Open Access Research article

Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

Aurélie Chambouvet1*, Cédric Berney23, Sarah Romac23, Stéphane Audic23, Finlay Maguire1, Colomban De Vargas23 and Thomas A Richards4

Author Affiliations

1 Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK

2 CNRS, UMR7144, Equipe Evolution du Plancton et Paleo-Ocean, Roscoff, France

3 UPMC Univ Paris 06, UMR 7144 Adaptation et Diversité en Milieu Marin, Roscoff, France

4 Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK

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BMC Microbiology 2014, 14:110  doi:10.1186/1471-2180-14-110

Published: 29 April 2014

Abstract

Background

Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations.

Results

We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms.

Conclusions

These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the ‘seed bank’ microbial community.

Keywords:
454 pyrosequencing; Perkinsus; Parvilucifera; Food web; Protist; Parasite