Soils harbour a great diversity of fungal species that have various ecological functions (Bridge & Spooner 2001; Havlicek & Mitchell 2014). Saprophytic fungi break down dead organic matter and, in turn, fertilise the soil (Setala & McLean 2004). Certain plant fungal pathogens are specifically adapted to infect plants through roots and to spread or survive in soils, while some pathogens affecting tissues of plants growing above the soil also have the ability to survive in soils. Propagules of more specialised below-ground fungi, such as mycorrhiza that form specialised root associations benefitting plant health, can also be found in surrounding soils (Moore, Robson & Trinci 2011). Similarly, propagules of various fungi occurring in different niches and substrates above ground can also be found in soils (Aylor 2003; Taylor & Bruns 1999).

Soil conditions can permit specific fungal species to grow and produce fruiting structures. Soil qualities such as pH and nutrient concentrations, soil types, temperature and humidity may influence optimal growth conditions for species (Rousk et al. 2010). Furthermore, types of vegetation in a particular area such as grasslands and forests, which harbour their own unique fungal communities, serve as inoculum sources for associated soils (Talbot et al. 2014). Similarly, propagules of coprophilous fungi (those closely associated with animal dung) can also be isolated from soil (Richardson 2001).

Fungi occurring asymptomatically within plant tissues are named endophytes and they play diverse roles (Rodriguez et al. 2009). These vary from highly symbiotic relationships, for example, conferring traits such as herbivore resistance to their hosts or boosting growth, to detrimental as is the case with latent plant pathogens. Other fungi do not have any specific known function, or simply have the ability to overcome plant resistance and infect the tissues (Rodriguez et al. 2009).

Endophyte communities can differ between plant tissues; for instance, some endophytes are better specialised to infect leaves (Khare, Mishra & Arora 2018). Roots also often harbour very specialised endophytes that have functions beneficial to their host (Sabra et al. 2018). Root endophytes can include fungi that infect through aerial tissues or from surrounding soils and often play beneficial roles for plant health (Glynou et al. 2016; Rodriguez et al. 2009). However, certain fungi have the ability to occur across various plant tissues.

Plant pathogens have varying biological compositions (Agrios 2005). As already mentioned, latent pathogens can reside inside plant tissues without causing disease symptoms until triggered by specific stimuli such as stress conditions (Slippers et al. 2007). Other pathogens do not follow this strategy and can only cause disease symptoms. Certain pathogens are also adapted to only infect aerial tissues or below-ground tissues such as roots. However, survival strategies of pathogens may enable them to survive in other substrates such as soil or water (Hargreaves et al. 2015; Havlicek & Mitchell 2014; Lareen, Burton & Schafer 2016).

The rhizosphere is an interface consisting of a zone of soil that is associated with the roots (Hiltner 1904). Often this area contains exudates of the plant, which select for specific fungal communities to be present (Lareen et al. 2016; Sasse, Martinoia & Northen 2018). This area has an important function where fungi, as well as other microbial organisms, can facilitate the movement of nutrients (Mommer, Kirkegaard & Van Ruijven 2016; Schippers, Bakker & Bakker 1987). Other functions include protection against organisms feeding on roots, or plant pathogens (Moore et al. 2011).

Grazing lawns are unique ecological phenomena (McNaughton 1984). Areas of grazing lawns contain natural vegetation significantly different from the surrounding area. The vegetation has a high nutritional value and productivity, attracting animals that in turn fertilise the soil again (Verweij et al. 2006). It is also known that these areas are self-sustaining although the mechanisms behind this phenomenon are still unknown (Archibald 2007; Hempson et al. 2015). Grazing lawns can form part of a catena system, such as the one forming the topic of this special issue. A catena consists of a serial soil group sequence from foothills to the crest, and that originated from the same geological material (Brady & Weil 2002).

The Kruger National Park (KNP) is one of the largest game reserves in Africa (Carruthers 2017). It covers the north-eastern part of South Africa and now forms part of the Great Limpopo Transfrontier Park, linking it with the Gonarezhou National Park in Zimbabwe, and the Limpopo National Park in Mozambique. Recently, four research ‘supersites’ have been identified and established in KNP, with each of these supersites representing catenas with distinct geological, ecological and climatic features (Rughöft et al. 2016; Smit et al. 2013). Such a site represents an ideal opportunity to determine if fungal communities will be uniform over niches and soil conditions within the system, or if the catena will harbour a complex and differing fungal community.

The study focuses on characterisation of the fungal communities from the root ecto- and endo-environments of one plant species which occurred within the different soils and soil conditions of the grazing lawn zone and the neighbouring hillside zone of the catena (Theron, Van Aardt & Du Preez 2020; Vermeulen, Casson & Swart 2020). Whether different plants in the catena will have similar specialised rhizosphere fungal communities was also investigated, as it would add to the complexity to properly conserve and manage the catena site should variations be observed.

A catena system, such as the Stevenson–Hamilton granite supersite in the KNP, represents an ideal system to study the fungal communities that are associated with plant roots in different soil types and conditions and from different plant species. Within only approximately 500 m, a range of soil types and conditions are found that was also reflected by differences in the plant community (Theron et al. 2020). Similarly, marked differences in the fungal communities existed in the plant–soil interface. Unique MOTUs and shifts in frequencies were observed between the inside (endophytes) and outside (rhizosphere) communities of S. cordifolia roots, and also between two different soils. Furthermore, differences were observed between the rhizosphere soils of three different plant species in one zone, although the dominant MOTUs were relatively similar.

Fungi specialised to occur in different substrates, for example, soil compared to plant tissues, are different because they require different dissemination strategies and may also have different functional roles (Bayman et al. 1997; Carroll 1988; Hardoim et al. 2015, Moore et al. 2011; Talbot et al. 2014; Yang et al. 2018). The root rhizosphere is also known to usually harbour selected species either from the general soil environment or the root, and are often specialised according to the plant species (Berlanas et al. 2019; Mohanram & Kumar 2019). Nonetheless, levels of overlap do occur (Tedersoo et al. 2016). Our results thus reflected previous literature and represent the first such study for the KNP. It also represents the first evidence regarding how fungal communities differ within a catena system.

Alternaria and Fusarium include species that are endophytic, saprobic in soils and pathogenic or beneficial to plants, and that occur in numerous habitats (Leslie & Summerell 2006; Woudenberg et al. 2013). Such cosmopolitan fungi can be dominant or omnipresent in communities because of their ability to easily colonise or disperse, as opposed to more specialised fungi that may not always have a rapid growth rate and that have evolved with their hosts or niche (Vujanovic et al. 2006). While such dominant MOTUs of Alternaria and Fusarium were detected, shifts in their frequencies occurred between different substrates (e.g. Alternaria was dominant in rhizospheres but less so as an endophyte) and soils (Fusarium was one of the dominant groups in all collections except in the slope rhizosphere of S. cordifolia; Fusarium was also almost five times as dominant as a root endophyte of S. cordifolia in the grazing lawn area compared to the slope). Plants that were selected were all healthy, and the presence of Alternaria within plants was latent and in low numbers, and the higher abundance of Fusarium could be because of non-pathogenic Fusarium species. An interesting result was that other fungi that can occur both in plants and soils, for example, Curvularia, Penicillium and Aureobasidium (Domsch, Anderson & Gams 1980; Haas et al. 2016) were selectively detected, and others were not detected at all, such as cladosporiod fungi.

Knowledge regarding the ecological functions of fungi associated with different soil types and those associated with plants is virtually non-existent for natural and pristine ecosystems in South Africa. The ecological functions of these fungi can only be guessed from the existing literature. Intensive studies are needed to elucidate the functions of the various fungi characterised in this study, and how changes will impact them and their associated hosts. The more rare fungal groups could be more specialised and sensitive, but without more surveys it will be difficult to identify them as important in the ecosystem or if they are promoting plant and soil health (Frac et al. 2018), as opposed to just being able to infect at a low frequency.

Sida cordifolia is not native to South Africa, but a declared invasive weed (Morris, Witkowski & Coetee 2011). It was chosen because of its ability to grow across the different soils of the catena system. Nonetheless, the communities involved with the rhizospheres and roots in the two sites of the catena showed telling variation. The invasive plant S. cordifolia appeared to attract only half of the number of MOTUs present in its rhizosphere compared to those in the native relative M. acuminata, and the other native plant K. angustifolia. However, more extensive sampling will have to be performed to really prove this statistically.

Various factors could possibly explain the differences observed between S. cordifolia and the two native herbs. Certain plants have been shown to have a stronger rhizosphere effect than others (Gomes et al. 2003), and what has been observed in this study could merely be such an effect. No studies have been conducted for comparing the microbial rhizosphere community of invasive plants, or even non-native plants, with those of native plants in the same area. Nonetheless, it could be hypothesised that the ability to attract a functional rhizosphere microbial community that benefits the plant will aid the establishment or invasiveness of a plant (Coats & Rumpho 2014), similar to what has been found with other types of microbes such as mycorrhiza (Nuñez & Dickie 2014; Rodríguez-Echeverría et al. 2009). Furthermore, it has been shown that some invasive plants can change the soil microbiome around their roots to their benefit (Dawkins & Esiobu 2017; Policelli et al. 2019). What has also been found in other groups of plant-associated microbes, such as endophytes, was that the endophytic community of non-native plants were composed of endophytes with wide host ranges and large geographical locations (cosmopolitan fungi), while the native plants had more specialised and diverse endophytes including those with narrow host ranges (Clay et al. 2016; Hoffman & Arnold 2008; Newcombe et al. 2009). Whether the native plant species in the KNP have closer evolved endophytic and rhizosphere fungi compared to introduced plants will have to be studied further.

Many of the MOTUs detected in all the samples were assigned names of genera known to include plant pathogens, such as Fusarium and Alternaria. However, these genera include a wide diversity of species with diverse ecological roles and life strategies, including pathogens, non-pathogens or latent pathogens (pathogens that can hide as endophytes) and endophytes. It is difficult to assess if the DNAs detected from the samples represented pathogenic species or not based on the limited sequence data, especially because the ITS regions commonly used in Next Generation Sequencing (NGS) studies, are known to be incapable of differentiating between species of these genera (Schoch et al. 2012).

An interesting result is that members of other important pathogen groups have been detected. Molecular Operational Taxonomic Units in the Botryosphaeriaceae and an MOTU from the Teratosphaeriaceae were detected as root endophytes. These fungi are not recorded as soil fungi and are mostly known from aerial tissues of woody plants, where they have latent pathogenic life stages before causing various disease symptoms (Crous, Wingfield & Groenewald 2009; Finlay & Clay 2007; Marsberg et al. 2014; Pillay et al. 2013; Sieber 2007; Slippers & Wingfield 2007). While their presence in the rhizosphere could be attributed to the presence of spores, the prominence of especially two MOTUs of the Botryosphaeriaceae (Botryosphaeria and Lasiodiplodia) from the roots of the herbaceous plant S. cordifolia is interesting. An MOTU that was prominent in all of the rhizosphere samples had the assigned name of Boletus (Boletaceae). The MOTU was not present in the root endophyte samples. Members of Boletaceae are important ecto-mycorrhizal partners of plant roots and can easily be seen by the production of mushroom-like fruiting bodies (Goldman & Gryzenhout 2019). South Africa does not have reported indigenous ectomycorrhizal fungi, while the only indigenous bolete species is Phaeogyroporus sudanicus or the bushveld bolete (Goldman & Gryzenhout 2019; Gryzenhout 2010; Tonjock et al. 2020; Van der Westhuizen & Eicker 1994). While the fungus is known to be ectomycorrhizal (Thoen & Ducousso 1990, as Phlebopus sudanicus), its host range throughout South Africa, including the KNP, has not really been fully established. This bolete has been observed in the KNP by the first author, and it is thus possible that the MOTU could represent this species, especially so because there are no Phaeogyroporus sequences currently present in the UNITE database (https://unite.ut.ee/). The absence of the MOTU from inside surface sterilised roots could indicate that it does not have ectomycorrhizal associations with the three plant species.

Ecto-mycorrhizal fungi such as boletes are more easily observed than other groups of mycorrhiza because they produce visible fruiting bodies above soil. The detection of a bolete sequence raises the question if other native ectomycorrhizal partners to indigenous plants in the KNP do not in actual effect exist. This is especially so because extensive surveys for the presence of such fungi have not yet been conducted in the KNP. Furthermore, species of some plant genera that are known to have ectomycorrhizal partners, such as Albizia, Terminalia and Combretum in neighbouring countries such as Zimbabwe (Tsamba et al. 2015) and even up to central Africa (Eneke, Njoh & Egbe 2018; Härkönen, Niemelä & Mwasumbi 2003; Härkönen et al. 2015), occur in the KNP. Related species such as Colophospermum mopane occur in the KNP, which belong to Detariodeae (Fabaceae). This family includes keystone genera known to have ecto-mycorrhizal partners in the iconic and widespread Miombo woodlands that are spread from Zimbabwe further north into Central Africa (Palgrave 2015). In fact, members of these named genera are present in the catena (Theron et al. 2020). Studying these special fungi is vital because they play an integral role in the health and resilience of their associated plants, and should they disappear for some reason, it will have grave consequences on plant survival in the KNP.

Other macrofungal MOTUs (fungi that can be seen without the need of a microscope) that were detected from all of the rhizosphere samples included the mushroom genera Agaricus and Amanita. Agaricus is known to be saprophytic while many species of Amanita are known ecto-mycorrhizal plant partners (Goldman & Gryzenhout 2019). However, certain Amanita species, including South African native species such as A. veldiei, are saprophytes (Goldman & Gryzenhout 2019). An MOTU assigned as Ganoderma was present in the rhizosphere samples of the three plant species from the slope. Ganoderma species are common throughout South Africa and include wood rotting bracket fungi that often are pathogens of plants (Goldman & Gryzenhout 2019; Tchoumi et al. 2019). A number of species of these genera occur in South Africa (Tonjock et al. 2020), and conducting more detailed surveys in the KNP to ascertain what species occur in the park will prove to be useful.

For the data analysis pipeline used in this study, the UNITE database (Nilsson et al. 2019) was used for taxonomic assignment. This database is better curated than general databases such as Genbank, and widely used for fungal environmental sequencing (Nilsson et al. 2019). However, taxonomic assignments must always be verified because the assignment process may not truly reflect the correct taxonomic identity even at the genus level, or may not reflect current taxonomies (Tonjock et al. 2019). The ITS region is also known to not always distinguish species in some genera, although it is still widely used as the barcode and minibarcode for fungi (Schoch et al. 2012). In practice, complicated taxonomic groups such as Phoma and Epicoccum cannot be distinguished based only on ITS data in routine ITS-based environmental sequencing studies (Tonjock et al. 2019). The conclusions from results of this study must thus be made with care considering that even generic names may not be accurate. However, in some cases, associations can be made if members of a particular family or genus have similar ecological attributes, such as the Boletaceae. In other cases, such as for Fusarium (Leslie & Summerell 2006), different species often have certain ecological roles (e.g. pathogen or latent pathogen or non-pathogenic, or pathogen with saprophytic survival phase). It is thus possible that an MOTU assigned as Fusarium (or previously used sexual names such as Gibberella and Haematonectria) from different niches and substrates may in fact represent different Fusarium species with different ecological roles.

Results from this study revealed a complex fungal community associated with the plant–soil interface within a catena system. This is despite the fact that the two sites occurred within a 500 m area. Results from other studies showed the effect of the different geological and hydrological processes on the plant and animal communities, while the biological communities also affect each other (Janecke 2020; Janecke & Bolton 2020; Theron et al. 2020; Vermeulen et al. 2020). This study also showed the need to include fungi in studying these interactions more thoroughly. Fungi provide fundamental ecosystem services as key saprophytes, plant degraders, pathogens and those providing benefits to the plant as mycorrhiza, endophytes or rhizosphere partners.

The complexity of fungal communities differing already in a small component of the entire ecosystem of the catena indicates that such a system with its differing communities will be sensitive to change and disturbances, both in the short and long runs. Similar results have also been obtained by looking at the bacterial communities (Vermeulen et al. 2020). This is despite the fact that the overall animal and plant communities may appear more uniform and thus do not indicate the importance to specifically also define differences of microbial communities on a micro-ecological scale. The same will be true for fungal communities associated with other plant species and soil types of the KNP.