﻿Checklist of the diatoms (Bacillariophyta) from Lake Naivasha, Kenya, with some historical notes

﻿Abstract Lake Naivasha is one of only two large freshwater lakes in the Eastern Rift Valley of Kenya, East Africa. Together with its satellite lakes Crescent Island Crater, Oloidien and Sonachi, it comprises a great variety of pelagic and benthic habitats for aquatic biota, and its sediment record represents a unique archive of past climate change and long-term ecosystem dynamics in equatorial East Africa. This is particularly so because local paleoenvironmental reconstructions can be checked against historical data on the composition of aquatic fauna and flora collected in Lake Naivasha since the early 20th century. Some of the most prominent biological proxies for reconstructing past changes in lakes are diatoms (Bacillariophyta), a group of unicellular autotrophic eukaryotes of which the siliceous skeletons (valves) preserve well in lake sediments and are good indicators for, among others, climate-driven changes in salinity. However, diatom taxonomy and species concepts have changed a lot in recent decades, making it sometimes difficult for non-taxonomists to know which species are concerned in different published studies. This paper provides the currently accepted taxonomic names of the 310 specific and infraspecific diatom taxa reported from Lake Naivasha and its satellite lakes to date, together with their synonyms used in literature concerning these lakes as well as other, commonly used synonyms. Further, a short overview is given of the history of diatom research conducted on materials from Lake Naivasha and its satellite lakes. The present checklist may facilitate the identification and interpretation aspects of future diatom studies on the wider Lake Naivasha ecosystem and on other East African lakes that are less well studied.


Introduction
Lake Naivasha is located at about 1885 m a.s.l. (above sea level) in the central valley of the Eastern (Gregory) Rift in Kenya between 0°43'08"S and 0°49'57"S and between 36°16'54"E and 36°25'46"E ( Fig. 1). With a surface area fluctuating around 135 km 2 , Lake Naivasha is, besides Lake Baringo, the only large freshwater lake in Kenya's portion of the Eastern Rift Valley, and consequently an important source of freshwater in the rift-valley region. It has two smaller satellite lakes, which, depending on the lake level, can be confluent with it or separated by a narrow sill: Lake Oloidien with a surface area of 5.1 km 2 at its southwestern corner, and Crescent Island Crater (1.9 km 2 ) along its eastern shore. Its third satellite lake is Lake Sonachi, also referred to as Crater Lake (e.g., Rich 1932) or Green Crater Lake (e.g., Damnati et al. 1991), is a very small saline crater lake (0.14 km 2 ) situated to the west and receiving underground water supply from the main basin of Lake Naivasha (MacIntyre and Melack 1982;Verschuren 1999a).
While the main basin of Lake Naivasha is hydrologically open, fed by the Malewa and Karati Rivers in the east and the Gilgil River in the north, and groundwater outflow to the south and the southeast, Lake Oloidien is hydrologically closed (Gaudet and Melack 1981;Verschuren et al. 2000b). Without its own river inflow, this lake depends on local rainfall and either direct confluence or subsurface inflow from Lake Naivasha . Crescent Island Crater Lake is hydrologically open through its direct confluence with the main lake. Only during periods of severe lowstands, when the connection with the main lake is fully interrupted, does it become a hydrologically closed system (Verschuren 2001; Van der Meeren et al. 2019).
During lake highstands, such as first recorded in 1897 but also the present-day situation after two episodes of strong transgression in 2011, 2012 and 2020, Lake Oloidien is broadly confluent with Naivasha and contains fresh water. However, when separated from Lake Naivasha during lake lowstands, it develops higher salinity because it then depends on local rainfall and subsurface inflow, while water losses are almost entirely due to evaporation ). Lake Sonachi is normally a strongly saline-alkaline ('soda') lake, but substantial changes in salinity during past episodes of wetter and drier climate conditions have also been reported in historical times . This implies that freshwater as as well as inland saline communities of aquatic biota, among others of diatoms, can be found in the lakes of this aquatic system, making Lake Naivasha and its satellite lakes ideal for paleolimnological research involving both climate reconstruction and long-term ecological dynamics (Verschuren et al. , b, 2000aMergeay et al. 2011; Van der Meeren et al. 2019; Van der Meeren and Verschuren 2021).
However, diatom taxonomy and species concepts have changed a lot since species description in this group of unicellular algae started in the 19 th century. After a period of species lumping in the 20 th century, the end of the last century saw the erection of new and restoration of many formerly described genera and species mainly due to better microscopes. Moreover, many new species were discovered, including tropical African taxa which had previously been assigned to European and/or North American taxa due to the use of identification guides from these north-temperate regions. This makes it often very difficult for non-taxonomists to know exactly which diatom species are involved in the older and the more recent literature on Lake Naivasha. Because of the importance of Lake Naivasha in East African paleoecological and paleoclimate Figure 1. A location of Lake Naivasha in Kenya, East Africa B bathymetric map of Lake Naivasha and its satellite Lakes Oloidien, Sonachi and Crescent Island crater, relative to a lake-surface elevation of 1885.8 m above sea level. White arrows show the direction of the groundwater flow. From , as modified after Gaudet and Melack (1981) and Åse et al. (1986). studies, and the fact that diatoms have proven to be good indicators (so-called 'proxies') for changes in salinity (and nutrients) and reconstruction of past environmental situations, we found it opportune to make a checklist of all the diatoms reported up to now from Lake Naivasha and its three satellite lakes. Notably, the present checklist covers both recent phytoplankton and periphytic collections as well as fossil diatom valves recovered from sediment cores. The current taxonomically accepted names are provided together with their synonyms used in different studies as well as references to the publications or materials in case of unpublished results.

Material and methods
The material used for the present checklist is twofold. On the one hand, all literature data known to us, published between 1932 and the present, among others Rich (1932), Bachmann (1938), Richardson and Richardson (1972), , Verschuren et al. (1999a), Verschuren et al. (1999b), Verschuren et al. (2000a), Verschuren et al. (2000b), Cocquyt and De Wever (2002), Stoof-Leichsenring et al. (2011 and Owino et al. (2020). On the other hand, counts of fossil diatom assemblages carried out on sediment cores from Naivasha, Crescent Island Crater, Oloidien and Sonachi, whose results are either unpublished, or were used for publications focusing on paleoenvironmental reconstruction that did not include full species lists.
The sediment sequences covered in this paper are listed in Table 1, with citation of the publication providing the most detailed information on their collection and characteristics.
All sediment cores were recovered from an anchored boat or platform using a combination of gravity coring and piston coring, except for NS93.2-F which was recovered using freeze coring (Verschuren 1999a).

Historical overview of diatom sampling and studies in Lake Naivasha
The first reports on diatoms from Lake Naivasha and its satellite lakes date back to the 1930s. Rich (1932) investigated samples collected between 18 April and 7 July 1929 by Miss Penelope Jenkin during the Percy Sladen Expedition to Kenya's Rift Valley Lakes (Jenkin 1936). From the 13 Naivasha samples she investigated, she only reported diatoms in three samples from near the mouth of the Gilgil River at the north end of the lake. In sample number 135 (surface) and number 193 (water over Ceratophyllum) Rich (1932) mentioned one and three diatom taxa respectively, and 30 diatom taxa in sample number 138 (mud) of which a diatom preparation was made. Besides the 30 taxa from the main basin of Naivasha, Rich (1932) reported one diatom, Rhopalodia ventricosa from one of the two samples collected in Lake Sonachi (referred to as 'Crater Lake'). Rich (1933) expanded the species list of Lake Naivasha by two taxa observed in samples taken in November 1930 andFebruary 1931. During the "Mission scientifique de l'Omo", organized by R. Jeannel and C. Arambourg, plankton samples from some Rift Lakes in Kenya were taken by hydrobiologist P.A. Chappuis, at the end of this expedition on the return from the Omo Valley (Ethiopia) to Mombasa (Kenya) from where the expedition members embarked back to France (Lester 1933). From the phytoplankton sample taken in Lake Naivasha on 12 April 1933 and which contained a lot of detritus from plant remains, Bachmann (1938) reported 14 diatom taxa. From the sample taken in 'Crater Lake' (= Lake Sonachi), which was dominated by Arthrospira platensis Gomont [as Spirulina platensis (Gomont) Geitler], Bachmann (1938) mentioned 4 diatom species.
By the end of the 1930s, 43 diatom species and infraspecific taxa were known from Lake Naivasha, distributed among 15 genera sensu lato; for Lake Sonachi this was only 5 species, belonging to five genera. However, Rhopalodia ventricosa was the only species from Lake Naivasha reported by both Rich (1932) and Bachmann (1938). About thirty years later, Richardson and Richardson (1972) reported 112 diatom taxa from a 28-meter long sediment sequence from Crescent Island Crater, covering the last ca. 9000 years and obtained by combining mutiple sediment cores taken between 30 December 1960 and 2 January 1961, and analyzed at 20-cm intervals. These taxa, 96 species and 16 varieties, are distributed among 25 genera, based on the taxonomy used. Of the 96 species, 15 are referred to as "cf." and 5 as "sp.".  studied six phytoplankton net samples from Lake Naivasha collected by herself on 5 December 1979 and by J. Kalff on 8 February,18 March,19 April, 2 May and June 1980, as well as one littoral mud sample collected by herself on 5 December 1979 and two bottom samples collected by C. Barton. From Crescent Island Crater she analyzed one phytoplankton net sample and one bottom mud sample collected by herself and C. Barton respectively. Finally,  reported on three samples from Lake Sonachi collected on 6 December 1979: a phytoplankton net sample, littoral mud and scrapings from dead trees. From this total of 11 samples,  reported 20 genera, 70 species, more than 14 varieties, two forms, one taxon with confer ("cf."), one taxon with affinity ("aff.") and two unknown species ("sp."). The exact number of varieties cannot be tracked down as it is not clear how many are included in the mentioned "and varieties".
In the 1990s, the growing interest in climate change in East Africa and worldwide led to several coring campaigns in Lake Naivasha and its satellite lakes followed by intensive paleolimnological studies of the recovered sediment cores (Verschuren et al. , 2000a. Diatoms were one of the paleoecological proxies studied in a 8.22-m long composite sediment core (NC93) from Crescent Island Crater covering the last ca. 1650 years (Verschuren et al. 2000a; Van der Meeren et al. 2019), and in a shorter sediment core of 71-cm from Oloidien (NO91.1-S) covering the last ca. 200 years . For Lake Sonachi diatom studies were performed on 50 samples from a 37.2-cm freeze-core (NS93.2-F) collected in 1993 . Diatoms from a sediment core taken in the main basin of Naivasha (NM93.1-S) were also investigated by one of us (CC) but these results have not been published to date.
The above mentioned paleoecological studies inspired Cocquyt and De Wever (2002) to study the epiphytic diatom communities in Lake Naivasha and its satellite lakes. For this purpose, herbarium specimens of aquatic plants collected in Lake Naivasha between 1909 and 1933, and kept in the collections of the Meise Botanic Garden (BR), were investigated: Nymphaea caerulea Savigny, Potamogeton pectinatus Linnaeus, P. schweinfurthii A.Bennett and Najas horrida A.Braun ex Magnus. Additional materials of Nymphaea caerulea and Cyperus laevigatus Linnaeus collected in 1999 in Lake Naivasha and Lake Sonachi respectively, were studied .
Based on microscopic (i.e., morphological) analyses of fossil diatoms in core NSA-3 from the main basin of Lake Naivasha, Stoof-Leichsenring et al. (2011) reported 39 diatom species, while in follow-up molecular analyses these authors could identify 28 different diatom haplotypes in bulk sediment samples . All haplotypes that differed < 8% to a species-specific GenBank sequence (corresponding to a similarity of 92-100%) were assigned to that species. Haplotypes with a similarity below 92% to any reference sequence, were not assigned to a species, but to the respective diatom family. This implied that the genetic survey did not reveal all species morphologically identified. However, all genetic information and morphological data were highly correlated but not fully identical . It is clear that the African diatom flora is still not well known either morphologically or molecularly.
This brief overview of the diatom research on Lake Naivasha and its satellite lakes covers only taxonomic relevant publications for diatoms ( Table 2). The numerous and important studies done on phytoplankton biomass, dynamics, chlorophyll, etc. and papers on algae other than diatoms, such as Kalff and Watson (1986), Harper et al. (1993Harper et al. ( , 2003 and Ballot et al. (2009), are not included in the present overview. However, the diatom species names mentioned in those ecological studies concern the most common diatoms, of which the taxon names can be found in this checklist either as a currently accepted name or as a synonym.

Results and discussion
Over the last decades, from the earliest start of diatom investigation of the Lake Naivasha system up to now, a total of 205 different species and infraspecific taxa have been reported: 132 from the main basin of Lake Naivasha, 123 from Crescent Island Crater, 43 from Oloidien and 15 from Sonachi (Table 2). When including unpublished studies of sediment core material this number increases to 310 (236, 149, 43 and 52 respectively) distributed over 66 genera. Cymatopleura and Rhopalodia are kept as separate genera and the species are not included in Surirella and Epithemia respectively as recently recommended (Ruck et al. 2016a, b;Cocquyt et al. 2018). However, some of the reported taxa are unidentified and referred to as "aff." (3), "cf." (38) and "sp." (14). Probably a number of these belong to already identified taxa and fall within the variability of a species, while others are potentially new to science and should be the subject of further taxonomic research. Taking into consideration only the identified species and infraspecific taxa, 7 taxa (3.4%) are considered to be endemic to tropical Africa (Sub-Saharan Africa without southern Africa), besides 4 pantropical (2.0%) and 2 taxa restricted to the African continent (1.0%). This proportion is very small compared to other tropical lakes such as Lake Tanganyika where in the northern part up to 13.1% of the reported diatoms have a distribution restricted to tropical Africa (Cocquyt 2000). However, the number of tropical African, pantropical and African diatom taxa can increase as the unidentified taxa and those referred to as "aff." and "cf." potentially are taxa with a restricted distribution. Two other remarks should also be noted, namely that it is quite possible that material from Lake Naivasha and adjacent lakes was misidentified, as often European and North American diatom floras were used, and secondly, that diatom species, originally described from tropical Africa, have erroneously been reported from other tropical regions or from temperate regions in Europe and North America. Examples of this second possibility are several Nitzschia species, such as N. accommodata, N. confinis, N. latens, N. spiculoides, N. subcommunis and N. tarda, all described by  from the formerly Albert National Park (Belgian Congo), nowadays the Virunga National Park in the eastern part of the Democratic Republic of the Congo and the Volcanoes National Park in Rwanda. Molecular analysis confirmed the morphological identification of 14 of the 49 species and infraspecific taxa observed in the sediment cores studied by Stoof- . This implies that slightly more than a quarter of the observed taxa are cosmopolitan. The genetically identified species had a higher internal similarity range than those that had been found in taxonomic studies on supposedly cosmopolitan species (Abarca et al. 2014). In addition, there are very few molecular data available of African taxa to serve as a reference library. The remaining three quarters of the reported taxa comprise species with restricted distribution, such as restricted to the tropics, to Africa, or to tropical Africa. This supports our hypothesis mentioned above that the number of tropical African, African and pantropical taxa must be higher than the number obtained by the results of the distribution of taxa present in this checklist.
In the overview below, taxa are listed according to the systematics of Round et al. (1990), with some adaptations to accommodate genera described after its publication. Although this classification is not the most recent one, and major changes have already occurred on higher taxonomic level (e.g. Adl et al. 2018), we believe it gives a clear and workable reference list of the diatom taxa known from Lake Naivasha, especially because many researchers who include diatoms in their research on Lake Naivasha are not taxonomists. The classification given here includes classes, orders, families and genera. Within each family, genera are arranged alphabetically and so are the species and infra-specific taxa within the genera. The authorities are compliant with the International Plant Names Index (2022). The most current used synonyms are given, as well as the synonyms used in the published papers. For each species the literature is cited where this taxon was mentioned for Lake Naivasha and its satellite lakes in the most important publications dealing with diatom taxonomy. With regards to our own unpublished observations, reference is made to the sediment core in which the species was observed. Crescent Island Crater: Richardson and Richardson (1972).
Occurrence. Plankton, bottom mud, sediment core. Richardson and Richardson (1972) distinguish a variety of A. granulata, "A. granulata var. (coarse variety)", which has much coarser areolae than the other valves of A. granulata and varieties observed in the studied sediment core materials. This taxon may be identified as Aulacoseira cf. goetzeana in core NC20. Occurrence. Plankton, bottom mud, sediment core. In NC93, the form curvata was distinguished within this taxon.
Remark. Besides the seventeen above mentioned Aulacoseira taxa, an unidentified species was reported in the main basin by Stoof-Leichsenring et al. (2011, and in NM91.1-S, NM93.1-S and NS93.2-F. In addition, Owino et al. (2020) erroneously mentioned two species with the generic name of Aulacoseira: A schroidera and A ulna. The latter is probably Ulnaria ulna. We have no idea which species is meant by the former but the most similar name is Melosira schroederi (Wołoszyńska 1914: 186, pl. III figs 11, 12, 14) described from Lake Victoria. Observation. Crescent Island Crater: NC20.

Class
Occurrence. Sediment core.
A unidentified Fragilaria sp. was observed in the sediment core NM91.1-S taken from the main basin of Lake Naivasha. However, as the diatom analysis was performed at the beginning of the 1990s before the delineation of many now accepted genera within Fragilaria s.l., we cannot determine the current genus of this species. Observation. Crescent Island Crater: Richardson and Richardson (1972) Observation. Crescent Island Crater: Richardson and Richardson (1972).
Occurrence. Sediment core. Occurrence. Sediment core. The observed valves of this taxon in the materials of NM93.1-S. appear morphologically closely related to Fragilaria nanana and F. tenera, especially the nearly straight valves that are only slightly constricted/deformed mid-valve. Lake Oloidien:   Observation. Crescent Island Crater: Richardson and Richardson (1972 Observation. Main basin: . Crescent Island Crater: . Lake Oloidien:   . 13.
Lake Oloidien: . Lake Sonachi: Cocquyt and De Wever (2002  Observation. Crescent Island Crater: . Main basin: . Lake Oloidien: . Occurrence. Plankton, littoral, bottom mud. Bachmann (1938) reported Cymbella ventricosa Kützing from the littoral zone of Lake Naivasha. According to Guiry and Guiry (2022) Cymbella ventricosa Kützing, 1844 is a nom. illeg. and the taxonomic or nomenclatural status (or both) of this entity is in some way unresolved and requires further investigation. Probably the taxon Bachmann observed is the same species as Encyonema ventricosum reported by .

Gomphonema lanceolatum
Occurrence. Plankton, bottom mud, sediment core. Gomphonema lanceolatum has long been a very common name of a diatom taxon by which various Gomphonema species and multiple forms of Gomphonema affine were referred to (Reichardt 1999). Gomphonema affine is a common species of tropical and sub-tropical regions and sometimes frequently found (Reichardt 1999). For this reason, in this paper we have not put the taxon observed in Lake Naivasha and its satellite lakes in synonymy with Gomphonema grunowii R.M. Patrick & Reimer (1975: 131, pl. 17 fig. 6) as mentioned by Guiry in Guiry and Guiry (2022).  Richardson and Richardson (1972), , NC20. Lake Oloidien: . Lake Sonachi: NS93.2-F. Occurrence. Plankton, littoral, bottom mud, sediment core. Cocquyt and De Wever (2002) reported Gomphonema cf. parvulum from epiphytic materials taken in Crescent Island, the main basin of Lake Naivasha and Lake Sonachi. Crescent Island Crater: NC20. Lake Oloidien: . Occurrence. Plankton, bottom mud, sediment core. Cocquyt and De Wever (2002) reported Gomphonema cf. pseudoaugur from epiphytic materials taken in the main basin of Lake Naivasha and Lake Sonachi. Observation. Crescent Island Crater: Richardson and Richardson (1972), core NC20.
Occurrence. Sediment core. Richardson and Richardson (1972) mentioned the name of this taxon as Navicula seminuloides var. sumatrana.

Genus
Occurrence. Bottom mud, sediment core Tropical African specimens of Amphora libyca (Ehrenberg) Cleve, 1895: 104 (synonym: Amphora ovalis var. libyca (Ehrenberg) Cleve, 1895: 104) were often put in synonymy with Amphora copulata. However, further investigation of the valves observed in Lake Naivasha and its satellite lakes is needed to see if these valves belongs to a cluster of different species. The revision work of the genus Amphora by Levkov (2009) suggests that we may indeed be dealing here with several species, as was the case for Lake Tanganyika where many new species were described. Cholnoky, 1953: 352, fig. 1. Observation. Crescent Island Crater: Richardson and Richardson (1972).

Nitzschia subcommunis
Occurrence. Sediment core. Richardson and Richardson (1972) reported Nitzschia cf. subcommunis from a sediment core taken in Crescent Island Crater. older taxonomy was used for identification. Moreover, it is well known that the more material is studied, the more species and infraspecific taxa will be observed, especially rare taxa. In addition, the present species richness is based only on morphological characteristics. Only a few studies exist at present on the molecular identity of the diatoms observed in tropical Africa. Available genetic data appears to be inadequate for most of the tropical African diatoms as shown by the results of Stoof-Leichsenring et al. (2012) where only less than 30% (14 out of the 49 species) could be more or less linked to a species present in the existing molecular library.
Extensive molecular investigation of the diatoms in Lake Naivasha and it satellite lakes, and in tropical Africa in general, would provide more information on the identity of the observed species and their endemic or cosmopolitan nature. We are convinced that the proportion of reported diatom species with a distribution restricted to tropical Africa (3.4%), to the African continent (1.0%), or to the pantropics (2.0%) based on the present checklist, will increase when molecular data of the observed taxa become available.
The checklist presented here will certainly provide a useful baseline for further diatom research in Kenya, and more generally in tropical Africa, in order to align molecular and morphological identifications.