• Loading metrics

Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens

Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens

  • Emile Gluck-Thaler, 
  • Jason C. Slot


Comparative genomic studies of microorganisms have disrupted the paradigm of vertical inheritance with modification. First in bacteria, and more recently in microscopic and even multicellular eukaryotes, horizontal gene transfer (HGT) has been implicated in genomic and ecological evolution. HGT is the exchange of genetic material between organisms that occurs independently of meiotic and mitotic recombination between mating or hybridizing individuals. HGT occurs as viral and plasmid-mediated transfer, and transformation by environmental DNA via known or yet-unknown mechanisms [1]. The existence of environmental gene pools and pan-genomes is supported by decades of functional and phylogenetic studies in bacteria that have highlighted the exchange and proliferation of virulence factors and antibiotic resistance mechanisms [24]. Presently, accumulating reports of HGT in eukaryotes raise similar questions of how exposure to such gene pools has impacted the evolution of eukaryotic microbes, and whether or not human activities influence HGT dynamics. Here, we describe the evidence supporting HGT in eukaryotic microbial pathogens from divergent lineages that impact human, animal, and plant health (S1 Table). We consider three interacting dimensions affecting the prevalence of HGT (genetic network structure, selectable functions, and opportunity for contact) in order to better understand how HGT manifests in this important group of organisms.

Does HGT Really Contribute to Eukaryotic Microbial Pathogen Genomes?

Reports of HGT among eukaryotic microbial pathogens have accumulated in recent years, largely driven by comparative genomic analyses showing an unexpected distribution and phylogenetic placement of gene sequences. However, these analyses require appropriate sampling and methodology, and should be interpreted with caution. Objections to the veracity and extent of HGT include the absence of a reproducible transfer mechanism in some lineages, and the plausibility of alternative explanations for the distributions and phylogenies of HGT candidate gene sequences [5]. The alternative interpretations of unexpected gene distributions and phylogenies hinge on different assumptions about the parsimony of a small number of gene transfer events versus a large number of the more widely accepted processes of gene duplication and loss [5]. Proponents of HGT hypotheses emphasize the importance of robust phylogenetic analyses coupled with multiple additional lines of evidence to support claims [6,7]. The most convincing cases have thus combined model-based phylogenetic approaches, which compare the topologies of gene trees to species phylogenies, with additional support from genome structure, sequence identity, codon usage, GC nucleotide content, and evidence of benefits to the recipient (S1 Table). Analyses relying on but a few of these methods, especially supporting methods in isolation, are rarely sufficient to strongly support HGT, and can result in false positive identification of HGT [7]. Unsampled genetic diversity at the population and species levels, which can impact reconstructions of gene distribution and inheritance, may also lead to false positive identification of HGT, underscoring the importance of robust taxon sampling [8]. For example, in a 2011 study, genes encoding the greatly expanded Crinkler protein family in the amphibian pathogen Batrachochytrium dendrobatidis had a distribution and phylogeny consistent with HGT from plant pathogenic oomycetes; however, the recent detection of Crinkler homologs in two additional fungal lineages opens the possibility that the current distribution is compatible with vertical inheritance and widespread gene loss [911]. Similar sampling biases can also lead to the underestimation of HGT in lineages of eukaryotic microbial pathogens, due to recent HGTs that are not fixed in populations and transferred genes that are prone to subsequent loss under changing selective pressures. This is illustrated by the rapid, differential degeneration of a horizontally acquired gene cluster among members of the necrotrophic fungal genus Botrytis [12]. More thorough sampling efforts currently underway may reduce erroneous inferences about HGT, help resolve the timing and direction of HGT events, and provide better estimates of their ecological contexts [13].

Does Genetic Network Complexity Influence HGT?

The complexity hypothesis posits that genes that are more modular in nature (i.e., residing at the periphery of gene connectivity networks) are more likely to be successfully transferred, because they are less disruptive to host networks and require establishment of fewer connections (Fig 1) [2,14]. This hypothesis is supported in bacteria, in which low network connectivity is found to enhance a gene’s “transferability,” which is largely independent of its specific biological function [15,16]. In eukaryotic microbial pathogens, genes encoding virulence factors may provide a fitness advantage to the recipient without extensive integration into genetic networks. Examples include genes encoding secreted effector proteins and specialized metabolic genes, especially those located in complete multigene clusters, which encode mechanisms for regulation, compartmentalization, secretion of products, and stoichiometric control of toxic intermediates [1724]. Biased rates of gene transfer and loss of function found in systematic investigations of pathogen genomes also support the complexity hypothesis. Notably, in the human pathogen Trichomonas vaginalis, only 2% of 152 horizontally transferred genes were “informational” (more often involved in highly conserved, connected cellular processes like transcription), compared to 65% that encoded metabolic enzymes, which are “operational” genes associated with less conserved processes [25,26]. However, a survey of metabolic enzymes in select pathogens found that the degree of network connectivity of horizontally transferred genes was not different from the connectivity of vertically inherited genes [27]. The authors note that this could be because the horizontally transferred genes integrated into existing networks during the extensive time period since they were acquired [28].

Fig 1. The interacting dimensions of horizontal gene transfer in eukaryotic microbial pathogens.

The probability of horizontal gene transfer (HGT) and retention of a gene in recipient organisms is proposed to be under three main interacting influences or dimensions: (1) the genetic network structure, defined as the sum of functional connections between the gene and all other genes within a genome; (2) the selectability of the phenotype conferred by its function in a host environment; and (3) opportunity for contact, i.e., the rate and intimacy of meetings between donor DNA and recipient organisms throughout their life cycles. In this depiction of a general model, the probability of HGT increases with increasing dot intensity and size. Some pathogen-specific parameters influencing each dimension are listed above each circle’s perimeter. While HGT and the subsequent maintenance of genes in recipient genomes might be possible under the influence of only one or two dimensions, it is predicted to have the highest probability when all dimensions interact.

A notable consequence of limited gene connectivity associated with horizontally transferred genes is the relaxation of network-imposed selection pressures, giving rise to sequence divergence, thus increasing the capacity for adaptive evolution. This effect has been reported in plant pathogenic Pyrenophora spp., in which ten horizontally transferred genes present significantly more diversifying sequence change compared to corresponding homologs in donor species [29].

What Biological Functions Favor Successful HGT in Eukaryotic Microbial Pathogens?

Environmental selection in pathogen niches may favor the acquisition of certain gene functions. To date, there have been few formal investigations of general trends in functions of genes transferred to eukaryotic microbial pathogens (but see [6,30,31] for discussion of trends in fungi and oomycetes), and few functional confirmations of the roles horizontally transferred genes play in virulence [27,28]. Individual reports suggest three functional categories that are often horizontally transferred to divergent pathogen lineages: secreted molecules, membrane modifications, and metabolism specialized to host interactions and environments (Fig 1). Secreted molecule genes that have been transferred include those for degradative enzymes, such as the 22 different plant polysaccharide depolymerization enzymes that were transferred from phytopathogenic fungi to oomycetes [18]. Genes for production of toxic metabolites that disrupt normal cellular function are also reported transferred, including the fumonisin mycotoxin gene cluster between phytopathogenic Fusarium and Aspergillus fungi [22]. Membrane modifications identified in HGT reports may directly mediate cellular contact between hosts and pathogens, or mask pathogen membranes from host defense responses [32]. For example, a septin trans-membrane protein acquired by the microsporidian Ordospora colligata may facilitate the endocytosis-mediated infection of its Daphnia hosts [33]. Finally, the environment, i.e., the host, selects for the ability in the pathogen to metabolize and/or utilize host defenses and resources, or other sources of fitness in or on the host. For example, osmoregulatory genes acquired by phytopathogenic fungi may facilitate cellular osmotic balance in vascular fluids, and an anaerobic sulfur mobilization gene may increase survival of Blastocystis (a stramenopile suspected to be a pathogen) in anaerobic gut environments [19,20]. Some genes or gene clusters may be considered “repeat offenders,” having been transferred multiple times, possibly due to advantages conferred in specific pathogenic ecologies. For example, the complex distribution of epipolythiodioxopiperazine toxin gene clusters in ascomycete fungi suggests at least three independent transfers between divergent lineages [23].

The extent to which de novo gene gain promotes rapid pathogen emergence is largely unknown. One apparently contemporary transfer of a secreted toxin-encoding gene required for complete virulence on wheat, from Stagonospora nodorum to Pyrenophora tritici-repentis, has been reported [17]. The role of HGT in pathogen emergence is additionally supported by functional studies of transferred genes. For example, deletions of two horizontally acquired genes from the grass pathogen Fusarium pseudograminearum, and of a horizontally acquired osmoregulatory gene from vascular wilt fungi, resulted in reduced virulence [19,34]. Conversely, gain of virulence was documented in a fungal endophyte transformed with a membrane modification gene that the related entomopathogenic fungus, Metarhizium robertsii, may have ancestrally acquired from insects [32].

The fitness benefits conferred by horizontally acquired genes may range from none to highly beneficial, and may not directly relate to pathogenesis. Some pathogens exhibit complex life cycles that alternate between pathogenic and non-pathogenic states, and alternatively the gain of adaptive genes with no pathogenic function could facilitate attenuation of pathogenicity or transition to free-living status under selection from host density. For example, it was speculated that the transfer of a nitrate assimilation gene cluster to the mycoparasitic Trichoderma fungi may promote a transition to the nitrogen-limited wood-decay niche, and the transfer of a sugar utilization gene cluster to Schizosaccharomyces yeast could be part of an ecological transition from pathogen to fermenter [35,36].

Do Eukaryotic Microbial Pathogens Become “Who They Meet?”

The frequency of physical contact between donors and recipients should be considered a driving force behind the likelihood of HGT events, and is a function of an organism’s ecology. Bacteria isolated from the same human body site, for example, exchange genes more frequently, and the genes they exchange are more frequently associated with niche-specific functions [3]. Three groups of ecologically adjacent organisms are often shown to be involved in horizontal gene exchange with eukaryotic microbial pathogens: co-infecting pathogens, non-pathogens symbiotically associated with the host, and the hosts themselves. Examples of transfers between potentially co-infecting pathogens include a host-specific toxin gene between two fungal wheat pathogens and a plant defense compound degradation cluster between fungal grass pathogens [17,21]. Non-pathogenic gut commensal bacteria are thought to have contributed diverse metabolic genes to Trichomonas vaginalis and Blastocystis genomes, including those involved in carbohydrate and amino acid metabolism [20,25,26]. Remarkably, there are cases of host-gene acquisition by insect- and plant-pathogenic fungi. These include the acquisition of a sterol binding protein by the entomopathogenic fungus Metarhizium robertsii that enables it to incorporate host-derived cholesterol into its cell membrane during infections, and the acquisition of a purine salvage pathway gene by obligate intracellular microsporidian pathogens, among others [32,33,37,38]. Considering the range of genetic exchange between ecological associates outside of predator–prey relationships, we suggest that the “you are what you eat” hypothesis proposed as a mechanism of HGT in phagotrophic eukaryotes may be rebranded “you are who you meet” for eukaryotic microbial pathogens [39]. We propose that the frequency of meetings between pathogens and specific classes of organisms may be influenced by virulence, localization in host, and host range (Fig 1). Less virulent pathogens may have sustained encounters with genomes of co-occurring pathogens, non-pathogenic symbionts, and the host because of their low impact on host mortality. In contrast, increasingly virulent pathogens may disproportionately encounter genomes from the greater environment as increased virulence correlates with increased survival time outside of hosts [40]. Obligate intracellular pathogens might be more frequently exposed to host genomes, while extracellular pathogens may often encounter genomes of other host-associated organisms. Similarly, generalists encounter a greater diversity of host genomes compared to specialists, and facultative pathogens may encounter more genes from the greater environment. Factors that contribute to a net increase in exposure to foreign DNA may favor acquisition of novel adaptive functions or drive an HGT ratchet by replacing pathogen genes with foreign genes (as proposed by Doolittle [39]). Furthermore, the gradually converging ecologies resulting from successive “meetings” may promote further transfers of ecology-specific genes such that decreasing ecological proximity results in acceleration of gene acquisition and vice versa. This could explain in part the repeated transfers of phytopathogenic genes from fungi to oomycetes, as well as the repeated acquisition of genes by the plant pathogenic Fusarium lineage from other plant pathogenic fungi, including the Verticillium, Aspergillus, and Collectotrichum genera [18,19,22,31,34]. It remains to be investigated whether specific pathogen lineages, virulence levels, host localizations, or specializations are more prone to horizontal gene exchange, but we note that lineage-specific biases in the rates of HGT were recently shown in a large comparative analysis of fungi [28].

Do Human Activities Impact HGT in Eukaryotic Microbial Pathogens?

Human activities that accelerate environmental changes may impose selection pressures and precipitate dispersal events, which can influence the likelihood of HGT among eukaryotic microbial pathogens. Strong selection pressures exerted by decreased host diversity and intensive management practices in agro-ecosystems, including antimicrobials and other chemical control agents, may be expected to increase the prevalence of horizontally transferred genes, similar to the horizontal proliferation of antibiotic-resistant genes in bacteria due to modern overuse [4]. Homogeneous host environments increase the density of host-specific pathogens, non-pathogens, and the opportunities for them to interact, while at the same time relaxing density-dependent selection against virulent pathogens. Other human activities, such as global trade and travel, influence both the frequency and diversity of the close physical encounters required for horizontal gene flow, which can lead to emergence and evolution of pathogens in the near-term [17]. Furthermore, the migration of host ranges associated with climate and land-use changes provides new opportunities for encounters between pathogens established in previously isolated environments [41]. The extent of human impact on HGT in eukaryotic microbial pathogens is not known, but recent HGT discoveries in these organisms argue for careful consideration of pathogen emergence by HGT as a consequence of ecosystem management.

Supporting Information

S1 Table. Well-supported reports of HGT in eukaryotic microbial pathogens.

This table details 21 references with at least one report of HGT among eukaryotic microbial pathogens. Recipient lineage, donor lineage, detection methods, putative contact opportunity, and information on gene functions are listed.



  1. 1. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Micro 3: 711–721.
  2. 2. Baquero F (2004) From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2: 510–518. pmid:15152207
  3. 3. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, et al. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241–244. pmid:22037308
  4. 4. Barlow M (2009) What antimicrobial resistance has taught us about horizontal gene transfer. Methods Mol Biol 532: 397–411. pmid:19271198
  5. 5. Kroken S, Glass NL, Taylor JW, Yoder OC, Turgeon BG (2003) Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc Natl Acad Sci USA 100: 15670–15675. pmid:14676319
  6. 6. Soanes D, Richards TA (2014) Horizontal gene transfer in eukaryotic plant pathogens. Annual Review of Phytopathology 52: 583–614. pmid:25090479
  7. 7. Zhaxybayeva O, Doolittle WF (2011) Lateral gene transfer. Current Biology 21: pR242–R246.
  8. 8. Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46: 239–257.
  9. 9. James TY, Pelin A, Bonen L, Ahrendt S, Sain D, et al. (2013) Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr Biol 23: 1548–1553. pmid:23932404
  10. 10. Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, et al. (2014) Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet 10: e1004078. pmid:24415955
  11. 11. Sun G, Yang Z, Kosch T, Summers K, Huang J (2011) Evidence for acquisition of virulence effectors in pathogenic chytrids. BMC Evolutionary Biology 11: 195. pmid:21740557
  12. 12. Campbell MA, Staats M, van Kan JA, Rokas A, Slot JC (2013) Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105: 1126–1134. pmid:23921237
  13. 13. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, et al. (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Research 42: D699–D704. pmid:24297253
  14. 14. Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96: 3801–3806. pmid:10097118
  15. 15. Pal C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37: 1372–1375. pmid:16311593
  16. 16. Cohen O, Gophna U, Pupko T (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol 28: 1481–1489. pmid:21149642
  17. 17. Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, et al. (2006) Emergence of a new disease as a result of interspecific virulence gene transfer. Nat Genet 38: 953–956. pmid:16832356
  18. 18. Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, et al. (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci USA 108: 15258–15263. pmid:21878562
  19. 19. Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, et al. (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog 7: e1002137. pmid:21829347
  20. 20. Tsaousis AD, Ollagnier de Choudens S, Gentekaki E, Long S, Gaston D, et al. (2012) Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis. Proc Natl Acad Sci USA 109: 10426–10431. pmid:22699510
  21. 21. Greene GH, McGary KL, Rokas A, Slot JC (2014) Ecology drives the distribution of specialized tyrosine metabolism modules in fungi. Genome Biol Evol 6: 121–132. pmid:24391152
  22. 22. Khaldi N, Wolfe KH (2011) Evolutionary origins of the fumonisin secondary metabolite gene cluster in Fusarium verticillioides and Aspergillus niger. International Journal of Evolutionary Biology 2011. Epub 2011 May 23.
  23. 23. Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, et al. (2007) Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol Biol 7: 174. pmid:17897469
  24. 24. Elmore MH, McGary KL, Wisecaver JH, Slot JC, Geiser DM, et al. (2015) Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biol Evol 7: 789–800. pmid:25663439
  25. 25. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, et al. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315: 207–212. pmid:17218520
  26. 26. Strese A, Backlund A, Alsmark C (2014) A recently transferred cluster of bacterial genes in Trichomonas vaginalis-lateral gene transfer and the fate of acquired genes. BMC Evol Biol 14: 119. pmid:24898731
  27. 27. Whitaker JW, McConkey GA, Westhead DR (2009) The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biology 10:R36. pmid:19368726
  28. 28. Wisecaver JH, Slot JC, Rokas A (2014) The evolution of fungal metabolic pathways. PLoS Genet 10: e1004816. pmid:25474404
  29. 29. Sun B-F, Xiao J-H, He S, Liu L, Murphy RW, et al. (2013) Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles. PLoS ONE 8: e60029. pmid:23555871
  30. 30. Richards TA, Talbot NJ (2013) Horizontal gene transfer in osmotrophs: playing with public goods. Nat Rev Micro 11: 720–727.
  31. 31. Savory F, Leonard G, Richards TA (2015) The role of horizontal gene transfer in the evolution of the oomycetes. PLoS Pathog 11: e1004805. pmid:26020232
  32. 32. Zhao H, Xu C, Lu H-L, Chen X, St. Leger RJ, et al. (2014) Host-to-pathogen gene transfer facilitated infection of insects by a pathogenic fungus. PLoS Pathog 10: e1004009. pmid:24722668
  33. 33. Pombert J-F, Haag KL, Beidas S, Ebert D, Keeling PJ (2015) The Ordospora colligata genome: evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. mBio 6: e02400–14 pmid:25587016
  34. 34. Gardiner DM, McDonald MC, Covarelli L, Solomon PS, Rusu AG, et al. (2012) Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLoS Pathog 8: e1002952. pmid:23028337
  35. 35. Slot JC, Hibbett DS (2007) Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study. PLoS ONE 2: e1097. pmid:17971860
  36. 36. Slot JC, Rokas A (2010) Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Natl Acad Sci USA 107: 10136–10141. pmid:20479238
  37. 37. Selman M, Pombert JF, Solter L, Farinelli L, Weiss LM, et al. (2011) Acquisition of an animal gene by microsporidian intracellular parasites. Curr Biol 21: R576–577. pmid:21820617
  38. 38. Armijos Jaramillo VD, Vargas WA, Sukno SA, Thon MR (2013) Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum. PLoS ONE 8: e59078. pmid:23554975
  39. 39. Ford Doolittle W (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14: 307–311. pmid:9724962
  40. 40. Walther BA, Ewald PW (2004) Pathogen survival in the external environment and the evolution of virulence. Biol Rev Camb Philos Soc 79: 849–869. pmid:15682873
  41. 41. Parmesan C, Yohe G (2003) A globally coherent fingerprint of climate change impacts across natural systems. Nature 421: 37–42. pmid:12511946