Microorganisms have been able to not only colonize but also thrive under unique or extreme environmental conditions characterizes by low/high pH, temperature, salt or pressure. Examples of extreme environments are soda lakes which are characterized by high alkalinity (with pH values ranging between 9 – 12) while Na+ concentrations can reach saturation. Their surface area fluctuates due to extensive evaporation attributed to the intense sunlight and low levels of precipitation experienced where they are located. Despite the extreme physicochemical conditions in the soda lake ecosystems, a high level of species diversity has been reported (Lanzen et al., 2013; Oren A. 2008; Lozupone and Knight, 2007, Mesbah et al., 2007). These habitats exhibit higher productivity as compared to freshwater bodies (Grum-Grzhimaylo et al., 2016).
Whereas most of the studies on extremophiles have focused on prokaryotes, there are reports of alkaliphilic and alkalitolerant fungi isolated from soda lakes and soda soils in different parts of the world (Orwa et al., 2020; Grum-Grzhimaylo et al. 2013a; 2013b; Oren and Gunde-Cimerman, 2012). Different species of black yeast have been isolated from hyper-saline waters of solar saltans (Gunde-Cimeman et al., 2009; 2000). Different genera, including Cladosporium, Aspergillus, Penicillium, Alternaria and Acremonium sp. have been reported to exist as either moderately or weakly alkali tolerant species in saline environments (Grum-Grzhimaylo et al., 2013b). Isolates affiliated to Chaetomium aureum, C. flavigenum, Emericella nidulans, and Eurotium amstelodami have previously been isolated from the Dead Sea (Buchalo et al., 2000). Orwa et al., (2020) describe isolates spread over 18 fungal genera namely Aspergillus, Penicillium, Acremonium, Phoma, Cladosporium, Septoriella, Talaromyces, Zasmidium, Chaetomium, Aniptodera, Pyrenochaeta, Septoria, Juncaceicola, Paradendryphiella, Sarocladium, Phaeosphaeria, Juncaceicola and Biatriospora from Lake Magadi in Kenya. Other reports include Chaetomium globosum from the Dead Sea as well as saline habitats of Wadi El-Natrun (Perl et al., 2018), Sarocladium kiliense from Lake Sonachi in Kenya (Ndwigah FI, 2017).
High-throughput sequencing allows rapid estimation and identification of microorganisms without cultivation (Tedersoo et al., 2015). Using this apprach, a high prokaryotic and eukaryotic diversity has been reported from several alkaline lakes such as Magadi in Kenya (Salano et al.,2017; Kambura et al., 2016), Ethiopian soda lakes (Lanzén et al. 2013), Central European hypersaline lakes (Keresztes et al. 2012) and sediments from Tibetan Plateau (Xiong et al., 2012). Therefore, a sequence-based approach has made it easier to understand diversity and structure of microbial communities in diverse environments (Han et al., 2017; Valenzuela-Encinas et al., 2008). Most of the next-generation sequencing technologies used in diversity studies have an amplification step. The earliest polymerase chain reaction (PCR) primers to gain wide acceptance in fungal studies were for the Internal Transcribed Sequences (ITS) described by White et al., (1990) and thereafter modified by several researchers (Scoch et al., 2012; Martin, K.J., Rygiewicz, P.T., 2005; Gardes M and Bruns TD, 1993). However, these primers have been reported to have poor resolution at lower level (Cavender-Bares et al., 2009) or are not good at resolving taxonomic groups that have highly hypervariable ITS regions (Nilsson et al., 2016; Thiéry et al., 2016; Tedersoo et al., 2015; Schoch et al., 2012; Stockinger et al., 2010).
Besides the ITS region, the small and large subunits of the rRNA gene have been targeted for amplification in fungal diversity studies (Xue et al., 2019; Tedersoo et al., 2015). Several group-specific 18S rRNA gene primers have been reported (Lefevre et al., 2010; Lee J, Lee S,Young JPW, 2008; Lazarus KL and James TY, 2005). However, coverage as well as phylogenetic resolution to lower taxonomic levels is always a challenge especially when dealing with less explored habitats. In this study, we designed a new set of primers for next generation sequencing and tested them using different samples collected from different soda lakes in Kenya. The main objective was to explore whether fungal diversity varies between lakes Magadi, Elmenteita, Sonachi and Bogoria and across each lake due to differences physicochemical parameters. The study provides new insights on the spatial diversity across various soda lakes and with varying physicochemical parameters.