The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages

Richards, Thomas A.; Vepritskiy, Alexey A.; Gouliamova, D.E.; Nierzwicki‐Bauer, Sandra A.

doi:10.1111/j.1462-2920.2005.00828.x

Cited by 151 publications

(149 citation statements)

References 42 publications

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“…However, in recent environmental surveys of freshwater lakes, the existence of taxa related to Perkinsea has been suggested (Richards et al, 2005;Lefèvre et al, 2008;Lepère et al, 2008). Nevertheless, as the analyses did not include any sequences from the MA or statistical support estimations for the tree topologies (Richards et al, 2005;Lefèvre et al, 2008;Lepère et al, 2008), it cannot be determined whether the sequences belong to Perkinsea or to any of the MA.…”

Section: Unknown Perkinsea Diversity In Marine and Freshwatersmentioning

confidence: 91%

“…To date, the Perkinsus and Parvilucifera (members of Perkinsea) and MA have only been identified in marine environments (Noren et al, 1999;Villalba et al, 2004;Groisillier et al, 2006;Guillou et al, 2008;Leander and Hoppenrath, 2008). However, microscopy observations, as well as reports of deeply diverging alveolate 18S rDNA sequences, point to the existence of freshwater Perkinsea species (Brugerolle, 2002(Brugerolle, , 2003Green et al, 2003;Richards et al, 2005;Davis et al, 2007;Lefèvre et al, 2008;Lepère et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

et al. 2010

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Protist parasites are ecologically important, as they can have great impact on host population dynamics and functioning of entire ecosystems. Nevertheless, little is known about their prevalence in aquatic habitats. Here, we investigate the diversity and distributional patterns of the protist parasites Perkinsus and Parvilucifera (Perkinsea). Our approach included 454 pyrosequencing of the 18S rDNA gene obtained from a high-altitude lake (Lake Finsevatn, Norway) and phylogenetic analyses of all publicly available sequences related to Perkinsea. The applied PCR primers target a 450 bp region that encompass the variable V4 region of the 18S rDNA gene and have been optimized for the Titanium upgrade of the 454 technology. Nearly 5000 sequences longer than 150 bp were recovered from nearly all eukaryotic supergroups, and of those, 13 unique sequences were affiliated to Perkinsea. Thus, our new strategy for 454 amplicon sequencing was able to recover a large diversity of distantly related eukaryotes and previously unknown species of Perkinsea. In addition, we identified 40 Perkinsea sequences in GenBank generated by other recent diversity surveys. Importantly, phylogenetic analyses of these sequences identified 17 habitat-specific marine and freshwater clades . Hence, only a few successful transitions between these habitats have taken place over the entire history of Perkinsea, suggesting that the boundary between marine and fresh waters may constitute a barrier to cross-colonizations for intracellular parasites.

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Section: Unknown Perkinsea Diversity In Marine and Freshwatersmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

et al. 2010

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“…As a rule, protists in marine and non-marine environments are largely distinct (Richards et al, 2005;von der Heyden & Cavalier-Smith, 2005;von der Heyden et al, 2004). Numerous major taxa are restricted to one or other habitat type.…”

Section: Discussion Single-gene Analysesmentioning

confidence: 99%

Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

Stoeck¹,

Jost²,

Boenigk³

2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicating cryptic species. One of the best-investigated morphospecies with respect to molecular and ecophysiological variation are flagellates of the Spumella morphotype. Here, we have phylogenetically analysed three protein-coding genes (actin, alpha-tubulin, beta-tubulin), internal transcribed spacers (ITS1, ITS2) and the 5.8S rDNA of 17 Spumella-like strains isolated from soil, freshwater and marine samples in order to (i) test the validity of the current Spumella-like phylogenetic classification system based exclusively on small subunit (SSU) rDNA, (ii) elucidate the phylogenetic associations of SSU rDNA-unresolved strains and (iii) evaluate the validity of the assignment of ecophysiological adaptations to previously identified SSU rDNA sequence clades. All single-gene analyses show different patterns of support, are incongruent and identify a number of conflicting nodes. Likewise, a concatenation of all protein genes fails to recover specific SSU rDNA clades. However, a combined analysis of all genes confidently resolved the conflicts of the single genes and the protein-gene concatenations and resulted in a tree topology that is identical to the SSU rDNA analysis, but with enhanced phylogenetic resolution and decisively greater support. We conclude that, depending on the genes concatenated, a 'supergene' analysis minimizes artefactual effects of single genes and may be superior in its performance in phylogenetically analysing cryptic species. We confirm the validity of the SSU rDNA Spumella-like phyloclades and support the suggestion that these clades indeed seem to reflect certain ecophysiological adaptations. INTRODUCTIONIn protistology, species descriptions often pragmatically conform to the morphological species concept: microbial eukaryotes have traditionally been identified on the basis of their morphological diversity (Finlay et al., 1996). In general, such a concept seems to work well for a number of larger protists. However, numerous smaller species (nanoand picoeukaryotes) are morphologically indistinguishable (Coleman, 2002;Hackstein, 1997;Nanney, 2004), as evolution and speciation in microbial eukaryotes are not necessarily accompanied by a perceptible morphological change (Machelon et al., 1984). As a consequence, distinct microbial eukaryote species are often classified as a single species (5cryptic species). The prevalence of such cryptic species impairs biodiversity estimates and analyses of spatial distribution patterns and ecological functions (Bickford et al., 2006;Coleman, 2002;Hackstein, 1997).A group of organisms that falls into this category are colourless chrysophytes often referred to as 'Spumella-like' flagellates or Spumella spp. (Auer & Arndt, 2001;Cleven & Weisse, 2001;Weitere & Arndt, 2003). These organisms account for a substantial proportion of the heterotrophic nanoflagellate (HNF) biomass, especially in freshwater systems (Domaizon et al., 2003;Felip et al., 1999;Zhao et al., 2003), and...

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“…PCR amplification of prokaryotic and eukaryotic small-subunit (SSU) rRNA used the following primer pairs: 27f/1492r targeting Bacteria (Lane, 1991), 21Fa/1492R targeting Archaea (DeLong, 1992) and both 3Fphp/1749Rphp (Richards et al, 2005) and 360Fe/1391Re (Dawson and Pace, 2002) targeting Eukarya. PCR amplification was performed using ThermoStart DNA polymerase (ABgene, Rockford, IL, USA) on a PTC-200 DNA Engine thermocycler (MJ Research, Watertown, MA, USA).…”

Section: Nucleic Acid Extractionmentioning

confidence: 99%

“…PCR amplification was performed using ThermoStart DNA polymerase (ABgene, Rockford, IL, USA) on a PTC-200 DNA Engine thermocycler (MJ Research, Watertown, MA, USA). Duplicate reactions were performed for each clone library using 0.5-25 ng DNA template in 25 ml volumes and the previously described cycling conditions (DeLong, 1992;Dawson and Pace, 2002;Richards et al, 2005;Liou et al, 2008). Pooled PCR products were examined by agarose gel electrophoresis, purified using the QIAquick gel extraction kit (Qiagen, Santa Clarita, CA, USA) and ligated into the vector pCR2.1 (TOPO-TA cloning, Invitrogen) or pSC-A (StrataClone PCR cloning, Stratagene, La Jolla, CA, USA), following the manufacturers' recommended protocols.…”

Section: Nucleic Acid Extractionmentioning

confidence: 99%

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

et al. 2009

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The propensity for groundwater ecosystems to recover from contamination by organic chemicals (in this case, coal-tar waste) is of vital concern for scientists and engineers who manage polluted sites. The microbially mediated cleanup processes are also of interest to ecologists because they are an important mechanism for the resilience of ecosystems. In this study we establish the long-term dynamic nature of a coal-tar waste-contaminated site and its microbial community. We present 16 years of chemical monitoring data, tracking responses of a groundwater ecosystem to organic contamination (naphthalene, xylenes, toluene, 2-methyl naphthalene and acenaphthylene) associated with coal-tar waste. In addition, we analyzed small-subunit (SSU) ribosomal RNA (rRNA) genes from two contaminated wells at multiple time points over a 2-year period. Principle component analysis of community rRNA fingerprints (terminal-restriction fragment length polymorphism (T-RFLP)) showed that the composition of native microbial communities varied temporally, yet remained distinctive from well to well. After screening and analysis of 1178 cloned SSU rRNA genes from Bacteria, Archaea and Eukarya, we discovered that the site supports a robust variety of eukaryotes (for example, alveolates (especially anaerobic and predatory ciliates), stramenopiles, fungi, even the small metazoan flatworm, Suomina) that are absent from an uncontaminated control well. This study links the dynamic microbial composition of a contaminated site with the long-term attenuation of its subsurface contaminants.

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The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages

Cited by 151 publications

References 42 publications

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

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