Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

López‐García, Purificación; Rodrı́guez-Valera, Francisco; Pedrós-Alió, Carlos; Moreira, David

doi:10.1038/35054537

Cited by 803 publications

(663 citation statements)

References 22 publications

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“…More recently, similar studies on eukaryotic diversity have also shown that, although eukaryotes are far more diverse than previously thought, most novel sequences determined from environmental surveys actually cluster into major acknowledged eukaryotic ''kingdoms'' (Berney et al 2004). To date, in contrast to the situation in prokaryotes, only very few environmental sequences could not be associated with any of the major eukaryotic kingdoms, for example the clade DH148-5-EKD18 (López-García et al 2001;López-García and Moreira 2008). At the next lower taxonomic level, however, the situation is far from being resolved.…”

Section: Introductionmentioning

confidence: 93%

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

Lara¹,

Moreira²,

López‐García³

2010

Protist

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Previous environmental surveys of eukaryotic diversity using the small subunit ribosomal RNA (SSU rRNA) gene have revealed many clone sequences that branch near the base of Fungi. In this work, we demonstrate that many of these sequences, including those of the environmental clade LKM11, form a monophyletic and strongly supported group that also includes two sequences derived from the parasitic genus Rozella. This novel clade, called here ''Rozellida'', is the deepest branch of true fungi so far identified, and appears to be extremely diverse in the environment.

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Section: Introductionmentioning

confidence: 93%

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

Lara¹,

Moreira²,

López‐García³

2010

Protist

Self Cite

163

116

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“…Thraustochytrids are distributed in saline lakes and in marine, estuarine, and deep-sea waters throughout the world (35,47,52), and they have been isolated from algal and plant material, as well as from sediments and water (14,37,55,59). Recently, a rapid direct detection technique for thraustochytrids using the fluorogenic acriflavine dye was developed (53).…”

mentioning

confidence: 99%

Isolation and Characterization of a Novel Single-Stranded RNA Virus Infectious to a Marine Fungoid Protist, Schizochytrium sp. (Thraustochytriaceae, Labyrinthulea)

Takao

Nagasaki

Mise

et al. 2005

Appl Environ Microbiol

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Thraustochytrids are cosmopolitan osmoheterotrophic microorganisms that play important roles as decomposers, producers of polyunsaturated fatty acids, and pathogens of mollusks, especially in coastal ecosystems. SssRNAV, a novel single-stranded RNA (ssRNA) virus infecting the marine fungoid protist Schizochytrium sp. (Labyrinthulea, Thraustochytriaceae) was isolated from the coastal water of Kobe Harbor, Japan, in July 2000, and its basic characteristics were examined. The virus particle is icosahedral, lacks a tail, and is ca. 25 nm in diameter. SssRNAV formed crystalline arrays and random assemblies within the cytoplasm of host cells, and it was also concentrated along the intracellular membrane structures. By means of one-step growth experiments, the lytic cycle and the burst size were estimated to be <8 h and 5.8 ؋ 10 3 to 6.4 ؋ 10 4 infectious units per host cell, respectively. SssRNAV had a single molecule of ssRNA that was approximately 10.2 kb long, three major proteins (37, 34, and 32 kDa), and two minor proteins (80 and 18 kDa). Although SssRNAV was considered to have some similarities with invertebrate viruses belonging to the family Dicistroviridae based on its partial nucleotide sequence, further genomic analysis is required to determine the detailed classification and nomenclature of SssRNAV. Our results indicate that viral infection is one of the significant factors controlling the dynamics of thraustochytrids and provide new insights into understanding the ecology of these organisms.

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“…Environmental DNA surveys are revealing a huge unknown diversity of microbial eukaryotes both globally and within individual samples (Epstein and Lopez-Garcia 2008;Lopez-Garcia et al 2001;Pawlowski et al 2012). This high diversity in turn suggests the existence of extremely complex, but mostly undocumented ecological interactions.…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

Kosakyan

Mulot

Mitchell

et al. 2015

European Journal of Protistology

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Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.

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Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

Cited by 803 publications

References 22 publications

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

Isolation and Characterization of a Novel Single-Stranded RNA Virus Infectious to a Marine Fungoid Protist, Schizochytrium sp. (Thraustochytriaceae, Labyrinthulea)

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

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