Ecological and evolutionary implications

Symbiotic relationships between (parasitic) protists and bacteria constitute a driver that has so far been under-represented in microbial ecology models. Endosymbionts undoubtedly play roles in the adaptation of their hosts to environmental challenges and likely in the origin of novel biochemical pathways. They have a number of functions in the host cell, some of which remain unknown (Archibald, Reference Archibald2015b; O'Malley, Reference O'Malley2015). It has been argued that in its extreme form, endosymbionts become completely integrated at the cellular level as organelles (Archibald, Reference Archibald2015a). By stretching the imagination, one can even predict that every stably entrenched endosymbiont may enter an (extremely) long evolutionary trajectory to become an organelle. Indeed, only recently commonalities and overlaps have been identified in the fields of symbiosis and organelle origin, leading to a proposal that there may, in fact, be a continuum between what has historically been labelled as ‘symbionts’, ‘parasites’, and ‘organelles’ (Keeling and McCutcheon, Reference Keeling and McCutcheon2017). For decades, organelles have been defined as cellular compartments with complex and dedicated targeting machineries embedded in their membranes (Cavalier-Smith, Reference Cavalier-Smith1987). However, now we know of prokaryotic proteins that are encoded in the protist nucleus and targeted into the endosymbiotic bacterium (Nowack and Grossman, Reference Nowack and Grossman2012; Morales et al., Reference Morales, Kokkori, Weidauer, Chapman, Goltsman, Rokhsar, Grossman and Nowack2016). Hence, the barrier between endosymbionts and organelles became blurred (Keeling et al., Reference Keeling, McCutcheon and Doolittle2015). Either of them can develop into a complex and versatile version of its initial form or can become subject to rampant simplification and/or degeneration, which we now know can lead, at least in the case of an organelle, to a complete elimination (Karnkowska et al., Reference Karnkowska, Vacek, Zubáčová, Treitli, Petrželková, Eme, Novák, Žárský, Barlow, Herman, Soukal, Hroudová, Doležal, Stairs, Roger, Eliáš, Dacks, Vlček and Hampl2016). The same may hold true for extant bacteria-free protists. It is plausible to speculate that they once harboured bacteria, similar to some of their present relatives, as in the case of diplonemids (Tashyreva et al., Reference Tashyreva, Prokopchuk, Votýpka, Yabuki, Horák and Lukeš2018). The reasons for their loss may vary from intolerable selfishness of the endosymbiotic organism to its degeneration to a point when it became fully dispensable for the host cell. The transition between stages may in some cases be surprisingly fast (Boscaro et al., Reference Boscaro, Kolisko, Felletti, Vannini, Lynn and Keeling2017).

It is generally accepted that all extant mitochondria arose from an α-proteobacterium sometime before the last common eukaryotic ancestor (Gray, Reference Gray2012) (although, see Martijn et al., Reference Martijn, Vosseberg, Guy, Offre and Ettema2018 for recent alternative views), whereas the origin of extant plastids was more convoluted. They arose by the acquisition of a cyanobacterium by a cell already containing a mitochondrion and subsequently spread throughout eukaryotic lineages by several rounds of secondary and tertiary symbioses (Archibald, Reference Archibald2015b).

Current models

Developing models for the basis of interactions between microbial species and how they affect their hosts is a major challenge and symbiotic interactions provide a wide range of opportunities to dissect the origin and profound impacts of close interactions. Another level of complexity of these interactions is produced by their multilayered nature or frequent transiency. In any case, symbiosis is now regarded as a major force for the creation of new biological complexity. This applies both to the deep evolutionary history when the eukaryotic cell came into being and to the functions and properties, it acquired afterwards thanks to the endosymbiotic systems (Archibald, Reference Archibald2015a; Keeling et al., Reference Keeling, McCutcheon and Doolittle2015).

The papers brought together in this volume provide evidence of the colourful and important roles (endo)symbionts and viruses play in the lives of parasites. Prior to the full entry of the sequencing era into this field, the information available about the bacterial endosymbionts and viruses in parasites was mainly confined to the electron microscopic pictures, in which they look pretty much alike or, in the case of bacteria, to their 16S rRNA sequences. However, now we can assemble the genomes of multiple endosymbionts and viruses at once, as well as dissect their metabolism, their interactions with the host cell metabolism and, in cases were more endosymbionts and viruses share the host cell, we can address mutual interactions among them. As a consequence, it is only now when the available sensitivity and range of methods allow researchers to start dissecting these complexities. This will eventually allow estimating the true impact of these interactions, which is clearly deeper than previously thought. In some cases, the host cell and its (endo)symbionts seem to be entwined as tightly as it gets in biology. Indeed, no eukaryotic organism lives in isolation. Each is influenced by omnipresent microbes and viruses, with their assemblages living inside of a given eukaryote being known as the microbiome and the virome (Angly et al., Reference Angly, Felts, Breitbart, Salamon, Edwards, Carlson, Chan, Haynes, Kelley, Liu, Mahaffy, Mueller, Nulton, Olson, Parsons, Rayhawk, Suttle and Rohwer2006).

Some of these systems are well-studied while others are relatively unknown. They include single- and/or multi-cellular parasites, bacteria and viruses since all of them play major roles in the population dynamics and effects on their hosts. Disentangling interactions among these players is currently easier in model systems and in those where these interactions are non-transient. These models can eventually be used to build a common evolutionary and ecological framework, informative for more complex and less studied systems.

Not surprisingly, the best-studied symbioses are those involving humans and mice and their intestinal microbiome. Intense research in the last few years dramatically reshaped our view on how the microbiome can impact human health and development (Knight et al., Reference Knight, Callewaert, Marotz, Hyde, Debelius, McDonald and Sogin2017). Moreover, the complex interplay between the mammalian host and its microbiome is further complicated by eukaryotes inhabiting the host, also called the eukaryome (Lukeš et al., Reference Lukeš, Stensvold, Jirků-Pomajbíková and Wegener Parfrey2015; Chabe et al., Reference Chabe, Lokmer and Segurel2017). Mostly due to technical reasons (extremely high sequence diversity), it is much more difficult to study the eukaryome as compared with the microbial community. As a consequence, the eukaryome remains a rather overlooked component of the holobiont which, however, must inevitably play a significant role in its life.

In their study, Jirků-Pomajbíková et al. (Reference Jirků-Pomajbíková, Jirků, Levá, Sobotková, Morien and Wegener Parfrey2018) dissected the complex relationships among the rat, the tapeworm Hymenolepis diminuta and the gut microbiome. Similar to several other intestinal parasites, H. diminuta is now considered a gut symbiont. It is frequently used by individuals for self-treating of inflammatory bowel disease and other intestinal inflammations and meets criteria for helminth therapy. For this purpose, its life stages are now being produced in semi-industrial amounts (Smyth et al., Reference Smyth, Morton, Mathew, Karuturi, Haley, Zhang, Holzknecht, Swanson, Lin and Parker2017). The authors convincingly demonstrated that a controlled infection with H. diminuta indeed protects rats against severe inflammatory colitis by inducing a type 2 immune response, resulting in faster recovery. The gut microbiome is disrupted during the artificially induced colitis in response to colonization by the tapeworm but, somewhat unexpectedly, does not play a major role in the H. diminuta-mediated protection.

The work of Rebello et al. (Reference Rebello, Andrade-Neto, Zuma, Motta, Gomes, de Souza, Atella, Branquinha, Santos, Torres-Santos and d'Avila-Levy2018) investigated the role of the HIV-1 peptidase inhibitor Lopinavir in Leishmania amazonensis metabolism and demonstrated that it induces lipid accumulation in promastigotes. Using this broad-specificity inhibitor against viral peptidases, they shed a new light on the first-line defense against viral infection in Leishmania and other trypanosomatids. This is particularly important because Leishmania treatment remains challenging and new therapies need to be developed (Gillespie et al., Reference Gillespie, Beaumier, Strych, Hayward, Hotez and Bottazzi2016; Aronson et al., Reference Aronson, Herwaldt, Libman, Pearson, Lopez-Velez, Weina, Carvalho, Ephros, Jeronimo and Magill2017). Understanding parasites’ response to different drugs is imperative in achieving this goal.

In his review of what is known about symbionts of blood-feeding organisms, Husník (Reference Husnik2018) seeks to identify some common trends in the varied landscape they represent. The blood-feeding strategy emerged multiple times independently in the evolution of notorious mosquitoes and tsetse flies, vectors of a range of serious diseases, as well as in the predecessors of less known vampire finches and lampreys. Regardless of their phylogenetic position and because of the highly specialized diet, the blood-feeders rely on either extracellular (usually located in the gut) or intracellular obligate symbionts (found in specialized bacteriocyte cells or even dedicated organs such as bacteriomes) that supply them with vitamins and potentially other compounds. The author also draws attention to the fact that in this complex system, represented here by the endosymbiont-loaded tissues of the tsetse fly, a prokaryote-to-eukaryote horizontal gene transfer event occurs much more frequently than in other systems (Husnik and McCutcheon, Reference Husnik and McCutcheon2018).

In their comprehensive review, Telleria et al. (Reference Telleria, da-Silva, Tempone and Traub-Cseko2018) summarized current knowledge of the sand fly microbiome. Phlebotomine sand flies are vectors of several etiological agents causing viral encephalitis, bartonellosis and leishmaniasis (Soares and Turco, Reference Soares and Turco2003; Akhoundi et al., Reference Akhoundi, Kuhls, Cannet, Votýpka, Marty, Delaunay and Sereno2016). The authors reviewed studies on viruses of public health importance, bacteria and fungi present in the sand fly gut and described them in the context of vector development and insect immune response. Finally, they highlighted the cellular mechanisms the insects utilize in order to survive the potential threats posed by viruses, bacteria and Leishmania spp. they transmit (Telleria et al., Reference Telleria, da-Silva, Tempone and Traub-Cseko2018).

Paranaiba et al. (Reference Paranaiba, Pinheiro, Macedo, Menezes-Neto, Torrecilhas, Tafuri and Soares2018) evaluated a group of Leishmania species non-infective to humans for the presence of double-stranded RNA viruses related to Leishmaniavirus belonging to the family Totiviridae. Two isolates of Leishmania enriettii were analysed and shown to be virus-free. This is an interesting result in the light of a recent broad survey of trypanosomatids, which also failed to document totiviruses outside of the genus Leishmania (Grybchuk et al., Reference Grybchuk, Akopyants, Kostygov, Konovalovas, Lye, Dobson, Zangger, Fasel, Butenko, Frolov, Votýpka, d'Avila-Levy, Kulich, Moravcová, Plevka, Rogozin, Serva, Lukeš, Beverley and Yurchenko2018). Moreover, in these understudied flagellates, Paranaiba et al. (Reference Paranaiba, Pinheiro, Macedo, Menezes-Neto, Torrecilhas, Tafuri and Soares2018) elaborated on the structure of glycoconjugates.

Harmer et al. (Reference Harmer, Yurchenko, Nenarokova, Lukeš and Ginger2018) offer a comparative view of endosymbiotic events during kinetoplastid evolution. While trypanosomatid flagellates are mostly known thanks to human pathogenic trypanosomes and leishmanias, their predecessors parasitizing insects occasionally acquired a bacterium, which provides them with essential vitamins and heme. From the comparison of two independently acquired bacteria belonging either to the family Burkholderiaceae or Alkaligenaceae, the authors concluded that these partnerships arrived at quite different outcomes. In the light of a recent finding that the basal trypanosomatid Paratrypanosoma confusum retains a cytostome (Skalický et al., Reference Skalický, Dobáková, Wheeler, Tesařová, Flegontov, Jirsová, Votýpka, Yurchenko, Ayala and Lukeš2017), they discuss possible alternative acquisition routes for the bacterium that turned into an endosymbiont. Moreover, Harmer et al., (Reference Harmer, Yurchenko, Nenarokova, Lukeš and Ginger2018) suggested that the endosymbiotic bacteria may also be found in free-living kinetoplastids (see the cover of this issue).

A particular case of Candidatus Kinetoplastibacterium sorsogonicusi, the bacterial endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae) was analysed by Silva et al. (Reference Silva, Kostygov, Spodareva, Butenko, Tossou, Lukeš, Yurchenko and Alves2018). The authors sequenced the whole genome of the endosymbiont and found it to be completely syntenic with the genomes of other known Ca. Kinetoplastibacterium spp., but more reduced in size. The most conspicuous loss is that of the heme synthesis pathway, making the host cell dependent on external heme. It remains to be investigated further why the ability to synthesize such an essential compound was lost in Ca. Kinetoplastibacterium sorsogonicusi, while it was retained in all other bacterial endosymbionts of trypanosomatids characterized thus far (Kořený et al., Reference Kořený, Oborník and Lukeš2013).

Agha et al. (Reference Agha, Gross, Gerphagnon, Rohrlack and Wolinska2018) investigated the life-history traits of a fungal parasite infecting the planktonic, bloom-forming protist Planktothrix spp. and report that the disease outcome is largely modulated by temperature. Yet the establishment of the infection and the exploitation of host resources were modulated differently. The authors conclude that parasite fitness results from the interplay of individual parasite traits that are differentially controlled by the host and external environment (Agha et al., Reference Agha, Gross, Gerphagnon, Rohrlack and Wolinska2018). The importance of this observation cannot be overestimated, as chytrid parasites in nature can inflict mass mortality on hosts, leading to changes in phytoplankton size distributions, and, potentially, the delay or even suppression of bloom events on a global scale (Frenken et al., Reference Frenken, Alacid, Berger, Bourne, Gerphagnon, Grossart, Gsell, Ibelings, Kagami, Kupper, Letcher, Loyau, Miki, Nejstgaard, Rasconi, Rene, Rohrlack, Rojas-Jimenez, Schmeller, Scholz, Seto, Sime-Ngando, Sukenik, Van de Waal, Van den Wyngaert, Van Donk, Wolinska, Wurzbacher and Agha2017).

The last paper of this series is devoted to Blastocystis, which colonizes the gut of about 1 billion people, yet there is still no consensus whether this stramenopile protist is a commensal or a parasite, linked to several gastrointestinal diseases. In their unique study, Scanlan et al. (Reference Scanlan, Hill, Ross, Ryan, Stanton and Cotter2018) show that Blastocystis is rare in healthy Irish infants, whereas every 2nd adult from the same region is positive. Consequently, the authors suggest that infants obtain Blastocystis by horizontal transfer. The microbiome (and likely the eukaryome) of an infant is shaped by many forces and may have a paramount impact on health status in adulthood (Blaser, Reference Blaser2014). Since recent studies have found Blastocystis at a higher prevalence in healthy individuals as compared with those with a gastrointestinal ailment (Rossen et al., Reference Rossen, Bart, Verhaar, van Nood, Kootte, de Groot, D'Haens, Ponsioen and van Gool2015), the results presented by Scanlan et al. (Reference Scanlan, Hill, Ross, Ryan, Stanton and Cotter2018) are actually good news, as they show that even in the Westernized world humans can acquire beneficial eukaryotes later in life.