Species (Prokaryote)

Depósito de investigación de la Universidad de Sevilla https://idus.us.es/ “This version of the chapter has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: http://dx.doi.org/10.1007/978-3-642-11274-4_1876” SPECIES (PROKARYOTE) Affiliation Antonio Ventosa, Cristina Sánchez-Porro Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla 41012 Sevilla, Spain [email protected] Definition A species is a category that circumscribes a (preferably) monophyletic and genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardized conditions (Rosselló-Mora and Amann 2001). Keywords Classification – Phylogeny – Average Nucleotide Identity – digital DNA-DNA hybridization – Genomic Indexes – Taxonomy Overview Species is the basic unit and most important taxonomic rank in prokaryote classification, represented by a group of microorganisms that share a common ancestor (monophyly) and have a genotypic relationship and coherent phenotypic features. The concept of species in prokaryotes is quite complex, since it is based on the premises of the species adopted for higher organisms, which are differentiated by the inability of reproduction among the organisms. However, this concept cannot be applied to prokaryotes, able to exchange genetic material easily among different species. Besides, morphologically they are not so diverse, and thus the relative morphologic simplicity of most prokaryotic microorganisms implies that morphology is, in general, of little importance in contrast with the classification of higher organisms. A species is represented by a type strain, a designated strain that is used as a reference specimen as a permanent example of the species. Traditionally, the definition of species in prokaryotes was based on the determination of the DNA-DNA hybridization values and ΔTm. It was generally accepted that strains with approximately 70 % or greater DNADNA relatedness and with 5 °C or less ΔTm should be considered as members of the same species (Wayne et al. 1987). However, certain drawbacks with respect to reproducibility, workability, and rigid application of DNADNA hybridization were reported (Stackebrandt et al. 2002). For those reasons, the prokaryote species delimitation has been based on a polyphasic approach which included phenotypic, genotypic, chemotaxonomic, and phylogenetic features. Phenotypic characteristics should agree with DNA-DNA hybridization values, and it was recommended that a distinct genospecies that cannot be differentiated from another genospecies on the basis of any known phenotypic property not be named until they could be differentiated by some phenotypic features. In recent years, new methods and techniques have been proposed to supplement or supplant the experimental DNA-DNA reassociation technique. The most extensively used is the 16S rRNA gene sequence analysis, a molecular marker to establish relationships among nucleotide sequences in the definition of prokaryotic species. On that basis, it was proposed that strains sharing 16S rRNA gene similarities below 97 % could be considered as different genospecies (Stackebrandt and Goebel 1994). More recently, this percentage has been fixed on a 98.7 %, (Kim et al. 2014; Chun et al. 2018), requiring a high quality of the 16S rRNA gene sequences under investigation (Chun et al. 2018). However, comparative studies clearly reveal the limitations of the sequence analysis of this highly conserved gene in the determination of relationships at the strain level. To overcome these limitations, MultiLocus Sequence Analysis (MLSA) based on conservative protein-coding genes, called housekeeping genes, had been developed for its applicability to genomically circumscribe the taxon species and differentiating it from neighboring species (Gevers et al. 2005). Such genes should be at diverse chromosomal loci and widely distributed among taxa. A more recent approach that advances the species definition for prokaryotes, as it is currently widely accepted is based on the whole genome sequence analysis, by using the overall genome related indexes (OGRIs) (Chun and Rainey 2014). The Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) are the most widely used. It has been estimated that ANI values of approximately 95-96 %, and dDDH 70 %, respectively, corresponded to the traditional 70 % DNA-DNA reassociation standard of the current species definition (Konstantinidis and Tiedje 2005; Goris et al. 2007; Richer and Rosselló-Móra 2009; Meier-Kolthoff et al. 2013; Chun and Rainey 2014; Chun et al. 2018). Further Reading Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12:406–411 Tindall BJ, Rosselló-Mora R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438 References Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324 Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X-W, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466 Gevers D, Cohan FM, Lwrence JG, Spratt G, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739 Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 Kim M, Oh H-S, Park S-C, Chun J (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:2567–2572 Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131 Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67 Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 Stackebrandt E, Frederiksen W, Garrity GM, Griment PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464