Skip to main content
SpringerLink
Log in

Acanthamoeba everywhere: high diversity of Acanthamoeba in soils

  • Original Paper
  • Published:
Parasitology Research Aims and scope Submit manuscript

Abstract

Acanthamoeba is a very abundant genus of soil protists with fundamental importance in nutrient cycling, but several strains can also act as human pathogens. The systematics of the genus is still unclear: currently 18 small-subunit (SSU or 18S) ribosomal RNA sequence types (T1–T18) are recognized, which sometimes contain several different morphotypes; on the other hand, some morphological identical strains belong to different sequence types, sometimes appearing in paraphyletic positions. In this study, we cultivated 65 Acanthamoeba clones from soil samples collected under grassland at three separate locations in the Netherlands, in Sardinia and at high altitude mountains in Tibet. We obtained 24 distinct partial sequences, which predominantly grouped within sequence type T4 followed by T2, T13, T16 and “OX-1” (in the T2/T6 clade). Our sequences were 98–99 % similar, but none was identical to already known Acanthamoeba sequences. The community composition of Acanthamoeba strains differed between locations, T4 being the dominant sequence type in Sardinia and Tibet, but represented only half of the clones from soils in the Netherlands. The other half of clones from the Dutch soils was made up by T2, T16 and “OX-1”, while T13 was only found in Sardinia and Tibet. None of the sequences was identical between localities. Several T4 clones from all three localities and all T13 clones grew at 37 °C while one T4 clone was highly cytopathogenic.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Amaral-Zettler LA, Nerad TA, O'Kelly CJ, Peglar MT, Gillevet PM, Silberman JD, Sogin ML (2000) A molecular reassessment of the leptomyxid amoebae. Protist 151:275–282

    Article  CAS  PubMed  Google Scholar 

  • Bagella S, Salis L, Marrosu GM, Rossetti I, Fanni S, Caria MC, Roggero PP (2013) Effects of long-term management practices on grassland plant assemblages in Mediterranean cork oak silvo-pastoral systems. Plant Ecol 214:621–631

    Article  Google Scholar 

  • Bonkowski M, Clarholm M (2012) Stimulation of plant growth through interactions of bacteria and protozoa: testing the auxiliary microbial loop hypothesis. Acta Protozool 51:237–247

    Google Scholar 

  • Booton GC, Kelly DJ, Chu Y-W, Seal DV, Houang E, Lam DSC, Byers TJ, Fuerst PA (2002) 18S ribosomal DNA typing and tracking of Acanthamoeba species isolates from corneal scrape specimens, contact lenses, lens cases, and home water supplies of Acanthamoeba keratitis patients in Hong Kong. J Clin Microbiol 40:1621–1625

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cavalier-Smith T (1998) A revised six‐kingdom system of life. Biol Rev 73:203–266

    Article  CAS  PubMed  Google Scholar 

  • Cavalier-Smith T, Chao EE (1995) The opalozoan Apusomonas is related to the common ancestor of animals, fungi, and choanoflagellates. Proc R Soc Lond B Biol Sci 261:1–6

    Article  Google Scholar 

  • Corsaro D, Venditti D (2010) Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida). Parasitol Res 107:233–238

    Article  PubMed  Google Scholar 

  • Corsaro D, Venditti D (2011) More Acanthamoeba genotypes: limits to the use rDNA fragments to describe new genotypes. Acta Protozool 50:49

    Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772

    Article  CAS  PubMed  Google Scholar 

  • Dyková I, Lom J, Schroeder-Diedrich JM, Booton GC, Byers TJ (1999) Acanthamoeba strains isolated from organs of freshwater fishes. J Parasitol 85:1106–1113

    Article  PubMed  Google Scholar 

  • Efron N, Young G, Brennan NA (1989) Ocular surface temperature. Curr Eye Res 8:901–906

    CAS  PubMed  Google Scholar 

  • Gast RJ, Ledee DR, Fuerst PA, Byers TJ (1996) Subgenus systematics of Acanthamoeba: four nuclear 18S rDNA sequence types. J Eukaryot Microbiol 43:498–504

    Article  CAS  PubMed  Google Scholar 

  • Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224

    Article  CAS  PubMed  Google Scholar 

  • Griffiths BS, Bonkowski M, Dobson G, Caul S (1999) Changes in soil microbial community structure in the presence of microbial-feeding nematodes and protozoa. Pedobiologia 43:297–304

    CAS  Google Scholar 

  • Hedlund K, Santa Regina I, Van der Putten WH, Lepš J, Díaz T, Korthals GW, Lavorel S, Brown VK, Gormsen D, Mortimer SR, Rodríguez Barrueco C, Roy J, Smilauer P, Smilauerová M, Van Dijk C (2003) Plant species diversity, plant biomass and responses of the soil community on abandoned land across Europe: idiosyncracy or above–belowground time lags. Oikos 103:45–58

    Article  Google Scholar 

  • Heger TJ, Mitchell EAD, Leander BS (2013) Holarctic phylogeography of the testate amoeba Hyalosphenia papilio (Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation. Mol Ecol 22:5172–5184

    Article  CAS  PubMed  Google Scholar 

  • Hewett MK, Robinson BS, Monis PT, Saint CP (2003) Identification of a new Acanthamoeba 18S rRNA gene sequence type, corresponding to the species Acanthamoeba jacobsi Sawyer, Nerad and Visvesvara, 1992 (Lobosea: Acanthamoebidae). Acta Protozool 42:325–329

    CAS  Google Scholar 

  • Horn M, Fritsche TR, Gautom RK, Schleifer K-H, Wagner M (1999) Novel bacterial endosymbionts of Acanthamoeba spp. related to the Paramecium caudatum symbiont Caedibacter caryophilus. Environ Microbiol 1:357–367

    Article  CAS  PubMed  Google Scholar 

  • Kreuzer K, Adamczyk J, Iijima M, Wagner M, Scheu S, Bonkowski M (2006) Grazing of a common species of soil protozoa (Acanthamoeba castellanii) affects rhizosphere bacterial community composition and root architecture of rice (Oryza sativa L.). Soil Biol Biochem 38:1665–1672

    Article  CAS  Google Scholar 

  • Łanocha N, Kosik-Bogacka D, Maciejewska A, Sawczuk M, Wilk A, Kuźna-Grygiel W (2009) The occurrence Acanthamoeba (free living amoeba) in environmental and respiratory samples in Poland. Acta Protozool 48:271–279

    Google Scholar 

  • Lara E, Berney C, Ekelund F, Harms H, Chatzinotas A (2007) Molecular comparison of cultivable protozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site. Soil Biol Biochem 39:139–148

    Article  CAS  Google Scholar 

  • Maciver SK, Asif M, Simmen MW, Lorenzo-Morales J (2013) A systematic analysis of Acanthamoeba genotype frequency correlated with source and pathogenicity: T4 is confirmed as a pathogen-rich genotype. Eur J Protistol 49:217–221

    Article  PubMed  Google Scholar 

  • Nuprasert W, Putaporntip C, Pariyakanok L, Jongwutiwes S (2010) Identification of a novel T17 genotype of Acanthamoeba from environmental isolates and T10 genotype causing keratitis in Thailand. J Clin Microbiol 48:4636–4640

    Article  PubMed Central  PubMed  Google Scholar 

  • Page FC (1988) A new key to freshwater and soil gymnamoebae with instructions for culture. Freshwater Biological Association, Ambleside

    Google Scholar 

  • Page FC, Siemensma FJ (1991) Nackte Rhizopoda und Heliozoea. Gustav Fischer Verlag, Stuttgart

    Google Scholar 

  • Pawlowski J (2000) Introduction to the molecular systematics of Foraminifera. Micropaleontology 46:1–12

    Google Scholar 

  • Pussard M, Pons R (1977) Morphologie de la paroi kystique et taxonomie du genre Acanthamoeba (Protozoa, Amoebida). Protistologica 13:557–598

    Google Scholar 

  • Qvarnstrom Y, Nerad TA, Visvesvara GS (2013) Characterization of a new pathogenic Acanthamoeba species, A. byersi n. sp., isolated from a human with fatal amoebic encephalitis. J Eukaryot Microbiol 60:626–633

    Article  CAS  PubMed  Google Scholar 

  • Risler A, Coupat-Goutaland B, Pélandakis M (2013) Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis. Parasitol Res 112:3807–3816

    Article  PubMed  Google Scholar 

  • Rodríguez-Zaragoza S (1994) Ecology of free-living amoebae. Crit Rev Microbiol 20:225–241

    Article  PubMed  Google Scholar 

  • Rodriguez-Zaragoza S, Mayzlish E, Steinberger Y (2005) Vertical distribution of the free-living amoeba population in soil under desert shrubs in the Negev desert, Israel. Appl Environ Microbiol 71:2053–2060

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rønn R, McCaig AE, Griffiths BS, Prosser JI (2002) Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68:6094–6105

    Article  PubMed Central  PubMed  Google Scholar 

  • Rosenberg K, Bertaux J, Krome K, Hartmann A, Scheu S, Bonkowski M (2009) Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana. ISME J 3:675–684

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual. 2nd ed Cold Spring Harbor Laboratory Press, New York

  • Sawyer TK, Griffin JL (1975) A proposed new family, Acanthamoebidae n. fam. (Order Amoebida), for certain cyst-forming filose amoebae. Trans Am Microsc Soc 94:93–98

    Article  Google Scholar 

  • Schuster FL (2002) Cultivation of pathogenic and opportunistic free-living amebas. Clin Microbiol Rev 15:342–354

    Article  PubMed Central  PubMed  Google Scholar 

  • Schuster FL, Visvesvara GS (2004) Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals. Int J Parasitol 34:1001–1027

    Article  PubMed  Google Scholar 

  • Smirnov AV, Brown S (2004) Guide to the methods of study and identification of soil gymnamoebae. Protistology 3:148–190

    Google Scholar 

  • Smirnov AV, Chao E, Nassonova ES, Cavalier-Smith T (2011) A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist 162:545–570

    Article  PubMed  Google Scholar 

  • Stothard DR, Schroeder-Diedrich JM, Awwad MH, Gast RJ, Ledee DR, Rodriguez-Zaragoza S, Dean CL, Fuerst PA, Byers TJ (1998) The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J Eukaryot Microbiol 45:45–54

    Article  CAS  PubMed  Google Scholar 

  • Vannini A, Bruni N, Tomassini A, Franceschini S, Vettraino AM (2013) Pyrosequencing of environmental soil samples reveals biodiversity of the Phytophthora resident community in chestnut forests. FEMS Microbiol Ecol 85:433–442

    Article  CAS  PubMed  Google Scholar 

  • Walochnik J, Obwaller A, Aspöck H (2000) Correlations between morphological, molecular biological, and physiological characteristics in clinical and nonclinical isolates of Acanthamoeba spp. Appl Environ Microbiol 66:4408–4413

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by a research grant from the EU-project ‘EcoFINDERS’ No. 264465.

Author information

Author notes

  1. Stefan Geisen

    Present address: Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands

Authors and Affiliations

  1. Department of Terrestrial Ecology, Zoological Institute, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany

    Stefan Geisen, Anna Maria Fiore-Donno & Michael Bonkowski

  2. Molecular Parasitology, Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria

    Julia Walochnik

Authors
  1. Stefan Geisen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anna Maria Fiore-Donno
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Julia Walochnik
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael Bonkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stefan Geisen.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

Phylogenetic analysis of Centramoebida based on 145 SSU sequences (all 18 described SSU types of Acanthamoeba represented) and 1,771 positions, with Balamuthia and Prothacanthamoeba as outgroups. Major clades and T4 are boxed. Only sequence types are named, while individual sequences were omitted for clarity, except for new sequences obtained in this study (in red). Support values >50 % (maximum likelihood, left) or >0.5 (posterior probability, right) are shown for branches leading to major clades. Filled circles represent full support in both analyses; boxes: clades of sequence types with bright boxes containing clones obtained in this study (JPEG 1116 kb)

High resolution image (TIFF 534 kb)

Supplementary Fig. 2

Phylogenetic analysis focusing on sequence types and sequences associated with the new sequences obtained in this study. In total, 116 sequences with 1,947 unambiguously aligned positions were used; the tree is unrooted; values higher than 60 for maximum likelihood analyses (left) and 0.60 for Bayesian analyses (right) are shown. Black circles represent full support; red: strains obtained in this study; boxes: associated sequence types with bright boxes containing clones obtained in this study (JPEG 3408 kb)

High resolution image (TIFF 2841 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Geisen, S., Fiore-Donno, A.M., Walochnik, J. et al. Acanthamoeba everywhere: high diversity of Acanthamoeba in soils. Parasitol Res 113, 3151–3158 (2014). https://doi.org/10.1007/s00436-014-3976-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00436-014-3976-8

Keywords

Search

Navigation