Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Dec;7(12):2387-99.
doi: 10.1038/ismej.2013.116. Epub 2013 Jul 18.

Vampires in the oceans: predatory cercozoan amoebae in marine habitats

Cédric Berney  1 , Sarah Romac, Frédéric Mahé, Sébastien Santini, Raffaele Siano, David Bass
Affiliations

Vampires in the oceans: predatory cercozoan amoebae in marine habitats

Cédric Berney et al. ISME J. 2013 Dec.

Abstract

Vampire amoebae (vampyrellids) are predators of algae, fungi, protozoa and small metazoans known primarily from soils and in freshwater habitats. They are among the very few heterotrophic naked, filose and reticulose protists that have received some attention from a morphological and ecological point of view over the last few decades, because of the peculiar mode of feeding of known species. Yet, the true extent of their biodiversity remains largely unknown. Here we use a complementary approach of culturing and sequence database mining to address this issue, focusing our efforts on marine environments, where vampyrellids are very poorly known. We present 10 new vampyrellid isolates, 8 from marine or brackish sediments, and 2 from soil or freshwater sediment. Two of the former correspond to the genera Thalassomyxa Grell and Penardia Cash for which sequence data were previously unavailable. Small-subunit ribosomal DNA analysis confirms they are all related to previously sequenced vampyrellids. An exhaustive screening of the NCBI GenBank database and of 454 sequence data generated by the European BioMarKs consortium revealed hundreds of distinct environmental vampyrellid sequences. We show that vampyrellids are much more diverse than previously thought, especially in marine habitats. Our new isolates, which cover almost the full phylogenetic range of vampyrellid sequences revealed in this study, offer a rare opportunity to integrate data from environmental DNA surveys with phenotypic information. However, the very large genetic diversity we highlight within vampyrellids (especially in marine sediments and soils) contrasts with the paradoxically low morphological distinctiveness we observed across our isolates.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Phase contrast light micrographs of our terrestrial isolates. (a) Isolate from Lake Baikal published previously (Bass et al., 2009). (b–d) Isolate WaAra (Wales, soil/ moss sample). Two different individuals (c and d are the same); this isolate was undistinguishable morphologically from the Baikal isolate, and with identical SSU rDNA sequence. (e–h) Isolate BAra1 (Amazon basin, associated with aquatic plants). Three different individuals (e and f are the same); cell body generally more compact than in the other soil isolates we observed. In all of these isolates, filopodia tend to be concentrated at the ends of cytoplasmic arms. The white arrow in b highlights a temporary anastomosis between two arms, and the black arrows in c and g show the typical pattern of rapid resorption of these arms when the cell changes direction. Scale bars: 20 μm in a–d; 10 μm in e–h.
Figure 2
Figure 2
Phase contrast light micrographs of isolates KibAr, V1ld4, En42C and V1ld9 (Cumbria, UK, marine sediment) and CAraX (California, USA, marine sediment). (a, b) Isolate KibAr (two different individuals). (c–f) Isolate V1ld4 (four different individuals). These two isolates have identical SSU rDNA sequences and were undistinguishable morphologically, with filopodia radiating from all around a generally compact cell body, only rarely assuming an elongated form (as in d). The closely related isolate V2ld4 looked very similar but died before good pictures could be taken. The cell shown in a illustrates the typical pattern of active movement for this morphotype, with regular resorption of the trailing cytoplasm (the arrow indicates the direction of movement). In b, the cell is shown attacking a cluster of diatoms. Occasionally two parts of a cell move in different directions, and instead of one being resorbed they can end up dividing into two viable smaller individuals by cell fission (illustrated in e). Arrows in c and f highlight the very thin cytoplasmic veil from which filopodia emerge. Temporary anastomoses at the base of filopodia are visible in f. (g) Isolate En42C (very small individual). This isolate died soon after initial observation. (h, i) Isolate V1ld9 (two different individuals). At maximum size the cells were highly reticulate with many lacunae; SSU rDNA sequence almost identical to that of isolate En42C. (j–m) Isolate CAraX (four different individuals). Highly branching morphotype similar to that observed in terrestrial isolates, with filopodia concentrated at the end of cytoplasmic arms. Scale bars: 20 μm in c, e, f, k; 15 μm in d, h, j, m; 10 μm in a, b, i, l; 5 μm in g.
Figure 3
Figure 3
Differential interference contrast light micrographs of isolate MVa1x (Thalassomyxa sp., Majorca, Spain, marine sediment) and phase contrast light micrographs of isolate NVam1 (Penardia sp., North Carolina, USA, brackish sediment). (a–g) Thalassomyxa sp. from Majorca; six different individuals (f and g are the same). Younger, more rapidly moving cells have a relatively compact (a) but sometimes elongated (e) morphology, similar to that of isolates KibAr and V1ld4 (see Figure 2). They can fuse into very large, slowly moving plasmodia (b, f, g) with lacunae in the cytoplasm and anastomoses between the peripheral filopodia (highlighted with arrows in f). Both smaller cells and giant plasmodia go into digestive cysts at regular intervals (c, d); a single plasmode can break up into many cysts of variable shapes and sizes (d). (h–k) Isolate NVam1 (Penardia sp.; four different individuals). Cell body generally intermediate between the more compact morphotype of some marine isolates and the branched morphotype of the terrestrial ones, but on average smaller than in all other isolates. Filopodia emerge from all around the cell; they are usually broader at the base and branching into thinner extensions. Temporary anastomoses frequently observed at the base of filopodia. Scale bars: 30 μm in a, e–g; 25 μm in b; 20 μm in d; 10 μm in h, i; 5 μm in c, j, k.
Figure 4
Figure 4
SSU rDNA phylogeny of vampyrellids in a cercozoan context, showing the position of our new isolates with respect to previously published isolates and identified environmental clones from GenBank. Alveolates and stramenopiles were used to root the tree. The ML topology is shown; bootstrap support values after 200 replicates and Bayesian posterior probabilities (see Materials and methods section) are indicated at nodes when above 50% and/or 0.70, respectively. Black blobs represent support values at or above 95%/0.95. Vampyrellids cluster in three main clades A, B and C. New and previously published isolates are highlighted in bold. Black squares identify marine sequences and white squares identify terrestrial (soil or freshwater) sequences; isolate NVam1 was found in brackish sediment. More details about the ecological provenance of environmental sequences from GenBank are given in Supplementary Table S2.
Figure 5
Figure 5
Graphical representation of the diversity of vampyrellid SSU-types found in the BioMarKs data in relation to sequenced isolates, highlighting their habitat preferences. A ML tree is used, based on the V4 region of the SSU rDNA; it was rooted with selected members of other endomyxan lineages. Clades and lineages are labelled consistently with Figure 4. Some branch lengths within fast-evolving lineage B3 have been reduced by half. Sequences from our new isolates are highlighted with arrows. The ecological provenance of environmental sequences from GenBank is listed (see also Supplementary Table S2). That of BioMarKs V4 SSU-types is indicated in the boxes (SED, sediment; DCM, deep chlorophyll maximum; SUR, surface waters). In the labels of the BioMarKs SSU-types, the number in brackets indicates how many individual sequences belong to that SSU-type. For each SSU-type, varying shades of grey in the boxes give an indication of the number of individual sequences found in each particular sample type: light grey for unique sequences, medium grey for 2 to 5 sequences, dark grey for 6 to 20 sequences, and black for >20 sequences. The two most diverse lineages (subclades P and T) were collapsed for clarity, but the V4 diversity and ecological provenance of all SSU-types within these lineages is provided in Supplementary Figure S1.
See this image and copyright information in PMC

References

    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. - PubMed
    1. Bass D, Cavalier-Smith T. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa) Int J Syst Evol Microbiol. 2004;54:2393–2404. - PubMed
    1. Bass D, Chao EEY, Nikolaev S, Yabuki A, Ishida K, Berney C, et al. Phylogeny of novel naked filose and reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea revised. Protist. 2009;160:75–109. - PubMed
    1. Bass D, Yabuki A, Santini S, Romac S, Berney C. Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases. PLoS One. 2012;7:e49090. - PMC - PubMed
    1. Berney C, Fahrni J, Pawlowski J. How many novel eukaryotic ‘kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol. 2004;2:13. - PMC - PubMed

Publication types

LinkOut - more resources