GLORIA — GEOMAR Library Ocean Research Information Access

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Sequence variations in the large-subunit ribosomal RNA gene of ammonia (foraminifera, protozoa) and their evolutionary implications (1996)

Holzmann, Maria ; Piller, Werner ; Pawlowski, Jan

Springer

Journal of molecular evolution 43 (1996), S. 145-151

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ISSN: 1432-1432

Keywords: Foraminifera ; Sequence dissimilarity ; LSU rRNA gene ; Phylogeny

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genusAmmonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens namedAmmonia sp. 1 andAmmonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% inAmmonia sp. 1 and from 0.7% to 2.3% inAmmonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally acaepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen ofAmmonia may reach up to 4.9%. Most of the observed variations result from multiplication of CA or TA serial repeats occurring in two particularly variable regions. For single base changes, C-T transitions are most frequently observed. We discuss the evolution of expansion segments and their use for phylogenetic studies.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF02337359

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Genetic diversity and distribution patterns of a group of foraminifera from the genus Bolivina (2017)

Kucera, Michal ; Silye, Lóránd ; Weiner, Agnes K M ; [et al.]

PANGAEA

In: Supplement to: Kucera, Michal; Silye, Lóránd; Weiner, Agnes K M; Darling, Kate F; Lübben, Birgit; Holzmann, Maria; Pawlowski, Jan; Schönfeld, Joachim; Morard, Raphael (2017): Caught in the act: Anatomy of an ongoing benthic-planktonic transition in a marine protist. Journal of Plankton Research, 39 (3), 436-449, https://doi.org/10.1093/plankt/fbx018

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Publication Date: 2023-03-03

Description: The transition from benthos to plankton requires multiple adaptations, yet so far it remains unclear how these are acquired in the course of the transition. To investigate this process, we analyzed the genetic diversity and distribution patterns of a group of foraminifera of the genus Bolivina with a tychopelagic mode of life (same species occurring both in benthos and plankton). We assembled a global sequence dataset for this group from single-cell DNA extractions and occurrences in metabarcodes from pelagic environmental samples. The pelagic sequences all cluster within a single monophyletic clade within Bolivina. This clade harbors three distinct genetic lineages, which are associated with incipient morphological differentiation. All lineages occur in plankton and benthos, but only one lineage shows no limit to offshore dispersal and has been shown to grow in the plankton. These observations indicate that the emergence of buoyancy regulation within the clade preceded the evolution of pelagic feeding and that the evolution of both traits was not channeled into a full transition into the plankton. We infer that in foraminifera, colonization of the planktonic niche may occur by sequential cooptation of independently acquired traits, with holoplanktonic species being recruited from tychopelagic ancestors.

Keywords: Center for Marine Environmental Sciences; MARUM

Type: Dataset

Format: application/zip, 4 datasets

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(Supplementary Table 2) Surficial sediment characteristics and interpretations for ANDEEP I-III stations based on sediment cores and surface and sediment profile images

Brandt, Angelika ; Gooday, Andrew J ; Brandão, Simone N ; [et al.]

PANGAEA

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Publication Date: 2023-05-12

Keywords: Area/locality; Bioturbation; Burrows; Depth, bottom/max; Description; Grain size description; Mounds; Number of stations; Occurrence; Sediment type; Station label; Surface description; Tubes

Type: Dataset

Format: text/tab-separated-values, 270 data points

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Occurence of monothalamous foraminifera in Admiralty Bay, King George Island, West Antarctica (Table 1, 2) (2007)

Majewski, Wojciech ; Lecroq, Beatrice ; Sinniger, Frederic ; [et al.]

PANGAEA

In: Supplement to: Majewski, Wojciech; Lecroq, Beatrice; Sinniger, Frederic; Pawlowski, Jan (2007): Monothalamous foraminifera from Admiralty Bay, King George Island, West Antarctica. Polish Polar Research, 28(3), 187-210

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Publication Date: 2023-07-10

Description: During the late 2007 austral summer, 20 sediment samples were collected in Admiralty Bay (King George Island, South Shetlands, West Antarctica) from 8 down to 254 m water-depth (mwd). The samples yielded abundant assemblage of monothalamous benthic foraminifera, belonging to at least 40 morphospecies. They constituted the first such collection from Antarctic Peninsula fjords and provided a new insight into this group's diversity and distribution. Among organic-walled taxa, Psammophaga sp., Allogromia cf. crystallifera, and three morphotypes of Gloiogullmia were especially abundant. Agglutinated forms were dominated by Hippocrepinella hirudinea, Psammosphaera spp., Lagenammina spp., and various mudballs. Although, the majority of the morphotypes were known from other high?latitude locations, somewere reported for the first time. Our quantitative data (〉125 µm) showed the greatest differences between monothalamous foraminifera assemblages at shallowest water depths above 50 mwd. The deepest assemblages from between 179 and 254 mwd, were most similar, suggesting uniform near-bottom conditions at ~200 mwd throughout the Admiralty Bay.

Keywords: Admiralty_Bay; Allogromia cf. crystallifera; Area; Armorella cf. sphaerica; Armorella sp.; Astrammina rara; Astrammina triangularis; Astrorhiza sp.; Bathysiphon cf. argenteus; Bathysiphon cf. flexilis; Calculated; Calculated after Shannon (1948); Counting 〉125 µm fraction; Crithionina cf. granum; Crithionina sp.; Depth, bathymetric; DEPTH, sediment/rock; Distance; Dominance; Foraminifera, benthic; Foraminifera, benthic dead; Foraminifera, benthic indeterminata; Foraminifera, benthic monothalamous; Fraction; Gloiogullmia sp.; Gromiids; Hippocrepina cf. crassa; Hippocrepinella alba; Hippocrepinella hirudinea; King George Island, Antarctic Peninsula; Lagenammina spp.; LATITUDE; LONGITUDE; Micrometula sp.; MULT; Multiple investigations; Nemogullmia spp.; Number of species; Pelosina aff. sphaeriloculum; Pelosina didera; Phainogullmia cf. aurata; Psammophaga sp.; Psammosphaera spp.; Sample code/label; Sample method; Shannon Diversity Index; Tinogullmia sp.; Vanhoeffenella gaussi

Type: Dataset

Format: text/tab-separated-values, 1015 data points

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List, processing details and taxonomic counts of planktonic foraminifera for the selected sediment samples of the study for morphologic analyses (Table S1) (2020)

Barrenechea Angeles, Ines ; Lejzerowicz, Franck ; Cordier, Tristan ; [et al.]

PANGAEA

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Publication Date: 2024-02-14

Keywords: 494-2; 496-2; 509-2; 511-2; 512-1; 513-2; 528-2; 528-3; 529-2; 530-1; 531-2; 532-2; 534-2; 535-2; 536-1; 537-2; 538-1; Center for Marine Environmental Sciences; Dentigloborotalia anfracta; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Elevation of event; Event label; Flemish Cap; Foraminifera; Foraminifera, planktic, total; GC; GeoB18515-2; GeoB18517-2; GeoB18530-2; GeoB18532-2; GeoB18533-1; GeoB18534-2; GeoB18549-2; GeoB18549-3; GeoB18550-2; GeoB18551-1; GeoB18552-2; GeoB18553-2; GeoB18555-2; GeoB18556-2; GeoB18557-1; GeoB18558-2; GeoB18559-1; Globigerina bulloides; Globigerina falconensis; Globigerinella calida; Globigerinella siphonifera; Globigerinita glutinata; Globigerinita minuta; Globigerinita uvula; Globigerinoides conglobatus; Globigerinoides elongatus; Globigerinoides ruber pink; Globigerinoides ruber white; Globorotalia hirsuta; Globorotalia inflata; Globorotalia menardii; Globorotalia truncatulinoides; Gravity corer; Latitude of event; Location of event; Longitude of event; Maria S. Merian; MARUM; Mass; Metabarcoding; microfossils; MSM39; MUC; MultiCorer; Neogloboquadrina dutertrei; Neogloboquadrina incompta; Neogloboquadrina pachyderma; North Atlantic; Orphan Basin; Orphan Knoll; Pulleniatina obliquiloculata; sedimentary ancient DNA; SE Grand Banks Slope; Size fraction; Split; SW Grand Banks Slope; Tenuitella fleisheri; Trilobatus sacculifer; Turborotalita quinqueloba; Wet mass

Type: Dataset

Format: text/tab-separated-values, 5199 data points

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(Supplementary Table 1) Expected number of species E(S100) of Isopoda in ANDEEP I-III stations (2007)

Brandt, Angelika ; Gooday, Andrew J ; Brandão, Simone N ; [et al.]

PANGAEA

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Publication Date: 2024-06-26

Keywords: Agassiz Trawl; AGT; ANT-XIX/3; ANT-XIX/4; ANT-XXII/3; Date/Time of event; Date/Time of event 2; EBS; Epibenthic sledge; Event label; Expected number of species; Haul length; Latitude of event; Latitude of event 2; Longitude of event; Longitude of event 2; MOOR; Mooring; Polarstern; PS61/041-3; PS61/042-2; PS61/043-8; PS61/046-7; PS61/099-4; PS61/105-7; PS61/114-4; PS61/129-2; PS61/131-3; PS61/132-2; PS61/133-3; PS61/134-3; PS61/135-4; PS61/136-4; PS61/137-4; PS61/138-6; PS61/139-6; PS61/140-8; PS61/141-10; PS61/142-6; PS61/143-1; PS61 ANDEEP 1; PS61 ANDEEP 2; PS67/016-10; PS67/021-7; PS67/059-5; PS67/074-6; PS67/078-9; PS67/080-9; PS67/081-8; PS67/088-8; PS67/094-14; PS67/102-3; PS67/110-8; PS67/121-10; PS67/133-2; PS67/142-5; PS67/150-6; PS67/151-7; PS67/152-6; PS67/153-7; PS67/154-9; PS67 ANDEEP 3; Sample elevation; Scotia Sea, southwest Atlantic; South Atlantic Ocean; Weddell Sea

Type: Dataset

Format: text/tab-separated-values, 120 data points

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Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers (2022)

Macher, J.N. (Jan) ; Bloska, Dimitra Maria ; Holzmann, Maria ; [et al.]

PeerJ

In: PeerJ vol. 10 no. e13952

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Publication Date: 2024-05-30

Description: Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 mm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.

Keywords: Foraminifera ; Metabarcoding ; Beach ; Community composition ; Intertidal ; Molecular ; biodiversity

Repository Name: National Museum of Natural History, Netherlands

Type: info:eu-repo/semantics/article

Format: application/pdf

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