulders are generally widely available (riffles, cobble beds, benches
and shelves), throughout the length of a river from headwaters to lowland stretches, and
throughout the year.
The type of stone sampled can usually be discounted when assessing the flora at a
particular site.
The performance of major diatom-based indices on this substratum is well understood.
The ecology of the epilithon is better known than any other group.
1.2 Alternative substrata (in order of preference)
Man made objects (bricks, pieces of concrete, bridge supports, cannel walls etc.).
Emergent macrophytes, such as Typha spp. or Phragmites spp.
Submerged macrophytes, such as Potamogeton spp, Ceratophyllum spp. etc. may be used
as an alternative substratum.
1.3 Introduced substrata
If pebbles, cobbles, boulders or macrophytes are absent from the sample site, artificial
substrata may be introduced into the stream. However sampling should only be attempted if
they have been submerged for at least four weeks.
The advantages of using introduced substrata include:
the ease of sampling from smooth surfaces,
greater control over the exact area of sampling,
standardisation of substrata,
less contamination by macrophytic algal growth and
the introduced substratum can be positioned exactly.
Some disadvantages to using artificial substrata include:
The community will be somewhat unnatural and biased towards those diatoms which are
fast growing and can attach to flat, smooth surfaces,

13
depending on the period of exposure prior to sampling, the flora may not represent a
‘climax’ community,
the smooth surfaces of some artificial substrata often lead to ‘sloughing off’ of the diatom
film.
substrata are often lost, removed or vandalised if the substratum is not fixed in position.
An appropriate method and apparatus needs to be devised for each site.
artificial substrata need to be immersed in the river for at least four weeks before
sampling (although this period is dependent on the trophic status of the water). This
causes a delay in the availability of data, as well as adding to the cost of the monitoring
program as transport costs to and from the site in question are doubled.
Further information about the use and application of artificial substrata can be found in
Cattaneo and Amireault (1992), Gold et al (2002) and Lane et al. (2003).
2. Sampling for aquatic bio-diversity studies
All the methods mentioned in this manual can be used for sampling diatoms from different
habitats for biodiversity studies. However, certain techniques are less suitable when sampling
diatoms to infer water quality. Phytoplankton drifts downstream and thus is not as stable or
reliable as the phytobenthos if an indication of a water quality impact at a specific point is
required.
2.1 Cobbles and small boulders (rocks)
See section 1.1.
2.2 Phytobenthos (“Floatation method” for epipsammon and epipelon)
The epipsammon and epipelon are components of the phytobenthos and yield very diverse
assemblages of usually motile diatoms. However, the “floatation method” discussed below
does not allow for the inclusion in the analysis of non-motile diatoms. The method has the
considerable advantage of extracting the motile living fraction of the diatom community for
subsequent analysis of the assemblage. Samples taken from the epilithon may contain many
attached and non-motile species which cannot be removed from the sample in the manner
below.
2.3 Qualitative sampling of sediments
The common method, described by Round (1991) is to use 5 mm Ø glass tube about a meter
long or more attached (splinted) to a rod (e.g. a broomstick) for deeper water at the margin of
a river.

14
Sampling may be achieved as follows:
Place a finger over the top end of the tubing and insert the bottom end under the water
and rest it on the sediment.
Release the finger pressure as the tube is drawn lightly over the sediment surface
horizontally (for about one meter) - as if gently scraping a line on the surface of the
sediment.
The pressure of the water will push the sediment material (with diatoms) into the tube.
Seal the top of the tube with your finger (to prevent loss of sample before you remove it
from the water) and carefully swing the tube out and transfer the collected material into a
sample bottle.
An alternative to this procedure in shallow water is to use a large syringe attached to the
upper end of a flexible latex tube. The contact end of the latex tubing is cut at an angle to
allow for oblique contact with the sediment containing the diatoms. Careful syringing action
will ensure that diatom material is sucked up with some surface sediment and this can be
discharged into an appropriate sample bottle until sufficient material is obtained.
Rapid qualitative sampling can also be achieved by scraping the surface of damp sediments to
a depth of 1 cm in several smaller areas in the stream bed. The accumulated material can be
stored in a damp environment within an ice-cream dish.
2.3.1 Quantitative sampling of sediments
To determine the biomass of a community (as reflected by chlorophyll measurements or cell
counts) quantitative samples are required and may be collected as follows:
Press the bevelled bottom end of a clear Perspex tube (~ 50 cm long and 20 mm in
diameter) into the sediment or sand and carefully section out a 1 cm deep core.
Remove the top 1 cm of the core containing surface diatoms using an extruder (i.e. push
the sediment out from the lower opening upwards).
The 1 cm surface core of the sediment sample usually retains its integrity as you remove
the sample unless the grains are very large and loosely compacted or too dry.
Typically, five 1 cm cores should be collected randomly for each sampling area.
Note: Cores collected in this manner can be used for chlorophyll ‘a’ analysis if placed into a
bottle containing 90% acetone. If the habitat is available this is the most suitable
technique for quantitative comparison of diatom populations between sites and over
time.

15
2.3.2 Examination of fresh material and extraction of diatoms for acid
treatment
The living, motile component of the sampled diatom population may be extracted and
separated in the following manner:
The fresh sediment/diatom mix is spread over the bottom of a petri dish or flat-bottomed
plastic tray and the heavier sediment is allowed to settle for a few hours (e.g. overnight).
The following day the excess supernatant is drained from the petri dish until the moist
sediment is exposed.
Several coverslips are allowed to gently ‘float’ and rest on the damp sediments for a 4
hour period of exposure to natural light.
The coverslips are then carefully removed and gently rinsed to remove unwanted sand
particles.
The coverslips are placed on a clean slide for examination of diatom cells.
2.3.2.1 Alternative separation techniques
Tissue paper
If the original sample contains large sand grains, it is advisable to place tissue paper between
the coverslip and the sediment. This allows the passage of the motile diatoms on to the
coverslip but prevents the transfer of unwanted sediment grains to the slide.
Submersed coverslips
It is not necessary to remove all the supernatant from the fresh material if living diatoms are
not required for initial examination. Coverslips are submerged and ‘floated’ on to the
sediment/diatom mix after the material has settled in a tray / petri dish. Living diatoms
actively adhere to the surface of the coverslip under the water. This technique ensures that
sand grains are washed off the coverslips as they are carefully withdrawn and placed in a
sample bottle containing ethanol for preservation or allowed to air dry for acid treatment.
2.4 Phytoplankton
Phytoplankton sampling can be achieved in one of two ways. The most simple method is to
collect water in a two litre container, add preservative (Lugol’s iodine), and allow the dead
planktonic organisms to settle out. The sedimentation rate of most phytoplankton allows for
complete settling within 16-24 hours from a two litre measuring cylinder.
Alternatively a plankton net may be used with a mesh size of not more than 25 µm. The
plankton net should be dragged back and forth just below the surface of standing waters or
held in the stream of moving waters for a few minutes. This should allow for the collection of

16
ample cells. The contents of the net should then be emptied into a wide-mouthed plastic
storage bottle and preservative added if required (see Section 11 for further details).
In standing waters (such as dams, lakes, estuaries) one should be aware of vertical
stratification of phytoplankton during certain times of the day. Where the system is deep
enough (i.e. >10m) take a vertical haul with the plankton net over a 5 metre depth to cover the
zone where light penetration is sufficient (euphotic zone) to encourage algal growth.
2.5 Terrestrial or soil diatoms
Soil diatoms and aerophilic diatoms have seldom been investigated in South Africa. These
diatoms are an interesting group with many adaptations for the arid climate in which they live.
Soil diatoms can be collected from moist sub-aerial habitats, as well as from aerial and arid
aerial habitats. Six sub-samples (± 5 cm2
) should be collected within a 10 m radius. Once the
site has been selected detritus or other material covering the surface of the soil should be
carefully moved aside. The soil should be collected to a depth of about 1 cm using a knife,
spoon, perspex corer or other similar implement (a slightly concave butter knife is ideal!). The
six sub-samples should, in total, amount to about 200 grams of soil. This soil should be stored
in a paper envelope to prevent the build up of moisture which promotes the growth of
undesirable fungi.
In order to separate the diatoms from the soil, a portion of the soil sample is placed in a sterile
petri dish and wetted with distilled water until the soil is saturated. One or two wettings may
be required before the soil becomes saturated depending on the amount of organic material
present. Once the soil is saturated it should be left for several days exposed to light (but not in
direct sunlight), where after pre-cleaned coverslips can be placed gently on the surface of the
soil. After two weeks the coverslips can be removed and the living cells examined under the
microscope. If cleaned material is required the coverslips may be treated using any of the
methods detailed below under Laboratory Procedures. A simple method to check for the
presence of diatoms is to invert the coverslips and heat them until the organic content is
burned away (incineration). Permanent mounts can then be made in the standard fashion see
Laboratory Procedures, section 2. Many soil diatoms are very small and are best examined
under the scanning electron microscope (SEM) - see details of preparation techniques below.

17
3. Toolkit for Fieldwork (field apparatus)
Plastic tray / clean 2 litre ice cream dishes with lids
Tooth brush or other similar brush
Knife or spoon
Envelopes (for soil samples)
Wide mouth sample bottles (~100 ml)
“Zip-lock” type plastic bags
Plankton net
Waterproof marking pen or labels
Field note book/field record forms
Pipettes
Depth gauging ‘broomstick’ / rod
100 ml syringe fitted with latex tubing / Turkey baster
Clear Perspex tubes (25 mm diameter)
Camera
1: Wide-mouth sampling bottle ~ 100 ml. 2: Turkey baster; useful for collecting sediment samples.
3: Pencil and labels, ethanol does not dissolve pencil markings. 4: Forceps for picking up
filamentous algae and detritus. 5: Water-proof marking pen. 6: Plastic Pasteur-pipette useful for
collecting small amounts of sediment. 7: Toothbrushes for scrubbing solid substrata. 8: Knife for
cutting the stems of aquatic vegetation. 9: White plastic tray with lip. 10: Fine-mesh plankton net.

18
4. Decision ‘tree’ for sampling for water quality monitoring
Sampling decision tree
SELECT LOCALITY
SAMPLING
PROCEDURE
2. Man made objects;
bricks, concrete
Note: All substrata should
have been submerged for a
period of a least 4 weeks
3.Bridge supports,
channel walls
Substratum selection
4.Emergent aquatic
macrophytes
5. Submerged aquatic
macrophytes
Free from
sediment
6.Sediment substrata
Introduce artificial
substrata
Free from marcophytic
algal growth
TAKE
SAMPLE
Not present / Non-
representative of substratum,
proceed with alternative
substrata in order of
preference
Narrow wadeable
stream
Sample in the centre
of the stream
Sample near to the
bank in an area of
accelerated flow
Broad deep river
1.Cobbles, boulders or
pebbles
No
Refer to Table 1 (Field
Procedures, Section 6)
TAKE
SAMPLE
No
Yes Yes
Yes
Yes
Yes
7. No suitable
substrata at site
Wait for at least 4
weeks
No
No
No
Record degree
of sedimentation
TAKE
SAMPLE
No
Yes Yes
TAKE
SAMPLE
Yes
TAKE
SAMPLE
Yes TAKE
SAMPLE
TAKE
SAMPLE
Proceed as for substratum 1 TAKE
SAMPLE
TAKE
SAMPLE
Yes
Yes

19
5. Site selection for water quality monitoring - Principles
The number and location of sampling sites should be designed according to the extent and
aims of the survey. Sites should be selected to provide representative samples, preferably
where marked changes in water quality are likely to occur or where there are distinctive river
features or human activities - for example confluences of sub catchments, major effluent or
dam discharges, flow regime changes through abstraction or flow augmentation from
interbasin transfers. Sampling both upstream and downstream of discharge points should be
carried out if sampling is intended to monitor the effects of such disturbances. Sampling
should extend for an appropriate distance downstream to assess the effects on the river and its
potential recovery.
Experience has shown that, in South African inland waters, diatom communities are at the
peak of their development in mid-winter to early spring. In addition, when sampling during
the winter low-flow regimes (in summer rainfall regions), water levels are receding rather
than rising and therefore the submerged substrata should have well-developed diatom
communities. Care, however, should be taken to avoid sampling after heavy or prolonged rain
events because scouring by high flows can displace diatom communities. Sampling conditions
in rivers may be less favourable at the height of the wet season due to the frequency of flood
events.
Sites for stream biomonitoring should be, if possible, in a “riffle”, where the water is flowing
over stones. However, “runs” and “glides” are also suitable if these have suitable substrata
Sampling in riffles or areas of moderate or high water velocity ensures continuous exchange
of the water surrounding the algae and prevents the build-up of a local chemical environment.
Furthermore, it prevents sedimentation of drifting organisms and particles, with the result that
only organisms living at that particular spot will be collected. The above recommendations
have, however, been made with wadeable rivers in mind and may not be applicable at all
times to deep rivers.
In broad, deep, slow-flowing rivers, such as the Vaal and Orange Rivers which are not
wadeable, cobbles or other substrata may be collected close to the riverbank from riffles with
flowing water or where flow is rapid enough (>20 cm sec-1
). The flowing water at the edge of
the main stream (littoral zone) is assumed to be of the same physical and chemical quality as
that in the main steam. Cobbles and boulders (but not macrophytes) should be gently agitated
in the river for a few seconds before removal. This should remove any surface contamination,
including small particles of organic matter and sediment.

20
The following aspects should be considered before selecting the reach and specific substrata
to be sampled:
Slight differences may occur between substrata from shallow water and those from deeper
water although there is a reasonably uniform distribution of the diatom flora at any given
sampling point. For this reason, sampling from depths greater than one metre should be
avoided, especially in turbid rivers where the euphotic zone (zone of effective light
penetration) may not extend to the riverbed. The performance of diatom indices is not
affected at depths of up to 0.5 m, provided that this is still within the euphotic zone.
Boulders with filamentous green algal growth should be avoided if possible, because
these growths of algae may support other unique diatom communities. However, if the
majority of the substratum is covered with filamentous green algae, sampling from un-
covered substrata would be non-representative. If this is the case, follow the
recommendations given below in Table 1.
TABLE 1 (DARES, 2004)
Percent cover of
filamentous green algae
Number of
cobbles
< 15% 0
≥ 15 < 29 1
≥ 30 < 44 2
≥ 45 < 59 3
≥ 60 < 75 4
<75 5
Boulders covered with a layer of sediment should also be avoided, if possible, as fine
sediments may modify substrate conditions. However, in lowland rivers it may be
difficult to avoid such boulders. The river bed in some coastal flood plains may be choked
with sand and sediment.
Although colonisation rates of diatoms are slower in fast-flowing than in slow-flowing
rivers, current speeds of 0.1 to 1.6 m.s-1
have little or no limiting effect on the
performance of diatom indices.
Repeated sampling at the same site requires the marking of sites with natural landmarks
in relation to immovable structures such as bridges.
To ensure the comparability of samples from other sites, the conditions of light, current
velocity, substratum etc. should be as similar as possible.

21
6. Sampling locality details and field notes/forms
Sample Field Record Form (modified from DARES, 2004)
River: _______________ Site: ____________________ Date: ________
DWAF #: _______________ Sample collected by: __________________________
Co-ordinates: __________________________ Elevation:___________________
Physical records
Width ______________ Depth:______________
Substrate (record estimated percentage)
bedrock boulders/cobbles pebbles/gravel
sand silt/clay peat
Estimate percentage of boulders and cobbles covered by:
Filamentous algae: other macrophytes
Shading (record estimated percentage)
Left bank None Broken Dense
Right bank None Broken Dense
Habitat Pool Run Riffle Slack
Water clarity Clear Cloudy Turbid
Bed stability Firm Stable Unstable Soft
Time since last spate
< 3 days 3 - 7 days 7 - 14 days > 14 days
not known
Photograph Facing upstream __________Facing downstream ___________
NB It is important to include an immovable structure in a photograph as a
referencefor future comparison e.g. a bridge
Use the reverse of this sheet for sketch map and other comments

22
7. Useful water quality variables and information to collect concurrently with
diatom samples for diatom index validation.
Note: The choice of which of the following variables need to be sampled will depend on the
design and outcomes of the particular study as well as monetary constraints.
7.1 Hydrological characteristics of the stream
7.1.1 Stream velocity
7.1.2 Channel depth
7.1.3 Channel breadth
7.2 Physical variables
7.2.1 Water temperature
7.2.2 Turbidity
7.3 Physico-chemical variables
7.3.1 pH, Conductivity/Total dissolved solids (TDS)
7.3.2 Nutrients
7.3.2.1 Orthophosphate-phosphorus (PO4-P), Total phosphate (TP)
7.3.2.2 Ammonium-nitrogen (NH4-N), Nitrite-nitrogen (NO2-N), Nitrate-nitrogen (NO3-
N), Total Kjeldahl nitrogen (TKN)
7.3.3 Major Cation/Anions (Budget constraints may provide for Conductivity values only;
Chlorides, sulphates and/or potassium may be essential to detect human intervention.
7.3.3.1 Magnesium (Mg2+
), Calcium (Ca2+
), Sodium (Na+
), Chloride (Cl-
)
7.3.3.2 Sulphates (SO4
-
)
7.3.4 Measures of Oxygen and Organic matter
7.3.5 Oxygen saturation
7.3.6 Chemical Oxygen Demand (COD) (preferred parameter for assessing performance
of sewage/industrial effluents and is aligned with DWAF monitoring programmes).
7.3.6.1 Biological Oxygen Demand - 5-day (BOD5), Total Organic Carbon (TOC)

23
8. Choice of substrata (detail)
Sampling should be representative rather than random. Operators should first decide which
areas in a river reach should be excluded and then search within the remaining areas for
substrata with obvious diatom growths, either by appearance or by feel.
Diatom growths can be identified by a golden-brown coloured mucilaginous layer on the
substratum or, if this is not visible, by the feel of the rocks, which will be slimy or slippery
because of the mucilage exuded by the diatoms for locomotion or attachment (see
Introduction).
8.1 Samples should be taken from five or more cobbles (diameter > 64, ≤ 265 mm) or
small boulders (> 256 mm diameter) where possible.
8.2 It is also acceptable to sample vertical faces of man-made structures such as quays and
bridge supports in the absence of appropriate stones at a particular site. Other hard
man-made surfaces, such as bricks, can also be sampled.
8.3 Alternative substrata, such as submerged or aquatic macrophytes, can also be
sampled, providing the stems are permanently submerged and not contaminated with
sediment. The type of macrophyte from which the sample is taken should always be
noted because it is important to sample the same species or, if this is not possible, the
same morphological type of macrophyte.
A useful identification guide for the identification of aquatic macrophytes is:
Gerber A, Cilliers CJ, van Ginkel Cand Glen R (2004) Easy identification of aquatic
plants. A guide for the identification of water plants in and around South African
impoundments. Department of Water Affairs, Pretoria.
This publication is available from:
Director; Resource Quality Services (RQS)
Department of Water Affairs and Forestry
Private Bag X 313, Pretoria 0001
Tel: 012 808 9500
or:
Annelise Gerber
gerbera@dwaf.gov.za
8.4 In order to compare downstream community composition, it is important to sample
from similar substrata along a river, as diatom communities vary according to
substratum
8.5 Samples should be taken in such a way as to obtain the greatest possible degree of
uniformity between sites.

24
9. Sampling
9.1 Solid substrata
9.1.1 Five to ten cobbles, boulders, pebbles or other substrata of similar proportions should
be collected from a reach of at least 10 m in the river or stream.
9.1.2 Gently rinse the substrata in the stream and carefully place in a sampling tray on the
river bank, together with about 50 ml of stream water.
NB If time limitations and safety factors are a concern; the cobbles/stones can be
placed in a large dish (e.g. an ice-cream container) and removed from the site for
attention in a safer environment.
9.1.3 Diatoms should be removed by vigorously scrubbing the upper surface of the
substratum with a small brush (e.g. clean toothbrush) to dislodge the diatom
community. Some diatomists prefer to scrape the substrata with a knife or a spoon as
these implements are easier to clean and reduce the possibility of contamination
between sites.
9.1.4 Only the upper side (the side most exposed to flowing water) of boulders should be
scrubbed to avoid contamination with sediment that might be present on the
undersides of the cobbles.
9.1.5 The resulting diatom suspension is then poured into a labelled wide-mouth plastic
sample bottle of 100 ml capacity or greater.
9.1.6 Care should be taken to avoid equipment contamination between sites by rinsing both
the toothbrush and the plastic tray in the river both before and after taking the diatom
sample.
9.2 Sampling from emergent aquatic macrophytes
9.2.1 The emergent macrophyte stem is cut with a knife above the water line.
9.2.2 A plastic bottle is then inverted over the remainder of the stem and the stem is cut
slightly above the point where it emerges from the sediment.
9.2.3 The bottle is inverted and brought to the bank.
9.2.4 This procedure needs to be repeated until five stems have been collected.
9.2.5 Scrubbing and removal of the diatom communities can then proceed in a similar
fashion to that described above for solid substrata (see 10)
9.3 Sampling from submerged aquatic macrophytes
9.3.1 Select replicates from five different plants growing in the main flow of the river.
9.3.2 Each replicate, consisting of a single stem plus associated branches of the plant from
the lowest healthy leaves to the tip, should be placed in a plastic bag together with 50
ml of stream water. Diatoms should be visible as a brown film associated with the
macrophytes (see Introduction).
9.3.3 The plants should be shaken vigorously and squeezed in the plastic bag and the
resulting brown suspension poured into a sample bottle.

25
10 Preservation of diatom material and labelling samples
Fresh diatom samples should be stored in the following manner:
In a refrigerator if the period of storage is to be less 24 hours.
If the samples are not going to be analysed immediately the samples may be fixed with
Lugol’s iodine, which may be used for short-term storage. (Lugol’s iodine is preferred if
material is to be examined prior to cleaning and should be added to reach a final
concentration of 1% by volume).
Lugol’s Iodine can be prepared by dissolving 2 g potassium iodide and 1 g iodine crystals
in 300 ml distilled water.
An alternative to Lugol’s iodine is ethanol. Ethanol should be added to reach a final
concentration of 20% by volume. Adding ethanol to a sample will destroy the
chloroplasts.
Ethanol is recommended for the long term preservation of un-cleaned material.
Formalin is NOT RECOMMENDED as a preservative although it is commonly used
for other algal samples. It should be avoided for diatom samples as it is carcinogenic and
in addition, even very weak formalin solutions might damage the fine structure of
diatoms.

26
SECTION 3: LABORATORY PROCEDURES
To facilitate the reading of this document references have been kept to a minimum. However
it should be mentioned that the methods described below have been based on several key
documents including: Kelly et al. (1998), CEN (2004), DARES (2004) and Taylor et al.
(2005).
1. Preparation
1.1 Toolkit
Beakers (easy to clean) - (50, 100, 250 ml)
Watch glasses to cover beakers (prevent cross-contamination between samples)
Test tubes
Pasteur pipettes (a cheap alternative is drinking straws)/Micro- Pipette with disposable
tips
Hot Plate for heating diatom material (inside a fume cabinet)
Vortex mixer (optional)
Separate hot-plate/slide dying bench for curing slides (inside a fume cabinet)
Reagents (clearly marked and correctly stored)
Waste bottles for disposal of hazardous compounds.
Health and safety of laboratory staff (general comments)
The specific health and safety risks involved in each of the diatom preparation
methods will be dealt with below. However, several general rules apply for safe
laboratory practice:
Always work in a well ventilated room.
If a reaction or procedure results in the production of vapors, fumes or smoke
ALWAYS work in a fume cabinet.
Proper care and attention should be paid to the storage and handling of
dangerous chemicals.
Do NOT dispose of hazardous chemicals or any other chemical compounds into
the municipal sewage system.
Avoid the use of dangerous chemicals if other less dangerous chemicals may be
substituted.
Work areas in the laboratory should be adequately delineated and carry the
appropriate warning and advisory signs

27
1: Micro-pipette 1 ml with disposable tips 2: Glass and plastic Pasteur-pipettes (2-3 ml). 3: Forceps.
4: Microscope slides. 5: Coverslips. 6: Diatom mountant. 7: 10 ml plastic gradated centrifuge tube.
8: 15 ml glass test tube. 9: 4 ml glass sample storage bottles with rubber seal inside cap. 10: Water-
proof fine marking pen. 11: Heat-resistant glass beaker ~ 100 ml. 12: Watch glass.

28
Section Summary
Preparation:
1. Pre-preparation examination for live cells.
2. Cleaning of cells:
a. In laboratory equipped with a fume cabinet: KMnO4 + hot HCl
method, hot H2SO4 + HNO3 (2:1) method, hot H2O2 method.
b. In WELL VENTILATED laboratory without fume cabinet: Cold
H2O2.
c. Rinsing: Centrifuge available: centrifuge with distilled water until
sample is circumneutral (4-5 runs for 10 min. at 2500 rpm)
d. No centrifuge available: decant supernatant using an aspirator.
Resuspend sample using distilled water and allow to settle for 8 hours
(repeat 4-5 times)
3. Slide preparation:
a. Concentrated diatom solution diluted with distilled water until only
slightly cloudy,
b. Add 1-2 drops of 10% NH4Cl to dilute solution to prevent clumping
of cells,
c. 1.5 – 2 ml of dilute solution is placed on cover slip, depending on size
of cover slip,
d. Sample allowed to air-dry ( Takes approximately 24 hrs),
e. Cover slip heated to drive off excess moisture and sublimate NH4Cl,
f. Sample mounted with high-resolution mountant.
Archiving:
1. Cleaned samples should be stored in ethanol, at a concentration high enough
to prevent the growth of bacteria and fungi and to prevent the dissolution of
silica.
2. Slides should be stored flat until mountant is dry.
3. All relevant information on the location, date of collection, substratum and
collector should be stored both with the sample and the slide, not simply a
reference number.

29
1.2 Pre-preparation examination of freshly sampled material
A quick examination of unpreserved fresh diatom material should be performed on return to
the laboratory to assess whether the diatom assemblage consists of predominantly of live cells
(It should be noted dead cells will also form part of the bio-film and are not necessarily
washed away under natural conditions).
If the majority of the diatoms in the freshly collected material are registered as dead cells
(empty frustules with no chloroplasts) the sample should be discarded, as further analysis will
not give a true reflection of recent water quality at the particular sampling site.
1.3 Cleaning techniques with rationale
Any method of preparation of diatoms for microscopy is acceptable, as long as the cleaned
material meets the following criteria:
Concentrations of cells in the cleaned sample should match as closely as possible the
concentration of cells collected in the original sample.
The organic matter in the sample should be completely removed.
Foreign matter should either be absent or insufficient to cause problems during the
enumeration or identification of the specimens.
1.3.1 Decalcification
Decalcification is ONLY necessary if samples are to be later treated with nitric or sulphuric
acid, as these acids combine with calcium causing the formation of an insoluble precipitate.
This stage can be omitted if you are sure that the sample does not come from a site with any
calcareous rock in the catchment or if using the Hot HCl and KMnO4 method
(recommended technique)
HEALTH AND SAFETY
Hydrochloric acid is CORROSIVE and OXIDATIVE. Do not perform any
analysis using this chemical outside of a fume cabinet.
When handling HCl wear acid resistant gloves, goggles and a lab coat.

30
1.3.1.1 On return to the laboratory, allow the samples to settle for 24 hours;
1.3.1.2 Pour off the supernatant liquid taking care not to loose any diatom material;
1.3.1.3 Shake the remaining suspension well and pour 5-10 ml (depending on the
concentration of the material) into a glass beaker;
1.3.1.4 In a fume cabinet, add a few drops of dilute HCl (e.g. 1 M) and agitate gently -
the material should effervesce as the carbonates are reduced to CO2. [If the
sample does not effervesce on addition of HCl there is not a significant amount of
Ca in the sample and it is not necessary to continue with decalcification];
1.3.1.5 Continue adding dilute HCl, and agitate the beaker gently until effervescence
stops;
1.3.1.6 Pour the solution into a centrifuge tube (10 ml);
1.3.1.7 Add distilled water to 1 cm below the rim of the centrifuge tube and centrifuge to
remove the acid;
1.3.1.8 The samples are rinsed by centrifuging with distilled water at 2500 rpm for 10
minutes;
1.3.1.9 After centrifugation the supernatant is decanted and the washing is repeated a
further 4 times until the sample is circumneutral.
1.3.2 Hot HCl and KMnO4 method (recommended technique)
This method is recommended by the authors as it has yielded good results with samples taken
from throughout South Africa, which usually have a high content of organic material. In
addition, there is no need to remove calcium (1.3.1) before processing the samples as in the
other techniques below (1.3.3 – 1.3.4).
1.3.2.1 Allow the diatom sample to settle for 24 hours after return to the laboratory;
1.3.2.2 Decant the clear supernatant liquid from the sample bottle taking care not to loose any
of the diatom material;
HEALTH AND SAFETY
Hydrochloric acid is CORROSIVE. CHLORINE GAS is emitted when combined
with potassium permanganate. Potassium permanganate is an OXIDATIVE
AGENT. Do not perform any analysis using these chemicals outside of a fume
cabinet. When handling HCl wear acid resistant gloves, goggles and a lab coat.

31
1.3.2.3 Shake the sample well and pour 5 to 10 ml (depending on the concentration of the
material) of thick suspension into a heat-resistant beaker;
1.3.2.4 Mark the beaker clearly with the sample number in several places;
1.3.2.5 Add 10 ml saturated potassium permanganate (KMnO4) solution, mix and leave for a
period of 24 hours;
1.3.2.6 In a fume cabinet, add 5-10 ml concentrated HCl (32%), taking care not to inhale
the gasses released. Cover the beaker with a watch glass and heat on a hot plate at
90°C for 1 to 2 hours until the solution becomes clear (usually the solution will have a
yellowish colour when clear);
1.3.2.7 After oxidation of organic material, add 1 ml of hydrogen peroxide to check if the
oxidation process is complete and no organic material remains, in which case the
hydrogen peroxide will not cause lasting foaming;
1.3.2.8 When oxidation is complete, the samples are allowed to cool and are then transferred
to 10 ml centrifuge tubes. Before pouring the diatom and acid samples from the
beakers, the beakers are vigorously swirled, the aim of the rotary movement being to
re-suspend the diatoms, whilst causing the stone and heavier sand particles to fall to
the bottom of the beaker;
1.3.2.9 The samples are rinsed by centrifuging with distilled water at 2500 rpm for 10
minutes;
1.3.2.10After centrifugation the supernatant is decanted and the washing is repeated a further
4 times until the sample is circumneutral;
1.3.2.11The supernatant should be poured off in a single movement, and care should be taken
not to lose any diatom material. After pouring off the supernatant fluid the diatoms
and small particles of sand at the bottom of the tube are loosened by means of a jet of
distilled water from a wash bottle. More water is then added until reaching the
required volume in the centrifuge tube;
1.3.2.12After the last wash, the diatoms are again loosened by means of a jet of distilled water
and then poured into small glass storage vials bearing the necessary sample
information. It is important to store diatom samples in glass as opposed to plastic
vials, as glass releases silica, which counters the dissolution of diatom valves.
Alternatively, the excess acid and soluble chlorides can be washed out by a series of timed
decantations.
1.3.2.13The beaker is filled with distilled water to within 1 cm if the top and the solution is
allowed to settle overnight;
1.3.2.14The clear supernatant is decanted;
1.3.2.15After each decantation, the remainder is swirled to get it into suspension and the
beaker is again filled with distilled water;
1.3.2.16This is repeated until the suspension is clear and it no longer turns blue litmus paper
red (i.e. the sample is circumneutral).

32
The supernatant may be decanted using an aspirator attached to a water suction pump or by
siphoning.
Tip: an aspirator can conveniently be made by heating and bending a glass Pasteur pipette
into a ‘u’-shape.
1.3.3 Hot HNO3/H2SO4 method
1.3.3.2 Decant the supernatant from the sample bottle taking care not to loose any of the
diatom material;
1.3.3.3 Check the sample for the presence of calcium and decalcify the sample if necessary
(see section 1.1);
1.3.3.4 Mix the diatom suspension carefully and pour a sub-sample (~ 5 to 10 ml) into a
beaker. The size of the sample is dependent on the sample density, which can be
judged by the visible concentration of suspended material;
1.3.3.6 Add 5 ml of a strong acid mixture (HNO3 + H2SO4, 2:1) and place the beakers on a
hot plate. The beakers should be covered with a watch glass to prevent contamination
between flasks if boiling becomes too vigorous and splashing occurs;
1.3.3.7 Heat the samples at 90°C for 2-3 hours, depending on the amount of organic matter in
the sample;
1.3.3.8 Rinse the samples and test for organic material as in points 1.2.7 – 1.2.12 in the
previous method.
1.3.4 H2O2 Methods
Hydrogen peroxide is much gentler than acid as it is not as corrosive. It is best used with
samples that require little cleaning, and where corrosion should be limited, as in SEM studies.
The choice of technique (either hot or cold) depends on the availability of a fume cabinet. If
HEALTH AND SAFETY
Both Nitric acid and Sulphuric acid are highly CORROSIVE OXIDISING agents.
Do not perform any analysis using these chemicals outside of a fume cabinet.
When handling HNO3 or H2SO4 wear acid resistant gloves, goggles and a lab coat.

33
one is available the peroxide can be boiled and, if not, a cold method should be used, but only
in a well-ventilated room.
Hot H2O2 method
1.3.4.2 Decant the supernatant from the sample bottle taking care not to loose any of the
diatom material;
1.3.4.3 Check the sample for the presence of calcium and decalcify the sample if necessary
(see section 1.1);
1.3.4.4 Mix the diatom suspension and place 5 to 10 ml of the suspension in a beaker;
1.3.4.6 Add 20 ml H2O2 and heat on a hot plate at 90°C for 1 to 3 hours;
1.3.4.7 The beakers should be covered with a watch glass to prevent contamination between
flasks if boiling becomes too vigorous and splashing occurs;
1.3.4.8 Add a few drops of HCl and leave to cool;
1.3.4.9 Rinse the samples as in method 1.2.7-1.2.12.
Cold H2O2 method
PAY ATTENTION TO THE HEALTH AND SAFETY WARNING FOR THE
PREVIOUS METHOD
1.3.4.10Proceed as in method 1.3.4, above, with the exception of using a hotplate;
1.3.4.11Cover beaker with watch glass and leave for a minimum of four days;
1.3.4.12Rinse the samples as in method 1.2.7-1.2.12.
Health and Safety
Hydrogen peroxide is an OXIDISING agent. Do not perform any analysis using this
chemical outside of a fume cabinet if heat is to be used to speed the reaction.
When handling H2O2 wear acid resistant gloves, goggles and a lab coat.

34
1.4 Other methods (Incineration)
The above methods (1.3.1 – 1.3.4) will completely destroy the organic material both inside
and outside of the diatoms cells including the organic materials used for colony formation.
Thus, by using these methods it will only be possible to observe single cells in the final
preparations. To make permanent slides which retain colony formation requires the use of a
different technique known as incineration. This technique may also be useful for particularly
delicate and weakly silicified diatoms that would be destroyed or badly damaged using other
techniques. The technique of incineration is described below:
Place 2-3 drops of fresh concentrated diatom suspension onto a coverslip.
Add distilled water until the surface of the coverslip is almost covered.
Gently heat the coverslip on a hot plate until all the liquid has evaporated.
Increase the heat to 350°C and continue to heat the sample.
Watch carefully for the changes in the colour of the diatom material.
The sample will first become brown as the chlorophyll and other organic material is
incinerated.
The sample will then turn black as all the organic material is converted into carbon.
As the carbon is incinerated the remaining material will turn a whitish colour.
When the sample is clean, i.e. has a white appearance, allow the coverslip to cool and
remove it from the hotplate.
Gently rinse the upper surface of the coverslip to remove any salts or other precipitates.
Heat the coverslip again until all the moisture has been removed from the sample.
The sample is now ready for mounting in a high resolution diatom mountant.

35
2 Preparation of diatom slides
As with of the cleaning of diatoms any method slide preparation is acceptable, as long as the
slide meets the following criteria:
The distribution of valves on the cover slip should not be significantly clumped, but be
evenly dense, without significant edge effects, over the whole area of the coverslip.
Ideally, there should be 5-15 valves, but not less than 1 and not more than 25 valves, per
field of view when viewed at 1000 x magnification.
The mountant should be properly cured, with no air bubbles, and should spread right to
the edge of the coverslip.
Most of the ultra-structural details of diatoms lie at the limit of resolution of light. In addition,
all generally used mounting media used in cytology have a refractive index similar to that of
diatom valves, with the result that slides with diatoms mounted in these media are too low in
contrast for satisfactory investigation. For this reason diatoms must be enclosed in a medium
of higher refractive index than that of the diatom valves. Four types of mounting media are
generally used: “Hyrax” r.i. (refractive index) 1.71; “Naphrax” r.i. 1.69, “ZRAX”, r.i. 1.7 and
“Pleurax”, r.i. 1.73
Naphrax is available from:
Brunel Microscopes Ltd,
Chippenham, SN14 6QA.
England
ZRAX is available from:
Professor W. P. Dailey
dailey@sas.upenn.edu
or
Mr. Klaus Kemp
Microlife Services,
Blautannen,
Wickham Way
East Brent,
Somerset, TA9 4JB
England
Tel: +44 1278 760 411
klaus.kemp@onetel.net
www.diatoms.co.uk
Pleurax is available from:
Mr. Jonathan Taylor
School of Environmental Sciences
Division Botany
North-West University
(Potchefstroom Campus)
Private Bag X6001
Potchefstroom, 2520
Tel: 018 299 4305
plbjct@puk.ac.za
Health and Safety
Many diatom mountants and the solvents used for these mountants contain harmful or
carcinogenic chemical compounds. Always make slides in a fume cabinet or under a
fume hood and never inhale the fumes and smoke released during this procedure.

36
2.1 Preparation
Principle: Slides should be free of contamination by other diatomaceous material and should
display an assemblage of diatoms that is as close as possible, in terms of composition, to that
of the original sample. For this reason strewn slides are used almost exclusively.
Note: It is always necessary to keep the sample well mixed or shaken, as the larger diatom
cells will tend to settle out of solution quicker than the smaller cells and thus the community
counts will be skewed and unreliable (a mechanical vortex mixer is very useful for this
purpose).
2.1.1 Slides and cover slips should be scrupulously cleaned with detergent soap and stored
in ethanol until needed.
2.1.2 Using a pipette, a portion is drawn from a well-shaken numbered vial of cleaned
material. The cleaned diatom suspension is diluted until it appears only slightly
cloudy to the naked eye.
Note: Obtaining the correct dilution is a matter of practice as the concentration of
diatom cells in the solutions will always differ from sample to sample.
2.1.3 A single drop of ammonium chloride (NH4Cl; 10% solution) is added for every 10 ml
of diluted diatom suspension to neutralise electrostatic charges on the suspended
particles and reduce aggregation. This is a very important step; if the diatoms and
other particles clump together this destroys the random distribution of the cells on the
slide which will in turn have an effect on the results of the analysis.
2.1.4 Using a pipette ~1.5 ml of this suspension is placed on a clean, dry cover-slip (22 x
32 mm). The amount of solution used will vary according to the size of the coverslip.
2.1.5 After being placed on the cover slip the diatom suspension should be allowed to dry
at room temperature in a dust free environment. It should not be disturbed until dry,
because vibration causes clumping of the diatom valves.
2.1.6 The drying of cover slips on a hot plate is not recommended because the resultant
convection currents form more or less concentric rings of diatoms, with consequent
overlying.
2.1.7 After the water has evaporated, diatom-coated cover-slips are placed on a hot plate at
~350ºC for 3 minutes to drive off the excess moisture and to sublimate the residual
ammonium chloride.
2.1.8 After the cover slips have cooled, they can be briefly examined under 400 x
magnification to determine if the concentration of diatoms in the solution was correct.
At least 10, but not more than 40, valves should be visible per field. When the sample
is finally viewed at 1000 x magnification there should ideally be between 5 and 15,
but not more than 20, valves visible in each field. If the concentration is too high or
low, steps 1-7 need to be followed again, using a more or less dilute suspension,
before proceeding further.

37
2.1.9 After the diatom-coated cover slips have been allowed to cool, one or two drops of
mountant are placed onto each by means of a glass rod or pipette.
2.1.10 A previously cleaned glass slide is then lowered onto the cover slip, inverted, and
then heated at 90-120 °C on a hot plate until the mountant ‘boils’ and all the solvent
evaporates.
2.1.11 The solvent of the mountant should be evaporated quickly. If this is not done a ring of
exuded medium will harden around the edge of the cover slip, while the mountant
under the cover slip remains more or less viscous.
2.1.12 Under no circumstances should the mountant be heated for too long, or at too high a
temperature, because then it will turn dark in colour.
2.1.13 Depending on temperature and the quality of the mountant, it will be necessary to
heat the slide on the hot plate for two to five minutes.
2.1.14 After the mountant has boiled for this length of time, but while it is still viscous, the
hot slide is quickly removed from the hot plate, and laid on the work bench.
2.1.15 The cover slip is then manoeuvred into position. If this operation is not successful the
first time, the slide need only be re-heated for another few moments and the
positioning repeated.
2.1.16 When the slide is thoroughly cooled, all the mountant should be hard and brittle and
capable of being easily chipped off with the point of a scalpel.
2.1.17 Surplus medium, which has been exuded and has set round the edge of the cover slip,
may be carefully removed with the point of a scalpel or cotton bud soaked in solvent,
after which the slide is then wiped clean with a soft rag soaked in the particular
mounting medium’s solvent (iso-propyl alcohol for “Pleurax” and toluene (which is
carcinogenic) for “Hyrax”).
2.1.18 The cover glass may then be ringed with shellac cement or Bio-seal®
.
2.1.19 The slide should be carefully labeled. Important details to be included on the slide
label are: Date of collection, site location and co-ordinates, habitat, collector and type
of mountant.
2.1.20 The slide is then ready for microscopic examination.

38
3. Preparation for Electron Microscopy (EM)
Diatoms provide an excellent subject for electron microscope studies. Both scanning electron
microscopy (SEM) and transmission electron microscopy (TEM) are useful but not essential
tools for diatom taxonomy. An impression of the three dimensional structure of diatoms is
gained using SEM, while the higher resolving power of TEM makes it useful for examining
fine structures and small, thin-walled diatoms (e.g. Fistulifera saprophila Lange-Bertalot &
Bonik). The silica frustule of diatoms is very robust and no special techniques such as those
used for soft-bodied algae are required to prepare these cells for electron microscopy.
2.2 Preparation for SEM
Freshly collected diatom material can simply be air dried onto a small coverslip (Ø 12
mm) or filtered through a 2.5 µm Millipore®
filter.
Cleaned material can be prepared in a similar manner.
When air dry the sample should be placed in a dessicator containing silica gel for 24
hours to make sure that it is completely dehydrated before continuing with further
preparation.
When dry the coverslip or filter should be mounted on an aluminium microscope stub
with carbon tape and sputter coated with gold palladium.
The samples are now ready for examination.
10 – 15 kV is usually adequate voltage for examining diatoms.
2.3 Preparation for TEM
The sample is suspended (or diluted) into water if possible and adsorbed onto a formvar
film which is attached to a copper specimen grid.
Once the diatom material has been adsorbed onto the film surface, the excess sample is
blotted off and the grid is covered with a small drop (5 µl) of stain solution (Aqueous
Uranyl Acetate).
This is left on the grid for a few seconds and then blotted off.
The sample is dried and examined in the TEM.

39
4. Archiving
It is important to retain a portion of the original sample throughout the preparation stage
until the final slide has been made and examined under a microscope.
After slide preparation, a portion of the cleaned suspension should be preserved and
stored in a labeled vial with ethanol added to reach a final concentration of more than
20% by volume, to prevent the growth of micro-organisms.
Alternatively, two or three drops of a 5% aqueous solution of phenol (caution: this
chemical is carcinogenic) may be added. The archiving of diatom material is necessary
in case further slides need to be made or if other workers wish to verify the results of a
diatom community analysis after mounting and examining the sample themselves, or if
SEM studies on the material are to be undertaken.
Finally, a slide should be stored in a herbarium or diatom collection to facilitate cross-
referencing. Diatom slides provide a permanent historical record of water quality
conditions at a site and should be stored in order to ensure that they can be accessed for
future analyses. It is recommended that at least two slides are prepared from each sample.
One of these should be lodged in the appropriate national herbarium, for future reference.
This is:
The North-West University,
Potchefstroom Campus,
School of Environmental Sciences and Development,
Division Botany,
Private Bag X6001,
Potchefstroom, 2520
Type material should be lodged at:
The Natural History Museum
Cromwell Road
London, SW7 5BD
UNITED KINGDOM
Diatom slides sent to such institutions should be labeled with the following minimum
information:
Location (place name not just a number)
Co-ordinates if available
Date on which the sample was collected
Substratum
Name of the sampler
Type of mountant
Date on which the slide was prepared.

40
5. Enumeration and simple biometrics
Diatom counts, when analysed may be used to infer the average water quality at a particular
sampling site. Once the sample has been counted in the correct manner the data can be
entered into a computer data-base (“Omnidia”, Lecointe et al., 1993) from which several
calculations can be made using a specific equation or using the sum of the water quality
optima of all the species in the sample.
Simply, each diatom species used in the calculation/equation is assigned two values; the first
value reflects the tolerance or affinity of the diatom to a certain water quality (good or bad)
while the second value indicates how strong (or weak) the relationship is. These values are
then, in addition, weighted by the abundance of the diatom in the sample i.e. how many of the
particular diatom in the sample occur in relation to the total number counted. Below is the
formula of Zelinka and Marvan (1961) on which most diatom indices are based:
Where aj = abundance (proportion) of species j in sample, vj = indicator value and sj =
pollution sensitivity of species j. The performance of the indices depends on the values given
to the constants s and v for each taxon and the values of the index ranges from 1 to an upper
limit equal to the highest value of s.
The aim of counting diatom units is to produce semi-quantitative data from which ecological
conclusions can be drawn. With this in mind it is important to know how many valves to
count to get a reliable estimation of the relative species composition at a specific sampling
site. The total number of valves to be counted for each sample varies according to the purpose
of the analysis and according to the need to produce statistically good results. The statistical
precision of percentage counting depends on the frequency of the taxon in the sample count in
relation to the size of the sample count. In a South African study Schoeman (1973) made a
series of experimental counts in which 200, 300, 400, 500 and 800 valves per sample were
counted and their relative abundance calculated. When only 200 valves were counted,
compared to when 800 valves were counted, the percentage differences of the relative
abundances of individual species were often as high as 6-7%. However, the results obtained
from counting 400 as opposed to 800 valves differed by only 1-2%. For this reason he
concluded that counting 400 valves was satisfactory for the calculation of relative abundance
of diatom species. Similarly, Battarbee (1986) demonstrated that there were marked
differences in the percentages between counts of 100 and 200 valves, while there was little
difference between counts of 400 and 500. For this reason he recommended that a count of
300 to 600 may be used for purposes of routine analysis. This range is supported by Prygiel et
al. (2002) who, in an inter-comparison exercise, found that diatom index scores were not
∑
∑
n
j
n
j
va
vsa
index
jj
jjj
1
1

41
affected at counts of 300 and above. Hence, it is recommended that, for diatom community
analysis in South Africa, 400 diatom valves should be counted in each sample.
Different conventions have been evolved for the enumeration of diatoms, using either valves
or frustules as the basic unit, or not distinguishing between valves and frustules. The effect
that such conventions have on the final results has not been evaluated, but is likely to be
small. However, it is important that the convention used be specified in advance and kept
consistent. In the case of small diatoms, such as some Achnanthidium and Naviculoid species,
it may not be possible to distinguish with certainty between intact frustules and isolated
valves on all occasions.
Suggested rules for counting diatoms can be summarised as follows:
Counts of diatom valves on slides should be made using a microscope equipped with
incident light (bright field illumination), phase contrast optics or differential interference
(Normarski) optics (DIC) at a magnification of 1000 x and higher (i.e. 100 x oil
immersion objective in combination with a 10 x eyepiece).
The eyepiece graticule or other measuring equipment must be calibrated against a stage
micrometer prior to the analysis to allow for measurement of dimensions and taxonomic
features.
Either the field of view or the grid of a graticule is used as the area defining the limits of
the count. All diatoms visible in the field of view (or within the grid of a graticule) are
identified and counted before moving along either a horizontal or vertical traverse to the
next field, or selecting a new field of view at random.
The edge of the dried sample suspension is recommended as the position to begin
counting, but if this rule is to be adopted, ensure that there are no significant “edge
effects”.
A rule is needed to cover situations where a diatom lies only partially inside a defined
counting area. For example, such a rule might include taxa that are only partially visible
at the upper but not the lower margin (in the case of vertical traverses) or the left but not
the right margin (in the case of horizontal traverses). The precise form of the rule is less
important than the consistency of its use when analysing samples.
Whether a horizontal or vertical traverse is used, it is important that each subsequent
traverse does not overlap with the previous one. No diatom valve should ever be counted
twice. The distance that the stage is moved on each occasion must also account for any
diatoms only partially visible in the field of view.
If sample analysis is unlikely to be completed in a single session, then it is useful to
record the position of each traverse. This ensures that subsequent traverses do not overlap
with those already completed.
Each individual specimen encountered is counted as a single unit, with no differentiation
between a valve and a frustule.
Girdle bands (copulae) should not be enumerated as being representative of diatom taxa.

42
Occasional filaments should be recorded as the corresponding number of diatom units. If
a large number of diatom units are found in filaments, a new preparation technique, using
a more aggressive mix of oxidising agents, should be considered.
In order to eliminate the risk of including separate fragments of broken valves or
frustules, a consistent approach must be decided on before starting a project. Valves
should be counted only if approximately three quarters is present, or alternatively broken
valves may be excluded from the count altogether. Since the scale of physical damage
during the sampling and preparation stages is unlikely to be significant, the presence of
many small fragments of diatoms may indicate that dead diatoms are being washed in
from upstream sites.
A diatom may not be identifiable for a number of reasons, including the presentation of a
girdle view, the presence of overlying material obscuring the view, or the taxon not being
recognised by the analyst. If many valves are obscured, then new slides should be
prepared using more dilute suspensions.
Some taxa are identifiable from girdle (side) views, either because the girdle view is
particularly characteristic (e.g. Rhoicosphenia abbreviata) or because the girdle view can
be assigned with confidence to a particular taxon by “matching” it with corresponding
valve views of taxa found in the sample. However, this is not always possible and, in
cases of doubt, the analyst should record the girdle views at the lowest level to which they
can be assigned with confidence (e.g. “unidentified Gomphonema sp.”, “unidentified
pennate girdle view”).
This convention should also be applied to other individuals found on the slide but not
identifiable by the analyst. A large number of such individuals may indicate a problem
either with the slide preparation or the identification skills of the analyst.
As most diatom indices presume that all taxa in a sample are identified, it is
recommended that not more than five per cent of the total count should comprise
unidentifiable individuals. If a diatom unit cannot be identified for any reason,
photographs, digital images or detailed drawings should be made. Notes should also be
taken of the shape and dimensions of the diatom unit, striae density and arrangement (at
the centre and poles), shape and size of the central area, number and position of punctae
and arrangement of raphe endings.
For some purposes, especially biodiversity studies, it is useful to continue to scan the
slide after the required number of diatom units has been counted, and any taxa
encountered that were not included in the count should be identified and recorded as
“present”.
A further scan using a medium power magnification (e.g. 400 x) may also be appropriate
in order to note any larger taxa (e.g. Gyrosigma spp.) which may be missed at higher
magnifications.

43
6. Counting records (electronic and manual methods)
A pro forma count sheet with a list of taxon names and space beside each on which the counts
can be made or a laboratory notebook organised in such a way that taxon identities and
numbers can be clearly recorded. Such sheets should be clearly marked with the details of the
sample, the date of the analysis and the analysis’s name.
Alternatively a computer program with facilities for direct entry of data can be used. These
programs (e.g. “Opticount”) allow the names taxa to be assigned to the different keys of a
computer keyboard. Each time a specific key is hit the program will record a single individual
of that specific taxon. Such programs greatly facilitate and speed counting and the storage and
archiving of counting records.
7. Microscopy
A compound light microscope, equipped with a mechanical stage and 100 x oil-immersion
lens is required for examining diatom slides. Use of a phase contrast or differential
interference (Nomarski) condenser is recommended, although brightfield light will give
satisfactory results. The microscope must incorporate facilities for measurements (e.g. an
eyepiece graticule) with a resolution of at least 1 m. Apparatus for photomicroscopy or
video capture are useful for taking pictures of difficult specimens. Image Analysis software is
also recommended for capture, storage and presentation of diatom images as well as
facilitating the measurement of cell dimensions. The eyepiece graticule, or other measuring
equipment, must be calibrated against a stage micrometer prior to the analysis. The results of
this calibration must be displayed in a position where users of the microscope can easily
consult them. The second eyepiece may be equipped with a second graticule to aid
enumeration.
8. Image capture, analysis and archiving
A problem affecting light microscopy of diatoms is diffraction. Many of the features of
diatom frustules – stria, puncta, spines, etc – are very small, approaching the same dimensions
as the wavelengths of visible light (c. 0.5 µm for blue-green light) and this means that
diffraction is the major factor determining whether or not structures can be seen. This in turn
means that microscopes must be of good quality and, perhaps even more importantly, they
must be used well if some of the fine details necessary for identification of diatoms are to be
observed.
A further peculiarity of ‘diffraction limited systems’ is that small structures, like puncta
(pores) or spines or the raphe system, appear in focus more than once, in different horizontal
planes. For example, in a normal light microscope as one focuses through a specimen

44
vertically, a feature may first appear in-focus dark against the background, then it will
virtually disappear, and then it will appear in-focus again, but now light against the
background. Neither of the in-focus images is ‘correct’. Both are artifacts of diffraction at the
interface between two transparent materials of different refractive index. In many ways, it
seems more reasonable to choose the ‘white-spot focus’ for small pores and the raphe slit,
because these are immaterial features – the absence of silica – whereas the ‘dark-spot focus’
seems more appropriate for solid structures like spines and warts. However, such choices are
arbitrary and observers choose on the basis of aesthetics and convention. So, for example, it is
more common to photograph most pennate diatoms with the striae (the lines of pores) and
raphe in ‘dark-spot focus’. However, Epithemia is usually photographed with the pores in
‘white-spot focus’ (Kelly et al., 2005).
Image analysis is the most advanced technology for a broad range of functions such as digital
image acquisition, image processing, sample analysis, database archiving and results/report
documentation. A recommended software package is “analySIS” which has several expansion
versions and configurations (Website: www.soft-imaging.net). Version 3.1 provides live
overlay, 3-D surfaces, automatic scale bar and many other functions. It is relatively user-
friendly but expert advice is required for the most benefit.
9. Sources of variation in diatom community analysis
When implementing monitoring programs based on assessments of diatom community
composition, we in South Africa have the advantage of looking to European and other studies
to identify sources of error in advance. Several sources of error, in all stages of the analysis,
have been highlighted by Prygiel et al. (2002) in an inter-laboratory comparison exercise.
According to these authors sampling appears to be a very important step. When the sampling
protocol is not strictly adhered to, variability in the end result of the analysis can be very
high.
Sampling-induced variations include:
Sampling from exposed substrata,
from areas subjected to water level change,
from areas of low-velocity flow as compared to other parts of the river and
sampling from stones covered by abundant filamentous algae.
Laboratory- and counting-induced variations may include:
The use of high temperatures when drying slides, leading to clumping of diatom valves,
the settling out of large taxa during the preparation of consecutive slides from a single
sample.

45
The main source of variability is, however, the identification of individuals, that is why
biological quality controls focus mainly on counts and misidentification. Diatoms are suitable
for such controls and proposals have been made by Kelly (1999).
Prygiel et al. (2002) made recommendations which should be seen as the way forward for
South Africa in terms of quality control and the validation of diatom analysis data:
Most of the variability due to sampling and slide preparation can be avoided by
organising comparisons between different studies. Such comparisons are very useful
because, with field and laboratory approaches, they make operators aware of the
consequences of not following protocols. They are also useful because they highlight
some taxonomic problems.
Diatoms are good subjects for photomicrography and therefore most diatomists use the
internet to check problematic identifications. This approach should be encouraged by
formalising expert-practitioner exchanges, by creating iconographic databases, and by
organising regular workshops to allow updating of knowledge.
The archiving of permanent slides also facilitates the creation of reference collections
which are particularly useful for the identification of difficult species.
10. Recommended software packages
Package Applications/comments Available from:
Opticount A counting program
especially designed for
the enumeration of algae
species and calculation of
biomass based on species
counts.
DoMix Software
Dr. Dominik Hepperle
Dorstrasse 20
D-18249 Klein Raden
Germany
info@do-mix.de
http://science.do-mix.de/software.php
Omnidia Diatom-based index
calculation and archiving
both diatom sample
information and species
counts. This is a very
valuable tool containing
about 11 000 diatoms
species with synonyms
and references.
CLCI
Mrs. Catherine Lecointe :
Fax: +33 5 53 61 26 73
Give your computer type (Mac or PC and
Windows version)
Payment can be made by cheques or
international postal order
PRICE: Euros 701,27 (07/2005)
clci@club-internet.fr
http://membres.lycos.fr/rimetfrederic/links.ht
ml
TaxIBD A pictorial key containing
the 209 species used for
the calculation of the
French Indice Biologique
Diatomées (IBD). This is
a simple key accompanied
by photographs and a
l'Agence de l'Eau Artois Picardie
200 Rue Marceline
BP 818
59508 Douai Cedex
France

46
short description of the
taxa used in the index.
Common
Freshwater
Diatoms of
Britain and
Ireland: A
multi-access
key
This electronic key is
based on LUCID software
and contains 379 river
diatom species commonly
encountered in Britain
and Ireland. This key
provides an introduction
to the morphology of the
diatoms, a detailed
description of each taxon
included accompanied by
photographs and
ecological information.
UK Environment Agency
http://www.environment-agency.gov.uk
Common
Freshwater
Diatoms of
South
Africa: A
multi-access
key.
This electronic key is
based on LUCID software
and contains ~ 200 river
diatom species commonly
encountered in South
African fresh waters. This
key provides a detailed
description of each taxon
included, accompanied by
photographs, drawings
and ecological
information
Private Bag X03
Gezina
0031
Mrs Rina Winter
Publications
Telephone: 012 330 0340
Fax: 012 331 2565
orders@wrc.org.za
http://www.wrc.org.za
AnalySIS Allows for image capture,
measurement, processing
and archiving
Wirsam Scientific & Precision Equipment
Mrs. Colleen Syrett
23 Menton Road
Richmond 2092
Johannesburg
Telephone: 011 482-1060
Fax: 011 726-6094
e-mail: wirsamjb@wirsam.com
http://www.soft-imaging.net

47
11. Key reference works
There are several key reference works as well as simpler illustrated keys and
introductory volumes on the diatoms that may be useful when first commencing the
study of diatoms, these include the following:
Title and authors Available from:
Suesswasserflora von Mitteleuropa: Band 2:
Bacillariophyceae. Tiel 1-4. K Krammer and
H Lange-Bertalot. (1986-1991)
Koeltz Scientific Books
Po Box 1360
D-61453
Königstien
Germany
E-mail: koeltz@t-online.de
www.koeltz.com
Suesswasserflora von Mitteleuropa: Band 2:
Part 5: English and French translation of the
keys. K Krammer and H Lange-Bertalot:
Bacillariophyceae. (2000)
Koeltz Scientific Books
Po Box 1360
D-61453
Königstien
Germany
E-mail: koeltz@t-online.de
www.koeltz.com
Guide méthodologique pour la mise en œuvre
de l'indice Biologique Diatomées NF T 90-
354. Agences de l'Eau-Cemagref de
Bordeaux, mai 2000, 134 pages + Clés de
détermination (89 planches) + cédérom
français-anglais (tax'IBD). J Prygiel and M
Coste M. (2000)
l'Agence de l'Eau Artois Picardie
200 Rue Marceline
BP 818
59508 Douai Cedex
France
Identification of common benthic diatoms in
rivers. MG Kelly (2002)
FSC Publications
Field Studies Council
Preston Montford
Shrewsbury SY4 1 HW
England
E-mail: fsc.publications@ukonline.co.uk
www.field-studies-council.org
A guide to the morphology of the diatom
frustule. HG Barber and EY Haworth (1981)
The Librarian
The Ferry House
Far Sawrey
Ambelside
Cumbria LA22 0LP
England
E-mail : EHaworth@fba.org.uk
An illustrated key to common diatom genera
from Southern Australia. PA Gell, JA
Sonneman, M Reid, MA Illman and AJ
Sincock (1999)
Murray Darling Freshwater Research Centre
PO Box 921
Albury NSW 2640
Australia
An illustrated guide to common stream
diatom species from temperate Australia. JA
Sonneman, A Sincock, J Fluin, M Ried, P
Newall, J Tibby and P Gell. (1999)
Murray Darling Freshwater Research Centre
PO Box 921
Albury NSW 2640
Australia

48
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HARDING WR, ARCHIBALD CGM, TAYLOR JC and MUNDREE S (2004) The South
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