Novel lineages of Southern Ocean deep-sea foraminifera revealed by environmental DNA sequencing

Pawłowski, Jan; Fontaine, Délia; Silva, Ana Aranda da; Guiard, Jackie

doi:10.1016/j.dsr2.2011.01.009

Cited by 38 publications

(30 citation statements)

References 27 publications

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“…We sequenced three 1-g surface sediment replicates per sediment core, subsampled consistently from each of the two cores obtained per multi-corer, deployed two to three times in 3 stations. We rely on an extensive reference database existing in our laboratory and partly included in Foram Barcoding project (Pawlowski and Holzmann, 2014) to assign the environmental sequences to taxa already recognized in previous genetic studies of deep Southern Ocean (Gooday et al, 2004a(Gooday et al, , 2004bBrandt et al, 2007;Cedhagen et al, 2009;Pawlowski et al, 2007Pawlowski et al, , 2011b. Some traditional studies based on morphological identification provide us with the comparison of foraminiferal patchiness inferred from eDNA data and microscopic counts (Cornelius and Gooday, 2004).…”

Section: Introductionmentioning

confidence: 99%

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Lejzerowicz

Esling

Pawłowski

2014

Deep Sea Research Part II: Topical Studies in Oceanography

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Section: Introductionmentioning

confidence: 99%

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Lejzerowicz

Esling

Pawłowski

2014

Deep Sea Research Part II: Topical Studies in Oceanography

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“…34. The second level corresponded to a family or clade defined by previous phylogenetic studies (9,27). Finally, the third level corresponded either to the genus level or to the species level for welldescribed voucher specimens.…”

Section: Methodsmentioning

confidence: 99%

“…The sequences of early lineages were particularly abundant in environmental DNA surveys of marine (6), freshwater (7), and soil (8) ecosystems. Eight new family-rank clades branching at the base of the foraminiferal tree were distinguished in DNA extracts of deep Southern Ocean sediments (9). However, all these studies relied on clone libraries, limiting the number of sequences available for analysis.…”

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confidence: 99%

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Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

Lecroq

Lejzerowicz

Bachar

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile, and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribosomal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational taxonomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) foraminifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology, the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach.DNA barcoding | next-generation sequencing | small subunit ribosomal RNA | microbial eukaryote | cosmopolitanism D eep-sea sediments are home for a wide range of small-sized metazoan and protistan taxa. The diversity of this meiofaunal community is difficult to estimate because its study suffers from undersampling, difficult access, and the problems involved in culturing deep-sea organisms. Additionally, most of the deep-sea species are tiny, fragile, and difficult to identify. Benthic foraminifera form one of the most abundant and diverse groups of deepsea meiofauna, found even in the deepest ocean trenches (1). Particularly in abyssal areas, a large proportion of deep-sea foraminifera belongs to early lineages characterized by simple, singlechambered (monothalamous), organic-walled or agglutinated tests, which are poorly preserved in the fossil record (2). These early monothalamous lineages traditionally classified in orders Allogromiida and Astrorhiza have been proposed to form a large radiation in the Neoproterozoic, well before the first multichambered foraminifera appeared (3). However, the assessment of their diversity is hampered by the fragment...

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“…Amphipods and polychaetes are consumed to a high percentage (50-80%), but other crustaceans and gastropods were also ingested . Using stable isotope Novel molecular methods revealed a pivotal role of a high biodiversity of foraminiferans for the food webs of the abyssal benthos, more than 90% of the identified phylotypes were reported to be new (Pawlowski et al, 2011).…”

Section: Deployed a Novelmentioning

confidence: 99%

The Southern Ocean deep sea—A benthic view to pelagic processes

Brandt

Würzberg

2014

Deep Sea Research Part II: Topical Studies in Oceanography

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Novel lineages of Southern Ocean deep-sea foraminifera revealed by environmental DNA sequencing

Cited by 38 publications

References 27 publications

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

The Southern Ocean deep sea—A benthic view to pelagic processes

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