Research article
Mirroring the effect of geological evolution: Protist divergence in the Atacama Desert

https://doi.org/10.1016/j.gloplacha.2020.103193Get rights and content

Highlights

  • Protist diversity in different habitats of the Atacama Desert is distinct and divergent from other regions on Earth

  • Due to the isolation of habitable microenvironments the Atacama region forms a center of radiation of protists

  • Time scales of the evolution of protists can be related to geological/tectonic events

Abstract

Unicellular eukaryotes, also called protists, are potentially fast evolving organisms. The small size of protists, their fast reproduction rate and ability to form cysts as well as their adaptability to extreme conditions allow them to associate to endemic animals, plants, saline lakes and soil even in extremely arid systems. These properties make unicellular eukaryotes ideal model organisms to combine studies on evolutionary processes of very different groups of organisms and across very different time scales comprising even geological ones. The hyperarid Atacama Desert offers a study area unique on Earth, where a predominantly arid climate was present for millions of years.

A comprehensive analysis of the diversity of unicellular eukaryotes in different habitats (endemic desert plant phyllosphere, the gut of endemic darkling beetles, isolated hypersaline waters) revealed a dataset distinct and divergent from other regions on Earth. We used standard isolation and cultivation protocols to elucidate divergence patterns for a variety of very different and independent taxonomic groups of protists such as gregarines and ciliates among alveolates, placidids among stramenopiles and choanoflagellates among opisthokonts. The ability to rapidly adapt to extreme environments, which enhance a fast divergence rate at high UV radiation, has only been reported for prokaryotes up to now. The establishment of arid to hyperarid conditions in the Atacama Desert about 20 Ma ago has obviously led to an isolation of protist populations followed by a radiation of species. There are only a few regions on Earth with similar extreme salinity conditions reducing the chance of an exchange between protist populations. Divergence patterns in unicellular eukaryotes in very different phylogenetic groups independently mirror the effect of geological evolution and climate variability during the Neogene.

Introduction

Recent fundamental studies of species diversity in surface waters of the oceans revealed protists (unicellular eukaryotes) to be the genetically most diverse group of organisms (e.g. de Vargas et al., 2015), which seems to be true also for terrestrial systems (Geisen et al., 2015; Venter et al., 2017). Still today, our understanding of the processes leading to this enormous diversity is rather poor. The high diversity of microbial eukaryotes forms an essential basis for understanding the evolution of multicellularity (King et al., 2008; Fairclough et al., 2013; Ratcliff et al., 2013). This is why protists have become important model organisms for experimental evolutionary studies (e.g. Fairclough et al., 2013; Ratcliff et al., 2013).

Evolution at the basis of the tree of life has been fascinating scientists for a long time(e.g., Margulis et al., 1990; Berney and Pawlowski, 2006; Parfrey et al., 2011). Reconstructing the phylogenetic tree that unites all lineages of eukaryotes is still a grand challenge (Hinchliff et al., 2015). The difficulty in defining homologous characters across the very different lineages makes it extremely difficult to resolve evolutionary processes and hence time scales. The incompleteness of consistent paleontological records of the delicate single-cell organisms which form the basis of the tree of life, makes calibration of evolutionary time scales imprecise. However, recent molecular biological studies provide a framework for a preliminary understanding of the timing of early eukaryote diversification, although estimated time scales differ greatly between the different investigations (e.g. Pawlowski et al., 1997; Berney and Pawlowski, 2006; Hinchliff et al., 2015).

Until recently, several protistologists have assumed that single cell eukaryotes as microbial organisms should be potentially homogeneously and globally distributed due to supposed missing biogeographies and low geographical heterogeneity (Finlay, 2002). However, an increasing number of scientists lead by the ciliatologist Wilhelm Foissner (e.g. Foissner, 2006, Foissner, 2007) has questioned the ubiquity model and proposed a so-called moderate endemicity model (e.g., Foissner, 2007; Weisse, 2008). Recently, studies based on next-generation sequencing support this idea: protists are extremely heterogeneously distributed in most aquatic and terrestrial habitats, even with local heterogeneities (de Vargas et al., 2015; Geisen et al., 2015).

However, it is unclear which processes have led to this enormous biodiversity. Investigating Earth evolution at the dry limit offers a unique research area to shed light on evolutionary processes and molecular substitution rates of protists. The extreme and distinct environmental conditions select for specific species molecular adaptations, supported by the well-defined fragmentation of the communities and populations by separation due to landscape and climate evolution in isolated populations (e.g. Gillespie and Roderick, 2014). Climatic thresholds that allow for a species migration may be different on species level. Unique to the research area is the fact that arid to hyperarid conditions in concert with high UV radiation create almost sterile conditions, especially in the core region of the Atacama (e.g., Azua-Bustos et al., 2012; Neilson et al., 2012; Valdivia-Silva et al., 2012), and spatially separate populations for different periods of time. The (hyper-) aridity of the Atacama Desert is mainly due to its geographic position in the subtropical high-pressure belt with its stable climate since the Late Jurassic (Hartley et al., 2005), the rain-shadow effect regarding Atlantic moisture transport established with the uplift of the Andes (Houston and Hartley, 2003), and to the restriction of humid onshore winds with the establishment of the cold Humboldt current in the Pacific (Rundel et al., 1991). Testing the mutual evolutionary relationship between biological evolution and geological (earth surface processes) processes, we aim to characterize thresholds for biological colonization (Fig. 1). In achieving these goals, we foresee major contributions to emerging concepts of evolutionary lag time (e.g. Guerrero et al., 2013), the interplay between geographical barriers and species migration in response to climate change (e.g. Burrows et al., 2014), species diversification in response to climate and geological processes (e.g. Gillespie and Roderick, 2014), and biogeomorphology (e.g. Corenblit et al., 2011).

The onset of aridity in the Atacama Desert is matter of an ongoing debate (e.g. Dunai et al., 2005; Evenstar et al., 2017; Ritter et al., 2018a; Hartley and Chong, 2002; Alpers and Brimhall, 1988). However, hyper-aridity is considered to be characteristic for parts of the Atacama Desert (between 21°–19°S in the Coastal Cordillera and partly Central Depression) since Miocene times (or even earlier Oligocene/Eocene, e.g. Dunai et al., 2005; Ritter et al., 2018a, Ritter et al., 2018; Evenstar et al., 2017). Subsequent expansion of arid conditions and intensification towards hyperaridity progressively expands from this core in all directions (Ritter et al., 2018a, Ritter et al., 2018). Therefore, hyperarid conditions in the Andean foothills to the east post-date the Miocene onset in the driest parts (Hartley and Chong, 2002). Long-term predominant arid to hyperarid climate was frequently punctuated by ‘wetter’ periods (still arid), that largely coincide with global climate events (e.g. Zachos et al., 2001; Jordan et al., 2014; Evenstar et al., 2017; Ritter et al., 2018).

Topography and climate gradients in the Atacama Desert may significantly control the recent distribution of organisms (Picard et al., 2008). Its extension is restricted by the Pacific Ocean to the west, and the rising Andes to the east, and covers the area from southern Peru in the north to the area around La Serena (Chile) in the south. Within this study, we will focus on the northern Atacama Desert, adumbrate by the 150 mm/yr precipitation isohyet (Fig. 2; Houston, 2006). Topography separates different habitats and strongly reflects climate conditions (‘aridity’). The Coastal Cordillera acts like a barrier for most of the drainages (‘migration corridors’) sourced in the Andes, resulting in a more or less endorheic system of the Central Depression. Coastal areas experience frequent moisture supplies by coastal fog (‘camanchaca’, Stoertz and Ericksen, 1974; Goudie et al., 2002; Cereceda et al., 2008) creating fog oases (Pinto et al., 2006; Latorre et al., 2011). Between 23°–19°S hyperarid conditions prevail in most parts of the Coastal Cordillera and in the Central Depression, where biological life is strongly dependent on locally adapted organisms or restricted to perennial or ephemeral drainages fed by groundwater from the Andes. In this hostile environment, photosynthetic activity and primary production are almost at its dry limit (Warren-Rhodes et al., 2006). To the east, the rising Andean foothills towards the Precordillera experience increase precipitation and indicate a stepwise increase in biological colonization. The corresponding runoffs from the Andean foreslope enable the existence of riparian biomes (Quade et al., 2008; Latorre et al., 2013). Pre-Andean depressions, such as the Salar de Atacama, are intramontane basins enclosed between the Precordillera and the Western Cordillera, which, with regard to the Salar de Atacama, exhibit a long history as depo-center for clastic and evaporitic sediments of Cenozoic age (e.g. Jordan et al., 2007). The Western Cordillera and western parts of the Altiplano Plateau (>4000 m a.s.l.) exhibit numerous endorheic basins, occupied by saline lakes and/or salt crusts, which are often delineated and created by volcanic activity and ignimbrite deposition. The adjacent Salar de Uyuni and corresponding other basins and salars, represent the main intramontane basin in the Altiplano, which repeatedly experienced lacustrine conditions in the past (e.g. Fritz et al., 2007, Fritz et al., 2012; Baker et al., 2001, Baker and Fritz, 2015). Most of the high Andean basins receive their major precipitation from Atlantic sources and are connected to large drainage catchments (Altiplano drainage catchment including Salar de Uyuni, Coipasa, Lake Poopo; e.g. Placzek et al., 2011).

Only a few plants, animals, and microbes managed to adapt to the extremely harsh environments of the Atacama region. Biologists were puzzled by the question of how living organisms could have adapted to survive in such a dry desert (e.g. Navarro-Gonzalez et al., 2003; Azua-Bustos et al., 2012). The patchy distribution of flora, fauna and microbiota in the Atacama Desert is assumed to be a result of contemporary environmental factors and historical contingencies. Landscape evolution should have influenced dispersal and thus the evolution and diversification of organisms, likewise climatic conditions and nutrient availability should have driven and should still drive dispersal and isolation processes of biological populations. The target areas are arid to hyper-arid systems, where the availability of water severely and predominantly limits both biota and Earth surface processes. In addition, the content of organic carbon in the soil as an energy source for heterotrophic life was estimated to be extremely low (Fletcher et al., 2012; Valdivia-Silva et al., 2012; Mörchen et al., 2019; Guerrero et al., 2013). Very high solar UV irradiance and the high concentrations of salts in the soil (Voigt et al., 2020) are additional factors limiting even microbial life in the Atacama Desert (Wierzchos et al., 2012; Mörchen et al., 2019)

The harsh environment in the Atacama forms one of the planet's most demanding conditions. This is reflected by the strong selection pressures for especially adapted organisms which have led to only a few evolutionary lineages coexisting under the extreme conditions. The strong fragmentation of plant populations (Böhnert et al., 2019; Merklinger et al., 2020) necessarily causes a strong fragmentation also of associated heterotrophic eukaryote populations e.g. in their phyllosphere or rhizosphere. The dominating insects are darkling beetles (Tenebrionidae) which are wingless and show a low passive dispersal (e.g., Cepeda-Pizarro et al., 2005). These insects are able to obtain water by digestion of dry organic matter or may collect moisture from fog (Hamilton and Seely, 1976; Willmer et al., 2000). Darkling beetles are known to harbour a diversity of endobiotic protists (e.g. gregarines), in many cases these associations of protists are known to be highly species specific (Desportes and Schrével, 2013) making them predestined model organisms for studies of co-evolution and associating molecular clock calibration for these protists (e.g. Ricklefs and Outlaw, 2010). It is believed that an extremely limited eukaryotic diversity mirrors the organic carbon restriction in these soil habitats. In contrast, aquatic protist communities in the very small ponds of the salars (highly hypersaline inland waters have been created by evaporating runoffs from Andean mountains) in the Atacama show a high number of unique protists, mostly not yet discovered and described (Triadó-Margarit and Casamayor, 2013). Diverse protists communities seem to be supported by diverse and productive prokaryote communities (Dorador et al., 2010).

As one hypothesis of our study it was assumed that plant radiation is younger than the onset of relatively constant hyperaridity (Picard et al., 2008; Böhnert et al., 2019) and that associated eukaryotic microbe communities show a relatively low divergence (if any) from related plant communities. Second, for several beetles, divergence has occurred already in the Atacama Desert (Zúñiga-Reinoso et al., 2019). Thus, those protists living as specific parasites/endobionts in beetles, which themselves may have been co-evolved with endemic plant communities, are assumed to show already a detectable divergence. Third, eukaryotic microbes living in salars may have adapted/co-evolved to the extreme environments independently and may reflect the extremely long stable geological conditions and geological isolation of the investigated water bodies in the Atacama Desert (Fig. 1).

The climatic and geological conditions have fragmented the area into habitats separated by nearly sterile regions without any eukaryotic life (Neilson et al., 2012; Valdivia-Silva et al., 2012). The habitable patches are several regions which allow a certain organic life due to specific adaptations to desert life or access to fragmented groundwater flow. In addition, short-term ‘wetter’ periods in the past could have enabled the opening (re-opening) and creation of biological migration corridors. We hypothesize that strong selection pressure may have led to only a few evolutionary lineages coexisting under these harsh conditions. To investigate our hypothesis, we combined studies on isolation, cultivation, morphology, ultrastructure, autecology, multi-gene phylogeny and next-generation sequencing on protist communities associated to the rhizosphere and phyllosphere of endemic plants (Eulychnia cacti), endemic species of darkling beetles (genera Scotobius and Psectrascelis), and on protists from hypersaline waters (salars). In the course of our studies, we intended to obtain different proxies to understand evolutionary processes at the dry limit due to interactions between evolutionary processes in the geo- and biosphere.

Section snippets

Study sites

Sampling was carried out during field trips in March 2015, 2017 and 2018 in the Atacama region of Northern Chile (Fig. 2). Samples were taken from hypersaline inland lakes, cacti phyllosphere and the gut of darkling beetles. The salinity of the original water samples taken from salars ranged between 6 and 310 PSU. Aquatic sampling sites included salars in the core of the Atacama (Salar de Llamará), in the Altiplano (Salar de Atacama, Salar de Huasco, Salar de Surire, Salar de Ascotan and Salar

Results

Overall, the studies revealed the presence of a large variety of protists from all major phylogenetic groups of protists. In hypersaline athalassic waters, stramenopiles from various groups (placidids, bicosoecids, chrysomonads) dominated regarding their abundance followed by ciliates and different groups of heteroloboseans, but also choanoflagellates were found to be present in all samples. The phyllosphere of cacti was mainly populated by colpodid ciliates, cercozoans, heteroloboseans,

General considerations

All groups of protists analyzed in this study and originating revealed a high degree of diversity in habitats of the Atacama region separated only by a few hundred kilometers. The lack of closely related sequences, in particular for choanoflagellates and placidids, from major databases like NCBI, VAMPS, ARB, PR2 or the Tara Ocean Project, supports a moderate endemicity hypothesis, stating that also unicellular organisms have biogeographies (Foissner, 2006), irrespective of their potential to

Conclusion

Our analysis of the diversity and divergence within several lineages of protists in different habitats of the Atacama revealed patterns fitting to the geological and climatic changes from the late Eocene to the onset of the Quaternary. Several coexisting species point to the repeated invasions, whereby some species already adapted to extreme environmental conditions. Multiple divergence/invasion events can be best explained by alternating climate variability favouring the re-opening and closure

Author contributions

All authors were involved in the sampling and preparation of samples; the geological context and age constraints were provided by B.R. and T.D.; investigations on the cultivation and isolation of protists was mostly carried out by S.S., A.R., F.N., H.A.; molecular investigations were conducted by F.N. and morphological analyses were done by S.S., A.R., F.N., H.A.; molecular clock analyses were made by F.N.; H.A., B.R. and F.N. were involved in the conceptualization and writing of the original

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

We are very thankful to Cristina Dorador, Chris Harrod, Sarah Carduck, Reinhard Predel, Alvaro Zúñiga Reinoso, Sonja Rueckert, Kathrin Lampert, Brigitte Gräfe, Linda Müller, and Nina Grella for their help in sampling and isolation of protists. Special thanks to Rosita Bieg for establishing a reliable protocol for gregarine lysis and amplification. We thank Tibor Dunai and Martin Melles in their role in setting up the Collaborative Research Centre 1211. The study was funded by the Deutsche

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