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abstract

Molecular tools are an important part to study the phylogeny and taxonomy of foraminifera. In the present chapter, isolation and extraction of these single-celled organisms will be described. Furthermore, the amplification of the 18S barcoding fragment in foraminifera and detection of amplified products by agarose gel electrophoresis will be detailed.

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Xenophyophores are large, agglutinated foraminifera that dominate the benthic megafauna in some parts of the deep sea. Here, we describe an assemblage of largely fragmentary specimens from the Clarion-Clipperton Zone (CCZ), an area of the eastern abyssal Pacific hosting large, commercially significant deposits of polymetallic nodules. We recognised 18 morphospecies of which eight yielded DNA sequences. These include two new genera and three new species, Claraclippia seminuda gen. & sp. nov., Stereodiktyoma mollis gen. & sp. nov., and Aschemonella tani sp. nov., three that are assigned to known species, Abyssalia foliformis, Aschemonella monilis and Shinkaiya contorta, and two assigned to open nomenclature forms Abyssalia aff. foliformis and Stannophyllum aff. granularium. An additional ten forms are represented only by morphology. The following seven are placed in known genera, species and open-nomenclature forms: Aschemonella? sp., Homogammina sp., Psammina multiloculata, P. aff. multiloculata, P. aff. limbata form 1 sensu Gooday et al., 2018, P. aff. limbata form 2 sensu Gooday et al., 2018, and Stannophyllum spp. The other three could not be identified to genus level. This new collection brings the total of described and undescribed species and morphotypes from the CCZ to 27 and 70, respectively, reinforcing the already high diversity of xenophyophores known from this part of the Pacific.

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abstract

Xenophyophores are large, agglutinated foraminifera that dominate the benthic megafauna in some parts of the deep sea. Here, we describe an assemblage of largely fragmentary specimens from the Clarion-Clipperton Zone (CCZ), an area of the eastern abyssal Pacific hosting large, commercially significant deposits of polymetallic nodules. We recognised 18 morphospecies of which eight yielded DNA sequences. These include two new genera and three new species, Claraclippia seminuda gen. & sp. nov., Stereodiktyoma mollis gen. & sp. nov., and Aschemonella tani sp. nov., three that are assigned to known species, Abyssalia foliformis, Aschemonella monilis and Shinkaiya contorta, and two assigned to open nomenclature forms Abyssalia aff. foliformis and Stannophyllum aff. granularium. An additional ten forms are represented only by morphology. The following seven are placed in known genera, species and open-nomenclature forms: Aschemonella? sp., Homogammina sp., Psammina multiloculata, P. aff. multiloculata, P. aff. limbata form 1 sensu Gooday et al., 2018, P. aff. limbata form 2 sensu Gooday et al., 2018, and Stannophyllum spp. The other three could not be identified to genus level. This new collection brings the total of described and undescribed species and morphotypes from the CCZ to 27 and 70, respectively, reinforcing the already high diversity of xenophyophores known from this part of the Pacific.

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Observations in 2022 of intertidal and subtidal foraminiferal faunas at four localities along the central-eastern side of Vancouver Island, British Columbia, Canada, and molecular analyses have documented the first occurrence of the nonindigenous Asian species Ammonia confertitesta Zheng in the northwestern Pacific Ocean. The species was present at three of these localities: Davis Lagoon south of Ladysmith (4% in the lagoon and 49% on the beach) and 0.6% in Nanaimo Harbor. The vector of introduction is thought to be the release of ballast water and associated sediment. These releases probably occurred in the Port of Vancouver, which were then transported by means of the cyclonic circulation across the Strait of Georgia, or from local anchorages close to the sampling sites. The timing of the introduction is impossible to determine because no stratigraphic record is presently available. However, foraminiferal studies in the late 1980s near the Port of Vancouver that recovered calcareous taxa did not report the presence of this species, nor was it found at 33 sites sampled from 1997 to 1999 throughout the Strait of Georgia.

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The abyssal Pacific Clarion Clipperton Zone (CCZ) hosts vast, commercially valuable seafloor deposits of polymetallic nodules. Foraminifera (testate protists) dominate benthic communities in this region. Here, we present a taxonomic survey, combining morphological and genetic data and focussing on mainly meiofauna-sized Foraminifera from the eastern CCZ. Sequences obtained from >100 specimens, the majority photographically documented, were analysed phylogenetically. Most were single-chambered Monothalamea (‘monothalamids’), a high percentage of them squatters inhabiting empty tests of mainly multi-chambered Foraminifera. The first sequences for the monothalamid genus Storthosphaera were obtained, while specimens assigned to Gloiogullmia, Hippocrepinella and Vanhoeffenella yielded new sequences. Among multichambered taxa, high-throughput Illumina sequencing (HTS) revealed a second haplotype of the calcareous rotaliid Oridorsalis umbonatus, possibly representing a distinct species. Additional HTS sequences were obtained from the rotaliids Nuttallides umbonifer and Globocassidulina subglobosa, confirming their wide distributions. We also obtained the first sequences for Cribrostomoides subglobosa, showing that it branches separately from other members of this genus. The fact that many sequences did not correspond to known morphospecies reflects the scarcity of reference barcodes for deep-sea Foraminifera, particularly the poorly known but highly diverse monothalamids. We recommend using HTS of single specimens to reveal further unknown species. Despite extensive research, much remains to be learnt about the true scale of foraminiferal biodiversity in the CCZ.

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Foraminifera are unicellular organisms that established the most diverse algal symbioses in the marine realm. Endosymbiosis repeatedly evolved in several lineages, while some engaged in the sequestration of chloroplasts, known as kleptoplasty. So far, kleptoplasty has been documented exclusively in the rotaliid clade. Here, we report the discovery of kleptoplasty in the species that belongs to the miliolid clade. The existence of kleptoplasty in the two main clades suggests that it is more widespread than previously documented. We observed chloroplasts in clustered structures within the foraminiferal cytoplasm and confirmed their functionality. Phylogenetic analysis of 18 ribosomal RNA gene sequences showed that branches next to symbiont-bearing Alveolinidae. This finding represents evidence of of a relationship between kleptoplastic and symbiotic foraminifera.. Analysis of ribosomal genes and metagenomics revealed that alveolinid symbionts and kleptoplasts belong to the same clade, which suggests a common ancestry.

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Non-marine monothalamous foraminifera are common in freshwater and soil habitats. They comprise a poorly-known group lacking sufficient information about diversity, morphology, reproduction, distribution and ecology. Based on an integrative morphological and molecular approach we describe a new family, a new genus and six new species of freshwater monothalamids from different localities in the Netherlands and France. We establish Astroperula as a new genus of organic walled freshwater foraminifera that contains two species, Astroperula dumacki and Astroperula parvipila. Furthermore, two new agglutinated freshwater monothalamids are described and illustrated, Limnogromia leanneae and Lacogromia pawlowskii, one new organic walled, Velamentofex dujardini, and a new naked monothalamid, Haplomyxa retiforma. Additional information is provided about a special form of cell division in Claparedellus lachmannii and L. leanneae, and feeding behavior in cultures of V. dujardini. Morphological observations are added for an unidentified Limnogromia sampled from the Netherlands and two types of Lacogromia sampled from an alpine region in the French Pyrenees and a karst sinkhole in Bosnia and Herzegovina. The present study provides additional insight into the ecology, diversity and occurrence of freshwater monothalamids and emphasizes the fact that a combination of morphological and molecular methods is necessary to clearly distinguish species in this group.

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Based on molecular and morphological characters, we describe a new species of monothalamous foraminifera, Psammophaga secriensia sp. nov., that was sampled from two coastal locations (48 m and 53 m depth) on the Romanian Black Sea continental shelf. Molecular data further confirm its presence in the northeastern part of the Black Sea (Balaklava Bay, 5–10 m depth). Specimens of Psammophaga secriensia sp. nov. are characterized by an elongate to broadly pyriform test and a simple rounded aperture. The wall is translucent and the cytoplasm contains mineral grains of different sizes. The genus Psammophaga, including Psammophaga simplora and several undetermined morphotypes, has been reported from different areas of the Black Sea. Previous research using an integrative taxonomic approach has identified two additional species (Psammophaga zirconia; Psammophaga sp., Gooday et al., 2011) occurring in the Black Sea. Monothalamids are an important part of the meiobenthos in the Black Sea and our results increase the knowledge of foraminiferal diversity in this marginal sea.

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The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the only valid species regularly recorded. To date, 16 species that are morphologically and/or genetically distinct have been described. While recent studies are documenting their diversity and their ecological importance, G. oviformis has been the sole gromiid species identified in the Black Sea, although unnamed Gromia species have also been recorded. We collected sediment samples from the Romanian continental shelf at varying depths (48 - 58 m) to study the morphological and genetic diversity of gromiids in this part of the Black Sea. Three new species, Gromia bugnae sp. nov., Gromia dianae sp. nov. and Gromia fabi sp. nov., were identified based on an integrative taxonomic approach, thus bringing the total described gromiid species to 19. Analysis of partial SSU rRNA gene sequences confirms that these are distinct species. Additionally, an undescribed species is represented by a sequence from the northern part of the Black Sea (Sevastopol, Kazachya Bay). The study provides further evidence of the diversity of gromiids in the Black Sea and underlines the importance of this little-known group in marginal seas.

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Most previous accounts summarising the biogeography and species durations of smaller calcareous benthic foraminifera have been based on literature reviews or on a massive North American database that had been taxonomically standardised. In this review we limit consideration to extant and fossil families or genera (from nearshore, open shelf, and deep-sea environments) with modern reviews that have standardised their global morphotaxonomy and where available, are complimented by molecular studies. We confirm previous studies that indicate most shelf species have limited geographic ranges and the majority of deep-water species are widespread and cosmopolitan or nearly so. In our intertidal and inner shelf groups only one species (molecular and morphological), Ammonia veneta, has a cosmopolitan distribution, although four warm-water morphospecies, of Ammonia and Rugobolivinella, have or had distributions that spanned more than one ocean in equatorial latitudes. The majority of both warm- and cool-water species in these groups are regionally or locally-restricted endemics (92% of Bolivinellidae, 100% of Tubulogenerina, 73% of Ammoniidae). The biogeographic distribution of the two rarer, warm-water groups (Bolivinellidae, Tubulogenerina) changed dramatically through the Cenozoic with the Paleocene–Eocene North American–European distribution of Bolivinellidae switching to purely Indo-Pacific by the Pliocene–Quaternary. In our shelf–upper bathyal groups (Notorotaliiidae, Plectofrondiculariidae), two genera have been restricted to the Southern Hemisphere since their Eocene originations with their greatest diversity throughout in New Zealand and Australia, respectively. The dominantly cold-water notorotaliid genus Buccella has a biogeographic distribution largely restricted to the Arctic Ocean and both coasts of North and South America. Most notorotaliid species are locally or regionally endemic (100% of Notorotalia, Parrellina, Porosorotalia, 75% of Buccella). At least 50–60% of species in five extinct mid-bathyal–abyssal families are cosmopolitan and have been throughout the Cenozoic since their originations. The majority of these deep-sea species with more-restricted distributions are rare, and many could possibly be more widespread with further extensive study. This review found that the shortest mean species durations (4–5 myrs) occur in two groups of rather rare, tropical–subtropical inner-shelf foraminifera with many locally endemic species. In cooler and progressively deeper water environments the mean species durations increase to 7–11 myrs for temperate shelf–bathyal taxa (Notorotaliidae), 20 myrs for an extinct mid-shelf to bathyal family (Plectofrondiculariidae) and 41–50 myrs for five extinct mid-bathyal–abyssal families (Chrysalogoniidae, Ellipsoidinidae, Glandulonodosariidae, Pleurostomellidae, Stilostomellidae). One species in each of four of these deep-water families had a species duration of 150–120 myrs.

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DNA sequencing shows that species of the genera Notorotalia, Porosorotalia and Buccella form a distinct branch (Notorotaliidae) of Rotaloidea, and cluster as sister to Elphidiidae. In this review we report on the sequencing of three species of Buccella (from the Arctic Ocean, Patagonia and Chile) and one each of Notorotalia (New Zealand) and Porosorotalia (Chile). This information has been combined with all the morphological descriptive information on species of these genera plus the genera Cristatavultus and Parrellina to provide a global synthesis of living species of the Notorotaliidae. We recognize 11 species of the southern hemisphere genus Notorotalia, which has a centre of diversity around New Zealand (8 species). A second southern-hemisphere-restricted genus, restricted to eastern Australia is Parrellina (3 species) although specimens (possibly introduced) have been recorded from the Mediterranean Sea. Cristatavultus has a single species, with a tropical west Pacific distribution.We synonymize Cribrorotalia under Porosorotalia, which has a disjunct distribution with one species in the northwest Pacific and a second around the southern parts of South America. Buccella is the most diverse and widespread genus (16 species recognized) with its greatest abundance in the Arctic Ocean and around subantarctic-temperate South America. Five species of Buccella live in a belt along the west coast of central America, from USA to Peru, with some spillage into the Caribbean Sea and Gulf of Mexico. Two new species of Buccella are recognized: B. dejardini (from South Georgia) and Buccella n. sp. A (from Chile).

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The invasive benthic foraminifera Trochammina hadai has been found for the first time in Europe along the coast of Normandy. Its native range of distribution is in Asia (Japan and Korea), and it has also been introduced along the coasts of western North America, Brazil and Australia. Morphological and molecular assessments confirm that specimens found in Le Havre and Caen-Ouistreham harbors belong to the Asiatic type. Like in Asia, T. hadai was found in transitional waters with muddy sediments. It exhibited high relative abundances (up to about 40%) confirming that T. hadai is a highly competitive species. In the present study, it was nearly absent from natural transitional waters and very abundant in heavily modified habitats like harbors, suggesting that ballast waters may likely be the vector of introduction. It was not recorded farther north along the coast of the Hauts-de-France. It is further hypothesized that the finding of a few specimens outside the harbor may facilitate the expansion of T. hadai in the English Channel by means of propagules dispersion.

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Single-chambered (monothalamous) foraminifera are poorly known compared to their multichambered relatives. In this first study of monothalamids from Greenland, we describe one new genus and two new species belonging to different clades from the Nuuk fjord system. Nujappikia idaliae Gooday & Holzmann gen. nov. sp. nov. (Clade Y) has a bottle-shaped test terminating in a single aperture located on a short neck. The flexible wall is basically organic but with a very fine agglutinated veneer. Bathyallogromia kalaallita Gooday & Holzmann sp. nov. (Clade C) has a broadly ovate test with an organic wall and a mound-like apertural structure. It is larger and genetically distinct from the two other Bathyallogromia species, both from the Southern Ocean. A survey of the morphological diversity of monothalamids in our samples revealed 49 morphospecies, of which 19, including the two new species, yielded DNA sequences. Five were assigned to the genera Bathysiphon, (Clade BM), Micrometula. (Clade BM), Psammophaga. (Clade E), Hippocrepinella (Clade D) and Crithionina (Clade J). The remaining twelve represented unknown taxa branching in clades A, C, F, and Y and one new clade. Our results add to growing evidence that monothalamids are common and diverse in fjords and other high-latitude settings.

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The genus Operculina, a large symbiont-bearing benthic foraminifer, is characterized by high morphological variability showing thick involute to intermediate semi-involute to flat evolute tests. Different morphotypes are either considered as ecophenotypes or distinct species. In order to test the hypothesis of ecophenotypes versus different species, a single cell high throughput sequencing approach was applied to assess the interspecific diversity of Operculina. This results in two groups of ribotypes, one corresponding to Operculina ammonoides/Operculina discoidalis, the other containing Operculina complanata/Operculina elegans. These groups can also be separated morphologically. Therefore, O. complanata and O. elegans represent a single species and the latter can be regarded as a junior synonym of O. complanata. Operculina ammonoides and O. discoidalis also form a single species, which makes the latter a junior synonym of O. ammonoides. Because generic differences in Operculina species are manifested in morphology and molecular genetics, the genus Neoassilina with the designated species Neoassilina ammonoides is installed. Additional analysis of ribosomal SSU rDNA data of eight recent nummulitid genera confirms the obtained high troughput sequencing results and further shows that Palaeonummulites venosus builds a clade with O. complanata that branches at the base of other Nummulitidae containing Planostegina, Planoperculina, Cycloclypeus, Heterostegina, Operculinella and Neoassilina.

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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 µm 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.

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Foraminifera, classified in the supergroup Rhizaria, are a common and highly diverse group of mainly marine protists. Despite their evolutionary and ecological importance, only limited genomic data (one partial genome and nine transcriptomic datasets) have been published for this group. Foraminiferal molecular phylogeny is largely based on 18S rRNA gene sequence analysis. However, due to highly variable evolutionary rates of substitution in ribosomal genes plus the existence of intragenomic variation at this locus, the relationships between and within foraminiferal classes remain uncertain. We analyze transcriptomic data from 28 species, adding 19 new species to the previously published dataset, including members of the strongly under-represented class Monothalamea. A phylogenomic reconstruction of Rhizaria, rooted with alveolates and stramenopiles, based on 199 genes and 68 species supports the monophyly of Foraminifera and their sister relationship to Polycystinea. The phylogenomic tree of Foraminifera is very similar to the 18S rRNA tree, with the paraphyletic single-chambered monothalamids giving rise to the multi-chambered Tubothalamea and Globothalamea. Within the Monothalamea, our analyses confirm the monophyly of the giant, deep-sea xenophyophores that branch within clade C and indicate the basal position of monothalamous clades D and E. The multi-chambered Globothalamea are monophyletic and comprise the paraphyletic Textulariida and monophyletic Rotaliida. Our phylogenomic analyses support major evolutionary trends of Foraminifera revealed by ribosomal phylogenies and reinforce their current higher-level classification.

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The foraminiferal order Carterinida is characterized by agglutinated tests consisting of calcareous spicules. Four species have so far been described from the tropical Pacific and the Caribbean Sea. We report here the first occurrence of Carterina from the Southeastern Levantine Shelf of the Mediterranean Sea. Based on molecular and morphological results, we describe Carterina labinea sp. nov., which is characterized by a trochospiral test with a conical, tapered spiral side and a concave umbilical side. The test is composed of elongate fusiform calcareous spicules. Tests have a mean diameter of 720 μm, which is twice the vertical height, and spicules vary in length and width from 112/15 μm to 73/14 μm. Our results show that the genus Carterina extends its distribution beyond tropical Seas and might be more widely distributed than previously thought. Moreover, the appearance of the new species in the study area suggests it is a new colonizer as continuous biomonitoring studies in the area show that it is absent in sediment samples taken before 2020. Our results highlight the importance of ongoing monitoring programs in high-risk basins such as the Levantine to gain more information about the biodiversity changes and improve environmental conservation of Eastern Mediterranean littoral areas progressively colonized by tropical species.

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The foraminiferal order Carterinida is characterized by agglutinated tests consisting of calcareous spicules. Four species have so far been described from the tropical Pacific and the Caribbean Sea. We report here the first occurrence of Carterina from the Southeastern Levantine Shelf of the Mediterranean Sea. Based on molecular and morphological results, we describe Carterina labinea sp. nov., which is characterized by a trochospiral test with a conical, tapered spiral side and a concave umbilical side. The test is composed of elongate fusiform calcareous spicules. Tests have a mean diameter of 720 μm, which is twice the vertical height, and spicules vary in length and width from 112/15 μm to 73/14 μm. Our results show that the genus Carterina extends its distribution beyond tropical Seas and might be more widely distributed than previously thought. Moreover, the appearance of the new species in the study area suggests it is a new colonizer as continuous biomonitoring studies in the area show that it is absent in sediment samples taken before 2020. Our results highlight the importance of ongoing monitoring programs in high-risk basins such as the Levantine to gain more information about the biodiversity changes and improve environmental conservation of Eastern Mediterranean littoral areas progressively colonized by tropical species.

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Based on molecular and morphological data, we describe three new genera and four new species of monothalamids from the sublittoral zone (21–250 m) in South Georgia fjords that belong to different monothalamid clades. Limaxia alba gen. nov. sp. nov. (Clade A) has an elongate, subcylindrical test, 359–688 µm long, with some detritus attached to the organic wall. Hilla argentea gen. nov. sp. nov. (Clade Y) has a cylindrical, finely agglutinated test, 535–755 µm long. Pseudoconqueria lenticularis gen. nov. sp. nov. branches separately. It has a spindle-shaped, finely agglutinated test, 280–574 µm long. Bathyallogromia olivacea sp. nov. (Clade C) has an ovate organic-walled test, 369–433 µm long. We present the first genetic data on two monothalamid species originally described from South Georgia, Hippocrepinella alba (Clade C) and Hippocrepinella hirudinea (Clade D), as well as a single sequence for C. delacai (Clade J) originally described from McMurdo Sound, Antarctica. In addition, we report nine undescribed species branching in six different monothalamid clades (A, B, BM, C, J, Y), eight of them sampled around South Georgia and one collected from the Falkland Islands near Stanley.

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Testate protists in the genus Gromia (‘gromiids’, supergroup Rhizaria) are common and diverse in marine settings. However, their ecological significance is not well understood, partly because they remain largely undescribed with most records being of the type species, G. oviformis. To enhance our knowledge of gromiid biodiversity, we use morphological and genetic data to describe four new species with tests of different shapes from sublittoral depths (21–136 m) in South Georgia fjords: G. pashukae (ovate), G. landrethi (spherical), G. amygdaliformis (almond-shaped), and G. saoirsei (elongate), maximum lengths 3.4, 2.5, 1.4 and 4.5 mm, respectively. We also describe two smaller ( ~1 mm) gromiid species from intertidal sites on the Falkland Islands: G. cedhageni (ovate test with finely granular, orange-coloured contents), and Gromia psammophila (subrectangular test with numerous small mineral grains embedded in pale, finely granular material). Gromia landrethi is also represented by DNA sequences from specimens collected in Ushuaia (Argentina) and G. psammophila by sequenced specimens from southern Chilean fjords, but the other species are known only from localities in South Georgia or the Falkland Islands. Analysis of partial SSU rRNA genes confirms the presence of these six new species, as well as an undescribed species represented by a clade of three sequences branching separately. Our results increase the number of described gromiid species from 10 to 16, and underline the importance of these poorly known relatives of the foraminifera in higher-latitude intertidal and fjord settings.

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An invasive foraminiferan is recorded for the first time in an Australian estuary. Trochammina hadai, originally described as endemic from Japan and subsequently found to be alien in coastal waters of California and Brazil, has been identified in estuarine sediment in the vicinity of Bunbury Port in Western Australia. Species determination is based on morphological, molecular and ecological similarities to the Japanese type. The species has not been recorded in other estuaries in Australia. Bunbury Port is a major exporter of woodchip to Japan and the introduction of T. hadai may have come from ballast water out of shallow-draught woodchip vessels. Small sediment samples of estuarine mud obtained at water depths of ~5 m contain abundant T. hadai (on average ~0.4 mm in adult diameter) that are easily recognised in microscopic view of the sediment surface by their bright reddish-brown colour. The collection of sediment samples from the estuarine floor and ballast water, and the examination of these for foraminifers, may provide a useful indicator in estuaries for the possible presence of other exotic species, particularly in the vicinity of ports.

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The Antarctic coastal fauna is characterized by high endemism related to the progressive cooling of Antarctic waters and their isolation by the Antarctic Circumpolar Current. The origin of the Antarctic coastal fauna could involve either colonization from adjoining deep-sea areas or migration through the Drake Passage from sub-Antarctic areas. Here, we tested these hypotheses by comparing the morphology and genetics of benthic foraminifera collected from Antarctica, sub-Antarctic coastal settings in South Georgia, the Falkland Islands and Patagonian fjords. We analyzed four genera (Cassidulina, Globocassidulina, Cassidulinoides, Ehrenbergina) of the family Cassidulinidae that are represented by at least nine species in our samples. Focusing on the genera Globocassidulina and Cassidulinoides, our results showed that the first split between sub-Antarctic and Antarctic lineages took place during the mid-Miocene climate reorganization, probably about 20 to 17 million years ago (Ma). It was followed by a divergence between Antarctic species ~ 10 Ma, probably related to the cooling of deep water and vertical structuring of the water-column, as well as broadening and deepening of the continental shelf. The gene flow across the Drake Passage, as well as between South America and South Georgia, seems to have occurred from the Late Miocene to the Early Pliocene. It appears that climate warming during 7-5 Ma and the migration of the Polar Front breached biogeographic barriers and facilitated inter-species hybridization. The latest radiation coincided with glacial intensification (~ 2 Ma), which accelerated geographic fragmentation of populations, demographic changes, and genetic diversification in Antarctic species. Our results show that the evolution of Antarctic and sub-Antarctic coastal benthic foraminifera was linked to the tectonic and climatic history of the area, but their evolutionary response was not uniform and reflected species-specific ecological adaptations that influenced the dispersal patterns and biogeography of each species in different ways.

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Foraminifera are a primarily marine taxon widespread in all oceanic habitats, from shallow, brackish-water settings to deep-seafloor and pelagic realms. Their diversity is remarkable with several thousand species described and a fossil record tracing back to the Cambrian. While foraminifera represent one of the best-studied groups of marine meiofauna, much less is known about their non-marine relatives. The first freshwater foraminifera were described in the 19th century by European and North American protozoologists, but interest in them lapsed during much of the 20th century and was not rekindled until the advent of molecular systematics provided a fresh impetus to their study. Several new species, genera, and families have been described recently based on morphological and molecular data derived from cultured specimens. In parallel, environmental genomic studies revealed that foraminifera are highly diverse and ubiquitous in freshwater and soil environments. Molecular phylogenetic analyses places non-marine foraminifera in a few clades among the large array of single-chambered (monothalamous) lineages, suggesting that several independent colonization events of freshwater and terrestrial habitats occurred. Non-marine foraminifera are turning from obscure curiosities to being recognized as an important part of soil and freshwater microbial communities, a major component of these complex environments.

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Benthic foraminiferal research in the North Pacific has a long history, with works published over a century ago providing important information about the taxonomy and distribution of morphospecies. These studies focused mainly on areas outside the Clarion-Clipperton Zone (CCZ). Our knowledge of foraminiferal faunas within the CCZ originates largely from recent baseline investigations related to likely future seabed mining of the polymetallic nodule deposits. These have revealed highly diverse assemblages of sediment-dwelling morphospecies among the meiofauna and macrofauna, as well as megafaunal xenophyophores and nodule-attached fauna. Morphological analyses have been complemented by metabarcoding studies that yielded even higher numbers of molecular species (Operational Taxonomic Units - OTUs). Monothalamids, the vast majority undescribed, constitute a substantial proportion of both morphological and molecular datasets, with multichambered agglutinated and calcareous foraminifera being less common. Their importance in this abyssal (>4,000 m depth) habitat likely reflects food limitation combined with carbonate dissolution close to and below the carbonate compensation depth. Literature records, supported in a few cases by genetic data, suggest that many morphospecies found in the CCZ have wide geographical distributions across the Pacific abyss and in other oceans. At smaller spatial scales (several 100s of kilometers) there is a general uniformity in assemblage composition. Nevertheless, many morphospecies are too rare to conclude anything about their geographical distributions. Similarly, the part played by benthic foraminifera in CCZ ecosystems is largely a matter of speculation, although their abundance across different size classes suggests that it is significant. Meiofauna-sized taxa that consume freshly-deposited organic detritus may be important in carbon cycling, particularly at the shallower, more eutrophic eastern end of the CCZ. Megafaunal xenophyophores can provide habitat structure for other organisms, potentially enhancing benthic biodiversity. Foraminifera of all sizes could be among the earliest recolonisers of disturbed or redeposited sediments. Their potential contributions in terms of both ecology and biodiversity make these protists significant members of benthic communities in the CCZ.

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Globally, one of the two most common shallow-marine and estuarine foraminiferal genera is Ammonia. Over the past 50 years, the majority of workers have identified specimens in this genus as belonging to just 1-3 cosmopolitan species - A. beccarii, A. tepida and A. parkinsoniana. This has been partly because of the problems of discriminating the Ammonia species based entirely on shell morphology and partly because of a 1974 laboratory study that claimed to have shown that all morphologies were merely ecophenotypic variants of one species - a conclusion that molecular studies have proven to be unequivocally wrong. In this study we recognize, describe and figure sixty-seven living species and infraspecies of Recent Ammonia and two closely-related genera (Acarotrochus, Pseudoeponides) from around the world and summarize their ecological and biogeographic distribution. Twenty-six species and two subspecies are recognized by DNA sequencing and shown to be morphologically distinguishable. A further 39 morphospecies and one subspecies, that have not yet been sequenced, have sufficiently distinct morphology to be recognized. Canonical variates analysis using 42 measured or assessed morphological characters shows that the majority of these species can be readily discriminated by their test morphologies, although a few of the less-ornamented molecular species are verging on being pseudocryptic. Molecular sequencing of the type species of Challengerella (C. bradyi) and Helenina (H. anderseni) places them within our Ammonia clade. Here we continue to recognize the morphologically highly distinct genera Pseudoeponides (subjective senior synonym of Helenina) and allied Acarotrochus. Twenty new species or subspecies are described (molecular T types in brackets): Ammonia abramovichae (T8), A. akitaae, A. aoteana australiensis (T5A), A. arabica (T26), A. ariakensis quiltyi, A. buzasi (T11), A. fajemilai, A. goldsteinae, A. goodayi, A. haigi (T25), A. hattai, A. jorisseni (T23), A. justinparkeri, A. kitazatoi (T10), A. morleyae (T12), A. shchedrinae, A. turgida almogilabinae (T22M), Acarotrochus lippsi, Pseudoeponides hottingeri and P. dubuissoni. Aneotype is designated for A. veneta (Schultze 1854) (T1). We recognize 67 Ammonia and related taxa in this study but speculate that there may be 30 or more additional living species that we are not yet confident to discriminate without molecular sequencing. Ammonia species live in most parts of the world between 62 degrees N (Faeroe Islands) and 55 degrees S (Strait of Magellan), where seasonal sea-surface temperatures are 4-10 degrees C and above. One estuarine species (A. veneta, T1) is cosmopolitan, euryhaline and eurythermic. Several species are widespread in one or two ocean regions (e.g., Atlantic and Mediterranean; South Pacific), whereas the majority are endemic to smaller areas (e.g., eastern Mediterranean; Caribbean-Gulf of Mexico). Eleven biogeographic "provinces" are recognized by cluster analysis of presence/absence records with the highest diversities in the Australian and northwest Pacific provinces with 18 and 19 species each). Levels of endemism in our "provinces" range between 0 (temperate Atlantic) and 44% (Australian).

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Species of large, testate, rhizarian protists in the genus Gromia are often common in high-latitude coastal environments, including fjords, but are frequently overlooked and almost all are undescribed. Here, we describe three new gromiid species from the Nuuk fjord system on the west coast of southern Greenland. Morphologically, the new species differ in the size and shape of the test. Gromia cucumiformis sp. nov. is elongate, up to 5.5 mm long, with a length:width (L/W) ratio of 4.3–5.5; Gromia botelliformis sp. nov. is up to 2.1 mm long, with a L/W ratio of 3.0–4.8; Gromia brevis is typically less than 1.0 mm long, with a L/W ratio around 2.0. Genetically, they are well-characterised and split between two clades. Gromia cucumiformis and G. brevis branch with several species of deep-water gromiids from the Arabian Sea and the Weddell Sea, while G. botelliformis branches with deep Weddell Sea species and several unnamed and morphologically uncharacterised gromiids from different parts of the world. Gromia botelliformis and G. brevis are currently known only from the Nuuk fjords, but sequences of G. cucumiformis from Greenland group together with sequences from Svalbard and the White Sea. Our genetic data reveal four additional clades of undescribed Gromia species. One contains sequences from Greenland, Svalbard and the White Sea, two comprises sequence from Greenland and the White Sea and one is limited to sequences from Greenland. These results demonstrate the high genetic diversity of gromiids and their widespread distribution in Arctic as well as in deep-sea environments.

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DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

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Foraminifera are single-cell eukaryotes common in all marine environments and generally characterized by shells, more specifically termed “tests”, which can either be organic, agglutinated, calcareous, and rarely siliceous. The diversity of foraminifera is commonly assessed microscopically based on morphological features of their tests. However, recent genetic and metagenetic studies show that this morphology-based diversity is largely underestimated. Many cryptic species and numerous lineages uncharacterized morphologically have been revealed, especially among the class of monothalamous (single-chambered) foraminifera. Here, we use an environmental DNA metabarcoding approach to explore the foraminiferal community in the Ubatuba region, northern São Paulo State coast, South-eastern Brazil, where no genetic foraminiferal studies have ever been conducted before. Our analyses revealed 42 phylotypes, among which 9 were identified as globothalamids and 31 have been assigned to monothalamids. All reported phylotypes are new to science and none of them could be assigned to species or genotypes present in foraminiferal barcoding database. These results demonstrate a huge gap that exist in our knowledge of the Southwest Atlantic shallow-waters foraminiferal genetic diversity. Filling this gap would be necessary for more accurate assessment of foraminiferal diversity in general and more specifically if DNA-based methods are to be used to identify potential foraminiferal indicators for ecological and biomonitoring studies in the future.

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The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it can be considered as potentially invasive. This species was recently discovered in Lake Geneva (Switzerland/France) and three other Swiss lakes. The aims of the present work are to report its repartition and abundance in Lake Geneva, to study its ecology and to determine its invasive potential in this lake. We also provide an identification key for correctly differentiating Q. multisetosus from the closely related species Spirosperma ferox Eisen, 1879 and Embolocephalus velutinus (Grube, 1879), and study the phylogenetic position of Q. multisetosus within several Tubificinae lineages based on the cytochrome c oxidase (COI) marker. Twenty-eight sites have been monitored since 2009 in Lake Geneva. In several sites, the COI sequence corresponding to this species was also searched for in sediment samples using high-throughput sequencing. In addition, we examined specimens collected in this lake before 2009 likely to belong to Q. multisetosus and to have been misidentified. We found that Q. multisetosus was only present in the lake downstream of a wastewater treatment plant and a combined sewer overflow in the Vidy Bay (near Lausanne) and at a site located nearby. These results confirmed the high tolerance of this species to organic matter pollution. Q. multisetosus was already present in this location in 1974 (misidentified as Spirosperma ferox), which suggests that Q. multisetosus has a limited capacity to disseminate in this lake. However, we recommend continuing monitoring its presence in Lake Geneva in the future, especially in the context of warming of waters that could contribute to the expansion of this species.

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Non-marine foraminifera are among the least known groups of protists and only a handful of species have been described since the 19th century. We collected one naked and five morphologically almost identical organic-walled monothalamid species from freshwater and terrestrial environments from Germany and Austria. One of the species was identified as Lieberkuehnia wageneriClaparède and Lachmann, 1859. As its original description is ambiguous and its type specimen has been lost, a neotype is proposed. We describe four new organic-walled monothalamous foraminifera and a novel Reticulomyxa species both morphologically and genetically. Analyses of molecular data of the different isolates revealed that they are distributed across six different clades. Two new genera, Claparedellus gen. nov. and Velamentofex gen. nov., and five new monothalamous families, Lacogromiidae fam. nov., Limnogromiidae fam. nov., Lieberkuehniidae fam. nov., Edaphoallogromiidae fam. nov. and Velamentofexidae fam. nov., are established.

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The Clarion-Clipperton Zone (CCZ) occupies a vast swathe of the Pacific with extensive polymetallic nodule deposits. Eastern and central parts host diverse assemblages of xenophyophores (megafaunal agglutinated foraminifera). Here we describe xenophyophores obtained using a Remotely Operated Vehicle from the western CCZ. Eleven distinct forms include two known species, Stannophyllum zonarium Haeckel, 1888 and Aschemonella monile Gooday and Holzmann in Gooday et al., 2017b. Another four are described as new species based on morphological and genetic data. In Abyssalia foliformis gen. nov., sp. nov. and Abyssalia sphaerica sp. nov. the flattened or spherical test comprises a homogeneous framework of sponge spicules. Psammina tenuis sp. nov. has a delicate, thin, plate-like test. Moanammina semicircularis gen. nov., sp. nov. has a stalked, fan-shaped test and is genetically identical to 'Galatheammina sp. 6' of Gooday and co-workers from the eastern CCZ. Sequence data revealed a spherical 'mudball', which disintegrated and cannot be formally described, to be a novel xenophyophore. Finally, four morphospecies are represented by dead tests: Psammina spp., Reticulammina sp., and an unknown genus with a unique test structure. This collection enhances our knowledge of Pacific xenophyophore diversity and provides the first genetic confirmation of wide geographic ranges for abyssal species.

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Benthic foraminifera are an abundant and important component of modern and ancient deep-sea ecosystems, and these single-celled organisms generate a fossil record that facilitates the assessment of paleoceanographic changes through time. Despite recent advances in taxonomic and ecological information about deep-sea foraminifera, many basic questions remain, requiring a better understanding of ecological tolerances, morphologic plasticity, and distribution of deep-sea foraminiferal species. This study focuses on the phylogenetics, morphology, and colonization dynamics of deep-sea foraminifera at abyssal Station M in the eastern Pacific Ocean. After 368 days at 4000 m on the Pacific Ocean seafloor, 546 foraminifera ~80% of which were calcareous species, occupied elevated substrate experiments. Genetic analyses of the most abundant calcareous foraminiferal taxon indicate that this trochospiral species is a morphological variant of Cibicidoides wuellerstorfi (referred to as C. wuellerstorfi var. lobatulus). Although Pyrgo and other milioline foraminifera are commonly found within sediments, two morphological variants of Pyrgo colonized elevated substrates at the Station M study site. Many Pyrgo spp. and C. wuellerstorfi var. lobatulus, were covered in an organic cyst, perhaps as a feeding structure. These results suggest that these calcareous foraminifera are able to flourish in deep-sea settings where hard substrates are available, and may be more widely distributed and diverse in lower bathyal and upper abyssal habitats when elevated substrates are present.

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A quest to collect live specimens of the well-known foraminifer Ammonia beccarii for sequencing has led to the recognition of five molecular species in Europe all related to it, but no live A. beccarii itself. The five molecular species all clump together in one clade (T3) of the Ammonia phylogenetic tree. All are characterized by large size, ornament on the umbilical side and a deep spiral, sutural fissure on the spiral side (beccarii morphogroup). All five molecular species can be discriminated based on distinct morphological differences as Ammonia batava (North Sea, northeast Atlantic, west Mediterranean Sea), A. corallinarum (northeast Atlantic, west Mediterranean Sea), A. pawlowskii n. sp. (Mediterranean Sea, west Indian Ocean), A. falsobeccarii (North Sea, east Atlantic seaboard, Mediterranean Sea, Persian Gulf), and A. neobeccarii (Mediterranean and Black seas). Using morphological characters, a further four species are recognized in the beccarii morphogroup for which no sequences are presently available: A. beccarii (Mediterranean Sea, northeast Atlantic), A. batava compacta (west Atlantic seaboard), A. debenayi n. sp. (west Indian Ocean), A. venecpeyreae n. sp. (west Mediterranean Sea, Gulf of Aden). One species, A. japonica (China, Japan, South Korea), for which sequences have been obtained, is included in the beccarii morphogroup based on morphological characteristics but differs genetically from the beccarii group. Another species, similar to A. falsobeccarii with secondary sutural openings on the spiral side but probably not part of the beccarii morphogroup because it lacks the spiral sutural canal typical of the group, is described as new – A. langeri (Indian Ocean, East Indies, south Australia). A growth series of A. beccarii topotypes from Rimini, north Adriatic Sea, is illustrated to aid in its recognition and a neotype designated and illustrated. Extinct fossil members of the beccarii morphogroup include A. ikebei, A. inflata, A. italica, A. nakazatoensis, A. punctatogranosa, A. reyi, A. togopiliensis, A. viennensis, and A. voorthuyseni.

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Xenophyophores are important megafaunal organisms in the abyssal Clarion-Clipperton Zone (CCZ; equatorial Pacific), a region hosting commercially significant deposits of polymetallic nodules. Previous studies assigned those with attached, fan-like tests to Psammina limbata, a species described from the central CCZ based on morphology. Here, we redescribe the holotype of P. limbata and then show that limbata-like morphotypes collected in the eastern CCZ include three genetically distinct species. Psammina aff. limbata is closest morphologically to P. limbata. The others are described as P. microgranulata sp. nov. and P. rotunda sp. nov. These fan-shaped species form a well-supported clade with P. tortilis sp. nov., a morphologically variable species exhibiting features typical of both Psammina and Semipsammina. A second clade containing Psammina sp. 3, and two species questionably assigned to Galatheammina branches at the base of this group. The genus Psammina includes another 9 described species for which there are no genetic data, leaving open the question of whether Psammina as a whole is monophyletic. Our study increases the number of xenophyophore species described from the eastern CCZ from 8 to 11, with a further 25 morphotypes currently undescribed. Many additional species of these giant foraminifera undoubtedly await discovery in abyssal settings.

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Xenophyophores are important megafaunal organisms in the abyssal Clarion-Clipperton Zone (CCZ; equatorial Pacific), a region hosting commercially significant deposits of polymetallic nodules. Previous studies assigned those with attached, fan-like tests to Psammina limbata, a species described from the central CCZ based on morphology. Here, we redescribe the holotype of P. limbata and then show that limbata-like morphotypes collected in the eastern CCZ include three genetically distinct species. Psammina aff. limbata is closest morphologically to P. limbata. The others are described as P. microgranulata sp. nov. and P. rotunda sp. nov. These fan-shaped species form a well-supported clade with P. tortilis sp. nov., a morphologically variable species exhibiting features typical of both Psammina and Semipsammina. A second clade containing Psammina sp. 3, and two species questionably assigned to Galatheammina branches at the base of this group. The genus Psammina includes another 9 described species for which there are no genetic data, leaving open the question of whether Psammina as a whole is monophyletic. Our study increases the number of xenophyophore species described from the eastern CCZ from 8 to 11, with a further 25 morphotypes currently undescribed. Many additional species of these giant foraminifera undoubtedly await discovery in abyssal settings.

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Based on a combination of morphological and molecular data, we describe five new species and two new genera of xenophyophores from the Clarion–Clipperton Zone (abyssal eastern Pacific), an area with commercially valuable seafloor deposits of polymetallic nodules. Bizarria bryiformis gen. et sp. nov. displays unusual features, notably an organic-walled test, largely devoid of agglutinated particles, comprising interconnected branches growing upwards from the nodule substrate; the bases of the branches contain dark masses of waste material (stercomare) and pale strands of cytoplasm (granellare), the whitish, tuft-like extremities contain sediment particles. Tendalia reteformis gen. et sp. nov. forms a delicate network of agglutinated tubes. Shinkaiya contorta sp. nov. is characterized by a contorted, partly reticulated plate-like test while the simpler plate-like test of Galatheammina interstincta sp. nov. combines characters typical of Galatheammina and Psammina. In Semipsammina mattaeformis sp. nov., a thin, delicate test with one or more tubular extensions forms a flat canopy over the mat-like stercomare encrusting the nodule substrate. Tendalia reteformis and S. contorta are free-living; the other species are sessile on nodules. Together, they illustrate the considerable morphological diversity of xenophyophores in a region where they dominate the megafauna, and highlight some major taxonomic challenges posed by these giant monothalamous foraminifera.

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We describe Aschemonella monile Gooday and Holzmann sp. nov. from the Clarion–Clipperton Zone (CCZ, abyssal eastern equatorial Pacific), a region characterized by commercially significant concentrations of polymetallic nodules. The new species is the most abundant xenophyophore (giant agglutinated foraminifera) in our main sampling area (12–14°N; 116°30′–117°26′W). Additional specimens originate from the central CCZ, and from a third area, ~900 km NW of the main area, where A. monile numerically dominates the megabenthos in photographic surveys of the seafloor (average densities 1.54 individuals/m2; peak densities > 3 individuals/m2). Aschemonella monile is much larger (≥ 7 cm in length) than previously described species of the genus, with a test comprising an irregular sequence of self-contained, partly overlapping ‘segments’, creating a multichambered structure. A similar, much rarer species from the main study area, described here as Aschemonella aspera Gooday and Holzmann sp. nov., has an unsegmented test with a very rough, coarsely agglutinated wall. Genetic data suggest that A. monile is distinct from A. aspera and most closely related to a group comprising Rhizammina algaeformis and Aschemonella ramuliformis. Both new species have delicate tests that are often attached to nodule surfaces, making them particularly vulnerable to seafloor disturbances.

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Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation.

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Ammonia aomoriensis (Asano 1951) was isolated from 78 samples collected from the Yellow Sea and East China Sea during 2010 to 2014. The species exhibits dimorphism (microspheric and megalospheric forms) and different coiling directions (dextral and sinistral). A fragment of SSU rDNA was sequenced for four specimens of A. aomoriensis exhibiting different morphologies (dextral vs. sinistral, microspheric vs. megalospheric). Our results show that A. aomoriensis from our study sites branch within previously obtained sequences of the same species. In order to test whether morphological differences are environmentally controlled we investigated 667 specimens from Qingdao and Jiaozhou Bay among which 290 were right coiled (dextral) and 377 were left coiled (sinistral). Similarly, 525 were microspheric and 142 were megalospheric. A correlation coefficient was computed to evaluate the relationship between foraminiferal morphology (dimorphism and coiling direction) and environmental parameters (temperature and salinity). A significant positive correlation was detected between the ratio of microspheric/megalospheric forms and salinity (r=0.719, p<0.001). No correlation was detected between morphological variations and temperature. Our findings suggest that the ratio of microspheric/megalospheric forms in A. aomoriensis can be used to infer past salinity conditions (and thus fresh water influx) in study areas off China.

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The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e., genus). This article is protected by copyright. All rights reserved.

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Most foraminifera inhabit marine habitats, but some species of monothalamids have been described from freshwater environments, mainly from Swiss water bodies over 100 years ago. Recent environmental DNA surveys revealed the presence of four major phylogenetic clades of freshwater foraminifera. However, until now only one of them (clade 2) has been associated to a morphologically described taxon-the family Reticulomyxidae. Here, we present morphological and molecular data for the genera representing the three remaining clades. We describe two new agglutinated freshwater genera from China and the Netherlands, Lacogromia and Limnogromia, which represent clades 3 and 4, respectively. We also report the first ribosomal DNA sequences of the genus Lieberkuehnia, which place this genus within clade 1. Our study provides the first morphotaxonomic documentation of molecular clades of freshwater foraminifera, showing that the environmental DNA sequences correspond to the agglutinated monothalamous species, morphologically similar to those described 100 years ago.

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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 data set 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 the plankton and benthos, but only one lineage exhibits 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.

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Rotaliida is the most diversified order of modern benthic foraminifera, comprising 73 extant families. The current classification of Rotaliida is based exclusively on morphological characters of their calcareous tests. Previous molecular phylogenetic studies partly confirmed morphological classifications but they were based on relatively limited taxon sampling and SSU rRNA gene sequences only. Here, we investigate phylogenetic relationships of rotaliid foraminifera by sequencing complete or partial SSU and LSU rRNA genes for 80 phylotypes representing 70 genera. The analysis of 87 sequences of concatenated genes enabled us to recognize seven rotaliid superfamilies, four of them being established ones (Planorbulinoidea, Discorboidea, Rotalioidea, Nummulitoidea) and three new ones (Glabratelloidea, Calcarinoidea, Serioidea). Although some of these superfamilies were not strongly supported in phylogenetic trees, due to a weak signal of ribosomal genes, they comprise genera and families of distinctive morphological features that have been often united in previous morphology-based classifications. A total of 34 families has been recognized, 10 of them being newly established ones. The placement of three families (Rubratelliidae, Cymbaloporidae, Murrayinelliidae), which occupied isolated branches among the seven superfamilies, could not be determined and they are considered here as incertae sedis. An assemblage of 22 genera representing several morphologically different families of small rotaliids (Clade 3) was not raised to superfamily level because of the lack of molecular and/or morphological support. The phylogenetic relations within this assemblage as well as within the superfamily Rotalioidea have been examined in detail by analyzing partial SSU rDNA sequences for large taxon sampling.

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Xenophyophores, giant, fragile, agglutinated foraminifera (protists), are major constituents of the abyssal megafauna in the equatorial Pacific Clarion-Clipperton Zone (CCZ), a region where seabed mining of polymetallic nodules may occur in the future. As part of a baseline study of benthic communities we made extensive collections of xenophyophores in two areas (UK-1 and OMS) licensed for exploration by the International Seabed Authority. Based on test morphology, we distinguished 36 morphospecies (34 new to science) among 130 specimens. Twenty of these morphospecies yielded 184 DNA sequences, a 14-fold increase in genetic data for xenophyophores that confirms their high diversity in the eastern CCZ. A further 15 morphospecies (8 new to science) were recognised in samples from two other areas (APEI-6 and Russian exploration license area) within or adjacent to the CCZ. This large number of species confirms that the CCZ is a focal area for xenophyophore diversity. More broadly, it represents an unprecedented increase in the known global diversity of xenophyophores and suggests that many species remain undiscovered in the World's oceans. Xenophyophores are often sessile on nodules in the CCZ, making these delicate organisms particularly vulnerable to mining impacts. They can also play a crucial role in deep-sea ecosystems, providing habitat structures for meiofaunal and macrofaunal organisms and enhancing the organic content of sediments surrounding their tests. The loss of xenophyophores due to seabed mining may therefore have wider implications for the recovery of benthic communities following major human disturbances on the abyssal seafloor.

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Benthic foraminifera are single-celled eukaryotes that make a protective organic, agglutinated or calcareous test. Some agglutinated, single-chambered taxa, including Psammophaga Arnold, 1982, retain mineral particles in their cytoplasm, but the selective mechanism of accumulation is not clear. Here, we report the ability of a foraminiferal species to select and accumulate zircons and other heavy minerals in their cytoplasm. In particular, the use of Scanning Electron Microscope coupled with an Energy Dispersive X-ray microanalysis system (SEM–EDS) enabled a representative overview of the mineral diversity and showed that the analysed Psammophaga zirconia sp. nov. individuals contained dominantly crystals of zircon (51%), titanium oxides (27%), and ilmenite (11%) along with minor magnetite and other minerals. The studied specimens occur in the shallow central Adriatic Sea where the sediment has a content of zircon below 1% and of other heavy minerals below 4%. For that reason we hypothesize that: (i) P. zirconia may be able to chemically select minerals, specifically zircon and rutile; (ii) the chemical mechanism allowing the selection is based on electrostatic interaction, and it could work also for agglutinated foraminifera (whether for ingestion, like Xenophyophores, or incorporation in the test as in many other described taxa). In particular, this aptitude for high preferential uptake and differential ingestion or retention of zircon is reported here for the first time, together with the selection of other heavy minerals already described in members of the genus Psammophaga. They are generally counted among early foraminifera, constructing a morphologically simple test with a single chamber. Our molecular phylogenetic study confirms that P. zirconia is a new species, genetically distinctive from other Psammophaga, and occurs in the Adriatic as well as in the Black Sea.

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We extracted and amplified a fragment of small subunit ribosomal DNA (SSU rDNA) from three Entzia macrescens speci- mens collected in Turda, Romania. The three sequences build a monophyletic group together with a sequence of E. macrescens obtained from Dovey Estuary, Wales, and branch as sister to five sequences of Entzia sp. specimens from Ca- margue, France. The two groups of E. macrescens and Entzia sp. build a strongly supported monophyletic clade with Hap- lophragmoides spp. and Arenoparella mexicana at its base. Calculation of pairwise distances shows that observed interin- dividual and intraindividual distances in E. macrescens and Entzia sp. are similar and lower than interspecific distances which indicates that the population from Camargue might belong to a different, cryptic species. Migratory birds might be responsible for the transport of E. macrescens to the land locked salt marshes of Romania. The sequences of E. macrescens from Dovey Estuary and Turda are almost identical, which would confirm the former hypothe- sis as flyways extend from Great Britain to the Southeast via Eilat to Africa that cross Romania. There is no migratory fly- way that crosses the European continent from the West (France) to the Southeast, which possibly limits the aerial distribu- tion of Entzia sp. found in Camargue.

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Textularia agglutinans d'Orbigny is a non-symbiont bearing and comparatively large benthic foraminiferal species with a widespread distribution across all oceans. In recent years, its populations have considerably expanded along the Israeli Mediterranean coast of the eastern Levantine basin. Despite its exceptionally widespread occurrence, no molecular data have yet been obtained. This study provides the first ribosomal DNA sequences of T. agglutinans complemented with morphological and ecological characterization, which are based on material collected during environmental monitoring of the hard bottom habitats along the Israeli Mediterranean coast, and from the Gulf of Elat (northern Red Sea). Our phylogenetic analyses reveal that all specimens from both provinces belong to the same genetic population, regardless their morphological variability. These results indicate that modern population of T. agglutinans found on the Mediterranean coast of Israel is probably Lessepsian. Our study also reveals that T. agglutinans has an epiphytic life mode, which probably enabled its successful colonization of the hard bottom habitats, at the Mediterranean coast of Israel, which consist of a diverse community of macroalgae. Our study further indicates that the species does not tolerate high SST (> 35°C), which will probably prevent its future expansion in the easternmost Mediterranean in light of the expected rise in temperatures.

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Carterina spiculotesta is a common tropical benthic foraminifer characterized by fusiform or rod-like calcareous spicules covering the surface of the test. Because of this peculiar wall feature, the genus Carterina was separated from other foraminifera and placed in its own suborder (Caterinina) or order (Carterinida). However, there is no agreement about the origin of Carterina spicules, which are considered either as being secreted by the foraminiferal cell or as agglutinated foreign particles; if the latter case, the genus was placed in the order Trochamminida. Here, we attempted to resolve this controversy by analysis of genetic data from various carterinids collected in New Caledonia. We obtained seven complete and 47 partial small subunit (SSU) rDNA sequences. Our results show that all specimens of spicule-bearing Carterina cluster together in a strongly supported clade. Sister to this clade are undetermined lineages of trochamminid morphospecies. Together with its sister groups, the Carterina clade forms an independent lineage at the base of Globothalamea within the paraphyletic radiation of textulariids and robertinids. Its exact phylogenetic position was difficult to establish because the used SSU rRNA genes lack resolution. As long as experimental data do not contradict the hypothesis of a secreted origin for Carterina spicules, we propose to retain the ordinal status of the Carterina clade, and consider it as one of the orders of the class Globothalamea. In view of our study, the diversity of this order may be much higher than traditionally accepted, including several genera and species, many of them new to science.

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DNA barcoding is the molecular identification of species using short, standardized gene sequences. Numerous applications of DNA barcoding in taxonomy, ecology, bioconservation, and biosafety contributed to a spectacular development of this initiative administered by the Consortium for the Barcode of Life (CBOL). Reference databases that assign DNA barcodes to particular morphospecies have been developed for almost all groups of animals, plants, and fungi, as well as some groups of protists (i.e., diatoms, ciliates, amoebae). However, such a database does not exist for foraminifera, despite large numbers of DNA sequences being available. To fill this gap, we initiated the Foram Barcoding (FB) project, whose objective is to create a curated molecular database for modern foraminifera. Each species included in our database is represented by one or several specimens, from which DNA was extracted and sequenced. Species entries include photos of processed specimens, taxonomic references, and DNA barcode sequences. A fragment of the 18S rRNA gene, commonly used in foraminiferal molecular studies, was chosen as the DNA barcode. We believe that the FB project will help resolve at least some misidentification problems that plague foraminiferal taxonomy. We also foresee its further applications in such domains of foraminiferal research as diversity assessment, ecology, biogeography, and biomonitoring. However, we are aware that the impact of the FB database depends mainly on its completeness and accuracy, and thus we appeal to the community of foraminiferologists to support this project by providing material for genetic studies and by contributing their taxonomic expertise in species identification and documentation.

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The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF) that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea) and from a known hotspot in Shikmona (northern Israel) that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.

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The limitations of a traditional morphology-based classification of Foraminifera have been demonstrated by molecular phylogenetic studies for several years now. Despite the accumulation of molecular data, no alternative higher-level taxonomic system incorporating these data has been proposed yet. Here, we present a new supraordinal classification of Foraminifera based on an updated SSU rDNA phylogeny completed with the description of major morphological trends in the evolution of this group. According to the new system, multi-chambered orders are grouped in two new classes: Tubothalamea and Globothalamea. Naked and single-chambered Foraminifera possessing agglutinated or organic-walled tests are arranged into a paraphyletic assemblage of “monothalamids”. The new system maintains some multi-chambered calcareous orders, such as Rotaliida, Miliolida, Robertinida and Spirillinida, although their definitions have been modified in some cases to include agglutinated taxa. The representatives of the planktonic order Globigerinida are tentatively included in the order Rotaliida. The agglutinated Textulariida are probably paraphyletic. The position of the order Lagenida is uncertain because reliable molecular data are only available for one species. The new classification system separates orders or families, which differ in basic chamber shapes, prevailing mode of coiling and distance between successive apertures. It appears that these features correspond better to the main evolutionary trends in Foraminifera than wall composition and structure, both used in traditional classification.

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The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

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A new monothalamous (single-chambered) soft-walled foraminiferal species, Arnoldiellina fluorescens gen. et sp. nov., was isolated from samples collected in the Gulf of Eilat, Israel. The species is characterized by a small elongate organic theca with a single aperture of allogromiids. It is characterized by the emission of green autofluorescence (GAF) that has so far not been reported from foraminifera. Phylogenetic analysis of a fragment of the 18S rDNA indicates that the species is related to a group of monothalamous foraminiferans classified as clade I. Although the morphology of the new species is very different compared to the other members of this clade, a specific helix in 18S rRNA secondary structure strongly supports this position.

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The diversity and distribution of modern benthic foraminifera has been extensively studied in order to aid the paleoecological interpretation of their fossil record. Traditionally, foraminiferal species are identified based on morphological characters of their organic, agglutinated or calcareous tests. Recently, however, new molecular techniques based on analysis of DNA sequences have been introduced to study the genetic variation in foraminifera. Although the number of species for which DNA sequence data exist is still very limited, it appears that morphology-based studies largely underestimated foraminiferal diversity. Here, we present two examples of the use of DNA sequences to examine the diversity of benthic foraminifera. The first case deals with molecular and morphological variations in the well-known and common calcareous genus Ammonia. The second case presents molecular diversity in the poorly documented group of monothalamous (single-chambered) foraminifera. Both examples perfectly illustrate high cryptic diversity revealed in almost all molecular studies. Molecular results also confirm that the majority of foraminiferal species have a restricted geographic distribution and that globally distributed species are rare. This is in opposition to the theory that biogeography has no impact on the diversity of small-sized eukaryotes. At least in the case of foraminifera, size does not seem to have a main impact on dispersal capacities. However, the factors responsible for the dispersal of foraminiferal species and the extension of their geographic ranges remain largely unknown.

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The majority of extant families of larger Foraminifera are hosts for cndosymbiotic diatoms, among them also Nummulitidae, which are the largest calcareous foraminiferans. Nummulitidae occur in reef environments and extend their depth distribution down to the base of the photic zone. They reach their highest diversity and abundance in the western Pacific. Some information about the diversity of nummulitid diatom symbionts has been gained by investigating morphological and ultrastructural…

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Xenophyophorea are giant deep-sea rhizopodial protists of enigmatic origins. Although species were described as Foraminifera or sponges in the early literature, the xenophyophoreans are currently classified either as a class of Rhizopoda or an independent phylum. To establish the phylogenetic position of Xenophyophorea, we analysed the small subunit (SSU) rRNA gene sequence of Syringammina corbicula Richardson, a newly described xenophyophorean species from the Cape Verde Plateau. The SSUrDNA analyses showed that S. corbicula is closely related to Rhizammina algaeformis, a tubular deep-sea foraminiferan. Both species branch within a group of monothalamous (single-chambered) Foraminifera, which include also such agglutinated genera as Toxisarcon, Rhabdammina, and Saccammina, and the organic-walled genera Gloiogullmia and Cylindrogullmia. Our results are congruent with observations of similar cytoplasmic organisation in Rhizammina and Syringammina. Thus, the Xenophyophorea appear to be a highly specialised group of deep-sea Foraminifera.

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We describe Bathyallogromia weddellensis gen. & sp. nov., a deep-water, monothalamous foraminiferan from bathyal and abyssal sites in the western Weddell Sea. The species is characterised by a delicate, almost spherical, organic-walled test, a low, broad projecting apertural region, and light grey or greenish cytoplasm containing mineral grains and other inclusions. Molecular phylogenetic analyses, based on small subunit rRNA gene sequences, indicate that Bathyallogromia is an independent lineage branching within a clade of monothalamous foraminiferans, which also includes such genera as Saccammina, Gloiogullmia, Cylindrogullmia, Rhabdammina, Toxisarcon and Pilulina (?). Lack of significant genetic differences between specimens collected at depths ranging from 1000 to 6300m suggests that B. weddellensis is adapted to conditions that span a broad bathymetric range.

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In this study, morphometric analysis has been performed on 178 Ammonia specimens belonging to 12 different molecular types, plus non-sequenced type specimens of Ammonia beccarii and A. tepida. Molecular type distinction is based on phylogenetic analysis of 267 partial LSU rDNA sequences, obtained from 202 living Ammonia specimens, sampled in 30 localities from 17 countries bordering the Pacific Ocean, Atlantic Ocean, Mediterranean Sea, Caribbean Sea and North Sea. Restriction fragment length polymorphism (analysis was carried out for another seven specimens. Morphometric analysis was based on measurements or assessments of 37 external test characters in spiral, umbilical, profile and close-up Scanning Electron Microscopic views. Cluster analysis, canonical variates analysis, and detrended correspondence analysis, performed on the morphological data set, suggest that each molecular type can be distinguished morphologically and can be regarded as a separate species. Primary types of A. tepida and topotypes of A. beccarii are shown to be morphologically separate from any of the molecular types so far recognised. We are aware of at least 9 more distinctive morphotypes that have not yet been sequenced, and thus we infer that the total number of genetically distinct and morphologically separable living species of Ammonia worldwide is likely to exceed 25–30. At this stage not all molecular types can be unequivocally assigned to formally described species. Several genetically-based species can be distinguished by the presence of one distinct character, but most are discriminated on the basis of a combination of many different characters. Morphological characters (e.g. test shape, chamber shape, porosity, prolocular diameter, folium shape, radial furrow length, umbilical diameter) are shown to be slightly more valuable in separating the molecular types than surficial ornament (beads, pustules, bosses, secondary calcite). One highly distinctive group (2–3 species – beccarii, batava, ?inflata) is readily discriminated on the basis of its large test size, strongly beaded and grooved ornament, and the presence of fissures along the sutures on the spiral side. The results of this study imply that the widespread practice of recognising only one, two or three species of Recent Ammonia worldwide should be abandoned. The most commonly used name, Ammonia beccarii, should be restricted to a large, compressed, highly ornamented species, so far not recognised beyond its type locality in the Adriatic Sea. Other commonly used names, such as A. parkinsoniana and A. tepida, apply to species with far more restricted distributions than the literature would suggest.

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Xenophyophorea are giant deep-sea rhizopodial protists of enigmatic origins. Although species were described as Foraminifera or sponges in the early literature, the xenophyophoreans are currently classified either as a class of Rhizopoda or an independent phylum. To establish the phylogenetic position of Xenophyophorea, we analysed the small subunit (SSU) rRNA gene sequence of Syringammina corbicula Richardson, a newly described xenophyophorean species from the Cape Verde Plateau. The SSUrDNA analyses showed that S. corbicula is closely related to Rhizammina algaeformis, a tubular deep-sea foraminiferan. Both species branch within a group of monothalamous (single-chambered) Foraminifera, which include also such agglutinated genera as Toxisarcon, Rhabdammina, and Saccammina, and the organic-walled genera Gloiogullmia and Cylindrogullmia. Our results are congruent with observations of similar cytoplasmic organisation in Rhizammina and Syringammina. Thus, the Xenophyophorea appear to be a highly specialised group of deep-sea Foraminifera.

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In 1926, Cushman described Rotalia beccarii var. tepida from San Juan Harbor, Puerto Rico. His publication illustrates a strew slide with many individuals, and no holotype was designated. Consequently, over the years, researchers have assumed that no holotype exists. A search of the Cushman Collection, however, discovered a slide labeled as holotype and it is so recorded in the Cushman Catalog of 1929. Here, this specimen is re-described and designated as a lectotype. All nine of the other surviving syntypes from the original collection in San Juan Harbor, Puerto Rico, now become paralectotypes. Hopefully, the designation of formal types for Ammonia tepida (Cushman) will help stabilize the taxonomy of this important species. Our study shows that the lectotype is morphologically distinguishable from other Ammonia types and that the distribution of Ammonia tepida is restricted to tropical shallow-water environments.

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Nummulitidae are the largest extant calcareous Foraminifera, and are widely distributed in tropical and subtropical shallow-water seas. Classical morphology-based taxonomy divides the Nummulitidae in two subfamilies, the Nummulitinae and Heterostegininae, according to the presence or absence of secondary septa. To test the evolutionary importance of this morphological feature, phylogenetic relationships of five Recent nummulitid genera were investigated by sequencing fragments of the SSU and LSU rRNA gene. According to our results, species characterized by septate chambers (Heterostegina depressa, Planostegina operculinoides, and Cycloclypeus carpenteri) either group with species lacking septate chambers (Operculina ammonoides, Nummulites venosus) or branch separately. This suggests that chamber subdivisions developed several times independently in the evolutionary history of the Nummulitidae, providing an example of parallel evolution in Foraminifera.

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Fossil Foraminifera appear in the Early Cambrian, at about the same time as the first skeletonized metazoans. However, due to the inadequate preservation of early unilocular (single-chambered) foraminiferal tests and difficulties in their identification, the evolution of early foraminifers is poorly understood. By using molecular data from a wide range of extant naked and testate unilocular species, we demonstrate that a large radiation of nonfossilized unilocular Foraminifera preceded the diversification of multilocular lineages during the Carboniferous. Within this radiation, similar test morphologies and wall types developed several times independently. Our findings indicate that the early Foraminifera were an important component of Neoproterozoic protistan community, whose ecological complexity was probably much higher than has been generally accepted.

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Sediment-dwelling protists are among the most abundant meiobenthic organisms, ubiquitous in all types of aquatic ecosystems. Yet, because their isolation and identification are difficult, their diversity remains largely unknown. In the present work, we applied molecular methods to examine the diversity of freshwater Foraminifera, a group of granuloreticulosan protists largely neglected until now. By using specific PCR primers, we detected the presence of Foraminifera in all sediment samples examined. Phylogenetic analysis of amplified SSU rDNA sequences revealed two distinct groups of freshwater foraminiferans. All obtained sequences branched within monothalamous (single-chambered), marine Foraminifera, suggesting a repeated colonization of freshwater environments. The results of our study challenge the traditional view of Foraminifera as essentially marine organisms, and provide a conceptual framework for charting the molecular diversity of freshwater granuloreticulosan protists.

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Vannella simplex (Gymnamoebia, Vannellidae) is one of the most common amoebae species, recorded from a variety of regions. It was originally described as a freshwater species, but has also been reported from shallow-water regions of the Baltic Sea. In the present work, we investigated the morphology and biology of three V. simplex isolates, originating from geographically distant regions. Among them is one brackish water strain, isolated from artificial cyanobacterial mats, which were originally sampled in Nivå Bay (Baltic Sea, The Sound). The strain is cyst-forming and can thrive at salinity ranges from 0-50 ppt. Phylogenetic relationships were investigated by sequencing partial SSU rDNA of the cultured V. simplex isolates. Additional sequences were obtained from four environmental DNA extractions of sediment samples collected from different localities in Switzerland. Analysis of all obtained sequences revealed a monophyletic group. Based on the analysis and comparison of morphological, ecological and molecular data sets we compiled a distribution map of V. simplex and propose an emendation of this species.

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Vannella simplex (Gymnamoebia, Vannellidae) is one of the most common amoebae species, recorded from a variety of regions. It was originally described as a freshwater species, but has also been reported from shallow-water regions of the Baltic Sea. In the present work, we investigated the morphology and biology of three V. simplex isolates, originating from geographically distant regions. Among them is one brackish water strain, isolated from artificial cyanobacterial mats, which were originally sampled in Nivå Bay (Baltic Sea, The Sound). The strain is cyst-forming and can thrive at salinity ranges from 0–50 ppt. Phylogenetic relationships were investigated by sequencing partial SSU rDNA of the cultured V. simplex isolates. Additional sequences were obtained from four environmental DNA extractions of sediment samples collected from different localities in Switzerland. Analysis of all obtained sequences revealed a monophyletic group. Based on the analysis and comparison of morphological, ecological and molecular data sets we compiled a distribution map of V. simplex and propose an emendation of this species.

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Allogromiids are classically defined as a group of monothalamous, soft-walled foraminiferans. Recent morphological, cytological, and molecular studies, however, challenge this view, showing that the soft-walled allogromiids are closely related to naked athalamids and unilocular agglutinated foraminiferans. To establish the phylogenetic relationships among these three groups we obtained partial small-subunit ribosomal DNA sequences of 50 species and undetermined morphotypes, and compared them to other foraminiferal taxa. Phylogenetic analyses of our data show that allogromiids, athalamids and astrorhizids comprise an assemblage of 13 lineages branching together at the base of the foraminiferal tree. Among these lineages, two are represented by a single species and four comprise similar genera, while the remaining seven are heterogeneous groups composed of several species having different types of wall structure and different test morphologies. All lineages are relatively well supported, yet the relationships among them are not resolved. In view of our data, we propose to revise the definition of allogromiids to include all naked and testate unilocular granuloreticuloseans that diverged early in the evolution of Foraminifera.

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Allogromiid foraminiferans are distributed over a wide range of marine habitats, but some are also reported from freshwater environments. Most of these descriptions date back to the 19th century. Among them, five species of freshwater foraminiferans have been described and redescribed from Lake Geneva by the Swiss protozoologist Eugène Penard. The different foraminiferal species were classified by Penard in the genus Gromia, which at that time included both, filosean and granuloreticulosan species and were later grouped by De Saedeleer in two allogromiid genera, Allelogromia and Diplogromia. We collected several sediment samples from Lake Geneva and from two other bodies of freshwater in Switzerland and investigated them subsequently under a stereomicroscope. None of the forms described by Penard were observed. On the other hand, we have obtained foraminiferal DNA sequences from DNA extracts of the same sediment samples. Phylogenetic analysis of these sequences shows that they branch with a clade of saccamminid foraminiferans, represented by the genera Ovammina and Cribrothalammina. This is in agreement with the observed morphological similarity between Penard’s species and the marine saccamminids used in our study. The possibility that our sequences belong to some undetermined naked foraminiferans, however, cannot be excluded and the molecular identification of the species described by Penard must await the confirmation by sequencing DNA of isolated specimens.

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Foraminifera are traditionally defined as marine granuloreticuloseans characterized by the presence of a membraneous, agglutinated or calcareous test. This definition has been recently challenged by molecular phylogenetic studies which showed that Foraminifera include both testate and naked species and that they occur in marine, freshwater, and terrestrial environments. Molecular data also revealed high taxonomic diversity of monothalamous (single-chambered) foraminiferans that developed different types of organic and agglutinated tests. First analyses of ribosomal DNA sequences suggested an early divergence of Foraminifera in the evolutionary history of Eukaryotes, but this result was not confirmed by later protein sequence data. Furthermore, analysis of variable regions in ribosomal DNA revealed the presence of several cryptic species, whose geographic distribution seems to be related to oceanic water mass circulation and productivity.

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The foraminiferal family Allogromiidae occurs mainly in marine environments, although some genera are described from brackish and freshwater habitats. We report here the occurrence of a terrestrial allogromiid foraminiferan. Phylogenetic relationships were investigated by sequencing part of the SSU rDNA. DNA sequence analysis confirms a close relationship of the new species to the genus Allogromia. Morphological studies corroborate the affiliation to the family Allogromiidae but the lack of an entosolenian tube and an internal septum as well as the different ecology do not allow a classification into a known genus of this family. Taking the molecular, morphological and ecological differences into account, a new genus Edaphoallogromia with the type species E. australica is erected.

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The foraminiferal superfamily Soritacea belongs to the suborder Miliolina and is divided in two families, Peneroplidae and Soritidae, the latter one comprising two subfamilies, Archaiasinae and Soritinae. Phylogenetic relationships of 11 genera of soritid foraminifera were investigated by sequencing the complete SSU rDNA gene for 25 specimens. Additionally, partial SSU rDNA sequences were obtained from another 15 specimens of Soritinae. DNA sequence analysis confirms the monophyly of each family. Caribbean Archaiasinae form a monophyletic clade with Pacific Laevipeneroplis at the base. The genus Parasorites apppears as a sister taxa to Soritinae. Complex morphological features that characterize the genus Marginopora seem to have evolved independently at least twice, as the examined representatives cluster within two other soritine genera. Molecular analysis further shows that Sorites orbiculus and Sorites marginalis represent two different morphotypes of one species. Our data indicate that morphological changes and acquisition of new endosymbiont types in each group played an important role in the adaptation and radiation of Soritacea.

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Large miliolid foraminifers of the subfamily Soritinae bear symbiotic dinoflagellates morphologically similar to the species of the "Symbiodinium" complex, commonly found in corals and other marine invertebrates. Soritid foraminifers are abundant in coral reefs and it has been proposed that they share their symbionts with other dinoflagellate-bearing reef dwellers. In order to test this hypothesis, we have analysed partial large subunit ribosomal DNA sequences from dinoflagellates symbionts obtained from 28 foraminiferal specimens, and compared them to the corresponding sequences of Symbiodinium-like endosymbionts from various groups of invertebrates. Phylogenetic analysis of our data shows that all soritid symbionts belong to the "Symbiodinium" species complex, within which they form seven different molecular types (Frl-Fr7). Only one of these types (Fr1) branches within a group of invertebrate symbionts, previously described as type C. The remaining six types form sister groups to coral symbionts previously designed as types B, C, and D. Our data indicate a high genetic diversity and specificity of Symbiodinium-like symbionts in soritids. Except for type C, we have found no evidence for the transmission of symbionts between foraminifers and other symbiont-bearing invertebrates from the same localities. However, exchanges must have occurred frequently between the different species of Soritinae, as suggested by the lack of host specificity and some biogeographical patterns observed in symbiont distribution. Our data suggest that members of the subfamily Soritinae acquired their symbionts at least three times during their history, each acquisition being followed by a rapid diversification and independent radiation of symbionts within the foraminiferal hosts.

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Large miliolid foraminifers bear various types of algal endosymbionts including chlorophytes, dinoflagellates, rhodophytes, and diatoms. Symbiosis plays a key role in the adaptation of large foraminifera to survival and growth in oligotrophic seas. The identity and diversity of foraminiferal symbionts, however, remain largely unknown. In the present work we use ribosomal DNA (rDNA) sequences to identify chlorophyte endosymbionts in large miliolid foraminifera of the superfamily Soritacea. Partial 18S and complete Internal Transcribed Spacer (ITS) rDNA sequences were obtained from symbionts of eight species representing all genera of extant chlorophyte-bearing Soritacea. Phylogenetic analysis of the sequences confirms the previous fine structure-based identification of these endosymbionts as belonging to the genus Chlamydomonas. All foraminiferal symbionts form a monophyletic group closely related to Chlamydomonas noctigama. The group is composed of seven types identified in this study, including one previously morphologically described species, Chlamydomonas hedleyi. Each of these types can be considered as a separate species, based on the comparison of genetic differences observed between other established Chlamydomonas species. Several foraminiferal species share the same symbiont type, but only one species, Archaias angulatus, was found to bear more than one type.

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The genus Ammonia is a common benthic foraminifer which is widely distributed in nearshore marine environments. Its large morphological variability causes considerable difficulties in species identification. In the present study, we investigated taxonomic relationships in Ammonia by using a molecular approach based on ribosomal DNA sequences. We obtained 149 partial large subunit ribosomal DNA (LSU rDNA) sequences and 23 small subunit ribosomal DNA (SSU rDNA) sequences from 88 living Ammonia specimens which were collected from free-living populations in 14 localities. Sequence analysis revealed the presence of eight distinct genotypic groups (T1–T7, T9) and one distinct genotype that is represented by one specimen (T8). Examination of morphological characters shows that only one genotypic group can be clearly distinguished by its morphology. Biogeographical and ecological features are used for an additional characterization and it seems that the different groups live in relatively well defined environmental conditions and that only one genotypic group is cosmopolitan, while the others have a rather restricted geographical distribution. According to our study, three of the genotypic groups can be regarded as distinct species.

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The genus Ammonia is one of the most common benthic foraminifer of considerable biogeographic importance. The taxonomic status of most of the described species of Ammonia, however, is yet unsettled. In the present study, we used the partial large subunit ribosomal DNA (LSU rDNA) sequences as an alternative approach to distinguish different specimens of Ammonia living in the Lagoon of Venice. We have obtained DNA sequences from 20 living specimens whose tests were examined previously by scanning electron microscopy (SEM). Sequence analysis revealed the presence of two groups, which differ by more than 10.5%. Within each group, the sequence divergence ranges from 0.2 % to 6.9 %. The two groups that can be separated genetically, are called Ammonia sp. 1 and Ammonia sp. 2. Their morphological distinction, however, is problematic. The tests of Ammonia sp. 1 are generally characterized by a more lobate periphery, more elevated dorsal sutures and larger perforations compared to those of Ammonia sp. 2, but none of these characters can be used with certainty for the morphological distinction of both groups.

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An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genus Ammonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens named Ammonia sp. 1 and Ammonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% in Ammonia sp. 1 and from 0.7% to 2.3% in Ammonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally accepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen of Ammonia 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.

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