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Ammonia is one of the most widespread foraminiferal genera worldwide. Three phylotypes (Ammonia sp. T1, T2 and T6), commonly encountered in the northeast Atlantic, are usually associated with the morphospecies Ammonia tepida. The biogeographic distribution of these three types was previously investigated in coastal environments around Great Britain based on genetic assignations. A new method was recently developed to recognize these three phylotypes based on morphological criteria (i.e. pore size and suture elevation on spiral side), avoiding the need to use molecular analyses to identify them. The results presented here allow us to validate the consistency of the morphometric determination method but also to define more precisely the pore size variability of each of the three phylotypes, which is a main criterion for their recognition. Moreover, these results, combined with earlier molecular and morphological data, enable us to refine the biogeographic distribution previously established by genetic analyses alone. The biogeographical distribution pattern presented here supports the putatively invasive character of Ammonia sp. T6, by suggesting that this phylotype is currently spreading out over large areas and is supplanting autochthonous phylotypes (T1 and T2) along the coastlines of the British Isles and northern France. In fact, only the southwest coast of England and Ireland and the northwest coast of France have not been colonized by Ammonia sp. T6 yet. Our results also suggest that within the areas colonized by phylotype T6, T2 may find refuges in the inner parts of estuaries. We further suggest that the absence of Ammonia sp. T6 in the western part of the English Channel may be explained by the general surface current circulation pattern, which impedes further expansion. The high reliability of the determination method of phylotypes T1, T2 and T6 based on morphology also allows us to quickly generate large datasets for sub-recent and fossil material. This new method will make it possible to gain an understanding of the ecological differences between the three phylotypes and of the historical changes in their distribution patterns (for example due to changing anthropogenic factors). Finally, it will allow us to confirm or invalidate the putative invasive character of phylotype T6.

Increasing occurrences of extreme weather events, such as the 2018 drought over northern Europe, are a concerning issue under global climate change. High resolution archives of natural hydroclimate proxies, such as rapidly accumulating sediments containing biogenic carbonates, offer the potential to investigate the frequency and mechanisms of such events in the past. Droughts alter the barium (Ba) concentration of near-continent seawater through the reduction in Ba input from terrestrial runoff, which in turn may be recorded as changes in the chemical composition (Ba/Ca) of foraminiferal calcium carbonates accumulating in sediments. However, so far the use Ba/Ca as a discharge indicator has been restricted to planktonic foraminifera, despite the high relative abundance of benthic species in coastal, shallow-water sites. Moreover, benthic foraminiferal Ba/Ca has mainly been used in open ocean records as a proxy for paleo-productivity. Here we report on a new geochemical dataset measured from living (CTG-labelled) benthic foraminiferal species to investigate the capability of benthic Ba/Ca to record changes in river runoff over a gradient of contrasting hydroclimatic conditions. Individual foraminifera (Bulimina marginata, Nonionellina labradorica) were analyzed by laser-ablation ICP-MS over a seasonal and spatial gradient within Gullmar Fjord, Swedish west coast during 2018–2019. The results are compared to an extensive meteorological and hydrological data set, as well as sediment and pore-water geochemistry. Benthic foraminiferal Ba/Ca correlates significantly to riverine runoff, however, the signals contain both spatial trends with distance to Ba-source, and species-specific influences such as micro-habitat preferences. We deduce that shallow-infaunal foraminifera are especially suitable as proxy for terrestrial Ba input and discuss the potential influence of water-column and pore-water Ba cycling. While distance to Ba-source, water depth, pore-water geochemistry, and species-specific effects need to be considered in interpreting the data, our results demonstrate confidence in the use of Ba/Ca of benthic foraminifera from near-continent records as proxy for past riverine discharge and to identify periods of drought.

Several foraminifera are deposit feeders that consume organic detritus (dead particulate organic material along with entrained bacteria). However, the role of such foraminifera in the benthic food-web remains understudied. As foraminifera may associate with methanotrophic bacteria, which are 13C-depleted, feeding on them has been suggested to cause negative δ13C values in the foraminiferal cytoplasm and/or calcite. To test whether the foraminiferal diet includes methanotrophs, we performed a short-term (1 d) feeding experiment with Nonionellina labradorica from an active Arctic methane-emission site (Storfjordrenna, Barents Sea) using the marine methanotroph Methyloprofundus sedimenti, and analyzed N. labradorica cytology via Transmission Electron microscopy (TEM). We hypothesized that M. sedimenti would be visible, as evidenced by their ultrastructure, in degradation vacuoles after this feeding experiment. Sediment grains (mostly clay) occurred inside one or several degradation vacuoles in all foraminifers. In 24 % of the specimens from the feeding experiment degradation vacuoles also contained bacteria, although none could be confirmed to be the offered M. sedimenti. Observations of the area adjacent to the aperture after 20 h incubation revealed three putative methanotrophs, close to clay particles. These methanotrophs were identified based on internal characteristics such as a type I stacked intracytoplasmic membranes (ICM), storage granules (SG) and gram-negative cell walls (GNCW). Furthermore, N. labradorica specimens were examined for specific adaptations to this active Arctic methane-emission site; we noted the absence of bacterial endobionts in all specimens examined but confirmed the presence of kleptoplasts, which were often partially degraded. Based on these observations, we suggest that M. sedimenti can be consumed by N. labradorica via untargeted grazing in seeps and that N. labradorica can be generally classified as a deposit feeder at this Arctic site. These results suggest that if methanothrophs are available to the foraminifera in their habitat, their non-selective uptake could make a substantial contribution to altering δ13Ctest values. This in turn may impact metazoans grazing on benthic foraminifera by altering their δ13C signature.

Benthic foraminiferal assemblage data have been derived from a marine sediment core collected in a cold-water coral (CWC) site off northwest Scotland (near the Wyville Thomson Ridge - WTR). The record covers the last glacial period to the late Holocene. Our reconstructions enable to better constrain the paleoenvironmental changes that took place in the study area since the last glacial time and define the environmental conditions that allowed the onset, formation and decline of CWCs in the area. The sedimentary record was characterized by three distinct foraminiferal assemblages, dominant during the pre-coral time interval (i and ii) and the coral period (iii): (i) the “Glacial” assemblage (>13 cal ka BP) was characterized by the dominance of Cibicides refulgens and Discanomalina coronata. Low foraminiferal densities and diversities indicated unfavorable ecological conditions (i.e., low temperature and food availability, coarse substrate) that were most likely related to the extended British Ice Sheet; (ii) the “Deglacial-Early Holocene” assemblage (~13–9 cal ka BP) was characterized by the cassidulinids-Lobatula lobatula association, indicating a progressive increase of organic matter content and influx of warm and saline North Atlantic surface waters. We hypothesize that these were the main environmental factors that thereafter allowed the settlement of CWCs in the WTR area around 9 cal ka BP; (iii) the “Holocene” (

We gathered total organic carbon (%) and relative abundances of benthic foraminifera in intertidal areas and transitional waters from the English Channel/European Atlantic Coast (587 samples) and the Mediterranean Sea (301 samples) regions from published and unpublished datasets. This database allowed to calculate total organic carbon optimum and tolerance range of benthic foraminifera in order to assign them to ecological groups of sensitivity. Optima and tolerance range were obtained by mean of the weighted-averaging method. The data are related to the research article titled "Indicative value of benthic foraminifera for biomonitoring: assignment to ecological groups of sensitivity to total organic carbon of species from European intertidal areas and transitional waters The authors are grateful to the Swiss National Science Foundation, the Agence de l'Eau Artois-Picardie, the Communauté d'Agglomération du Boulonnais, the Université de Lille, the Université du Littoral Côte d'Opale, the Laboratoire d'Océanologie et de Géosciences for their financial support to FOBIMO workshops in Fribourg (Switzerland), Wimereux (France) and Texel (The Netherlands); Additional funding was provided by Spanish MINECO (RTI2018-095678-B-C21, MCIU/AEI/FEDER, UE)

International audience; This work contributes to the ongoing work aiming at confirming benthic foraminifera as a biological quality element. In this study, benthic foraminifera from intertidal and transitional waters from the English Channel/European Atlantic coast and the Mediterranean Sea were assigned to five ecological groups using the weighted-averaging optimum with respect to TOC of each species. It was however not possible to assign typical salt marsh species due to the presence of labile and refractory organic matter that hampers TOC characterization. Tests of this study species’ lists with Foram-AMBI on two independent datasets showed a significant correlation between Foram-AMBI and TOC, confirming the strong relation between foraminifera and TOC. For one of the validation datasets, associated macrofaunal data were available and a significant correlation was found between the foraminiferal Foram-AMBI and the macrofaunal AMBI. The here proposed lists should be further tested withsensitivity-based indices in different European regional settings.

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, (undefined)

Funding: UK Natural Environment Research Council (NERC) grant NE/G020310/1 (K.D., W.E.N.A. and M.S) and the Carnegie Trust for the Universities of Scotland. The genetic diversity, morphology and biogeography of Ammonia specimens was investigated across the Northeast (NE) Atlantic margins, to enhance the regional (palaeo)ecological studies based on this genus. Living specimens were collected from 22 sampling locations ranging from Shetland to Portugal to determine the distribution of Ammonia genetic types across the NE Atlantic shelf biomes. We successfully imaged (via scanning electron microscopy, SEM) and genotyped 378 Ammonia specimens, based on the small subunit (SSU) rRNA gene, linking morphology to genetic type. Phylogenetic analyses enabled identification of seven genetic types and subtypes inhabiting the NE Atlantic margins. Where possible, we linked SSU genetic types to the established large subunit (LSU) T-type nomenclature of Hayward et al. (2004). SSU genetic types with no matching T-type LSU gene sequences in GenBank were allocated new T-numbers to bring them in line with the widely adopted T-type nomenclature. The genetic types identified in the NE Atlantic margins are T1, T2, T3, T6, and T15, with both T2 and T3 being split further into the subtypes T2A and T2B, and T3S and T3V respectively. The seven genetic types and subtypes exhibit different biogeographical distributions and/or ecological preferences, but co-occurrence of two or more genetic types is common. A shore-line transect at Dartmouth (South England) demonstrates that sampling position on shore (high, middle or low shore) influences the genetic type collected, the numbers of genetic types that co-occur, and the numbers of individuals collected. We performed morphometric analysis on the SEM images of 158 genotyped Ammonia specimens. T15 and the subtypes T3S and T3V can be morphologically distinguished. We can unequivocally assign the taxonomic names A. batava and A. falsobeccarii to T3S and T15, respectively. However, the end members of T1, T2A, T2B and T6 cannot be unambiguously distinguished, and therefore these genetic types are partially cryptic. However, we confirm that T2A can be assigned to A. aberdoveyensis, but caution must be taken in warm provinces where the presence of T2B will complicate the morphological identification of T2A. We suggest that T6 should not currently be allocated to the Pliocene species A. aomoriensis due to morphological discrepancies with the taxonomic description and to the lack of genetic information. Of significance is that these partially cryptic genetic types frequently co-occur, which has considerable implications for precise species identification and accurate data interpretation. Postprint

The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a ~ 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study 13C-bicarbonate, 15N-ammonium and 34S-sulfate uptake. In addition, respiration rate measurements were determined to assess the response of N. labradorica to light. The DNA sequences established that over 80% of the kleptoplasts belonged to Thalassiosira (with 96%–99% identity), a cosmopolitan planktonic diatom. TEM-NanoSIMS imaging revealed degraded cytoplasm and an absence of 13C assimilation in foraminifera exposed to light. Oxygen measurements showed higher respiration rates under light than dark conditions, and no O2 production was detected. These results indicate that the photosynthetic pathways in N. labradorica are not functional. Furthermore, N. labradorica assimilated both 15N-ammonium and 34S-sulfate into its cytoplasm, which suggests that foraminifera might have several ammonium or sulfate assimilation pathways, involving either the kleptoplasts or bona fide foraminiferal pathway(s) not yet identified. (Less)

Due to climate warming and increased anthropogenic impact, a decrease of ocean water oxygenation is expected in the near future, with major consequences for marine life. In this context, it is essential to develop reliable tools to assess past oxygen concentrations in the ocean, to better forecast these future changes. Recently, foraminiferal pore patterns have been proposed as a bottom water oxygenation proxy, but the parameters controlling foraminiferal pore patterns are still largely unknown. Here we use scaling laws to describe how both gas exchanges (metabolic needs) and mechanical constraints (shell robustness) control foraminiferal pore patterns. The derived mathematical model shows that only specific combinations of pore density and size are physically feasible. Maximum porosity, of about 30%, can only be obtained by simultaneously increasing pore size and decreasing pore density. A large empirical data set of pore data obtained for three pseudocryptic phylotypes of Ammonia, a common intertidal genus from the eastern Atlantic, strongly supports this conclusion. These new findings provide basic mechanistic understanding of the complex controls of foraminiferal pore patterns and give a solid starting point for the development of proxies of past oxygen concentrations based on these morphological features. Pore size and pore density are largely interdependent, and both have to be considered when describing pore patterns.

The aim of this work is to document the complex nutritional strategy developed by kleptoplastic intertidal foraminifera. We study the mixotrophic ability of a common intertidal foraminifer, Elphidium williamsoni, by (i) investigating the phylogenetic identity of the foraminiferal kleptoplasts, (ii) following their oxygenic photosynthetic capacity and (iii) observing the modification in cellular ultrastructural features in response to photoautotrophic conditions. This was achieved by coupling molecular phylogenetic analyses and TEM observations with non-destructive measurements of kleptoplast O2 production over a 15-day experimental study. Results show that the studied E. williamsoni actively selected kleptoplasts mainly from pennate diatoms and had the ability to produce oxygen, up to 13.4 nmol O2 cell-1 d-1, from low to relatively high irradiance over at least 15 days. Ultrastructural features and photophysiological data showed significant differences over time, the number of lipid droplets, residual bodies and the dark respiration increased; whereas, the number of kleptoplasts decreased accompanied by a minor decrease of the photosynthetic rate. These observations suggest that in E. williamsoni kleptoplasts might provide extra carbon storage through lipid droplets synthesis and highlight the complexity of E. williamsoni feeding strategy and the necessity of further dedicated studies regarding mechanisms developed by kleptoplastidic foraminifera for carbon partitioning and storage.

The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a similar to 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study C-13-bicarbonate, N-15-ammonium and S-34-sulfate uptake. In addition, respiration rate measurements were determined to assess the response of N. labradorica to light. The DNA sequences established that over 80% of the kleptoplasts belonged to Thalassiosira (with 96%-99% identity), a cosmopolitan planktonic diatom. TEM-NanoSIMS imaging revealed degraded cytoplasm and an absence of C-13 assimilation in foraminifera exposed to light. Oxygen measurements showed higher respiration rates under light than dark conditions, and no O-2 production was detected. These results indicate that the photosynthetic pathways in N. labradorica are not functional. Furthermore, N. labradorica assimilated both N-15-ammonium and S-34-sulfate into its cytoplasm, which suggests that foraminifera might have several ammonium or sulfate assimilation pathways, involving either the kleptoplasts or bona fide foraminiferal pathway(s) not yet identified.

Genetic characterisation (SSU rRNA genotyping) and Scanning ElectronMicroscope (SEM) imaging of individual tests were used in tandem to determine the modern species richness of the foraminiferal family Elphidiidae (Elphidium Haynesina and related genera) across the Northeast Atlantic shelf biomes. Specimens were collected at 25 locations fromthe High Arctic to Iberia and a total of 1013 individual specimenswere successfully SEMimaged and genotyped. Phylogenetic analyses were carried out in combination with 28 other elphidiid sequences from GenBank and seventeen distinct elphidiid genetic types were identified within the sample set seven being sequenced for the first time. Genetic types cluster into sevenmain cladeswhich largely represent their generalmorphological character. Differences between genetic types at the genetic morphological and biogeographic levels are indicative of species level distinction. Their biogeographic distributions in combination with elphidiid SSU sequences from GenBank and high resolution images from the literature show that each of them exhibits species specific rather than clade specific biogeographies. Due to taxonomic uncertainty and divergent taxonomic concepts between schools we believe that morphospecies names should not be placed onto molecular phylogenies unless both the morphology and genetic type have been linked to the formally named holotype or equivalent. Based on strictmorphological criteriawe advocate using only a three stage approach to taxonomy for practical application in micropalaeontological studies. It comprises genotyping the production of a formal morphological description of the SEM images associated with the genetic type and then the allocation of the most appropriate taxonomic name by comparison with the formal type description. Using this approach we were able to apply taxonomic names to fifteen genetic types. One of the remaining two may be potentially cryptic and one is undescribed in the literature. In general the phylogeographic distribution is in agreement with our knowledge of the ecology and biogeographical distribution of the corresponding morphospecies highlighting the generally robust taxonomic framework of the Elphidiidae in time and space.

The assimilation of inorganic compounds in foraminiferal metabolism compared to predation or organic matter assimilation is unknown. Here, we investigate possible inorganic-compound assimilation in Nonionellina labradorica, a common kleptoplastidic benthic foraminifer from Arctic and North Atlantic sublittoral regions. The objectives were to identify the source of the foraminiferal kleptoplasts, assess their photosynthetic functionality in light and darkness and investigate inorganic nitrogen and sulfate assimilation. We used DNA barcoding of a ~ 830 bp fragment from the SSU rDNA to identify the kleptoplasts and correlated transmission electron microscopy and nanometre-scale secondary ion mass spectrometry (TEM-NanoSIMS) isotopic imaging to study

Most environmental bio-monitoring methods using the species composition of marine faunas define the Ecological Quality Status of soft bottom ecosystems based on the relative proportions of species assigned to a limited number of ecological categories. In this study we analyse the distribution patterns of benthic foraminifera in the Mediterranean as a function of organic carbon gradients on the basis of 15 publications and assign the individual species to five ecological categories. Our categories (of sensitive, indifferent and 3rd, 2nd and 1st order opportunists) are very similar to the ecological categories commonly used for macrofauna, but show some minor differences. In the 15 analysed publications, we considered the numerical data of 493 taxa, of which 199 could be assigned. In all 79 taxa were classified as sensitive, 60 as indifferent, 46 as 3rd order, 12 as 2nd order and 2 as 1st order opportunists. The remaining 294 taxa are all accessory, and will only marginally contribute to biotic indices based on relative species proportions. In this paper we wanted also to explain the methodology we used for these species assignments, paying particular attention to all complications and problems encountered. We think that the species list proposed here will constitute a highly useful tool for foraminiferal bio-monitoring of soft bottoms in the Mediterranean Sea, which can be used in different ecological indices (Foram-AMBI and similar methods). With additional information becoming available in the next few years, it will be possible to expand the list, and, if necessary, to apply some minor corrections. As a next step, we intend to test this species list using several biotic indices, in a number of independent data sets, as soon as these will become available.

International audience; Assimilation, sequestration and maintenance of foreign chloroplasts inside an organism is termed “chloroplast sequestration” or “kleptoplasty”. This phenomenon is known in certain benthic foraminifera, in which such kleptoplasts can be found both intact and functional, but with different retention times depending on foraminiferal species. In the present study, seven species of benthic foraminifera (Haynesina germanica, Elphidium williamsoni, E. selseyense, E. oceanense, E. aff. E. crispum, Planoglabratella opercularis and Ammonia sp.) were collected from shallow-water benthic habitats and examined with the transmission electron microscope (TEM) for cellular ultrastructure to ascertain attributes of kleptoplasts. Results indicate that all these foraminiferal taxa actively obtain kleptoplasts but organized them differently within their endoplasm. In some species, the kleptoplasts were evenly distributed throughout the endoplasm (e.g., H. germanica, E. oceanense, Ammonia sp.), whereas other species consistently had plastids distributed close to the external cell membrane (e.g., Elphidium williamsoni, E. selseyense, P. opercularis). Chloroplast degradation also seemed to differ between species, as many degraded plastids were found in Ammonia sp. and E. oceanense compared to other investigated species. Digestion ability, along with different feeding and sequestration strategies may explain the differences in retention time between taxa. Additionally, the organization of the sequestered plastids within the endoplasm may also suggest behavioral strategies to expose and/or protect the sequestered plastids to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats.

Silicoflagellate double skeletons are commonly considered to be pre-division stages, even though their life cycle is only partially resolved, especially with respect to reproduction. Double skeletons of the modern silicoflagellate genera Dictyocha Ehrenberg, Distephanus Stohr, and Octactis Schiller are for the first time examined in detail by scanning electron microscopy in order to improve our understanding of how skeletal morphology relates to paired skeletons. A number of genus-specific mechanisms enable sibling skeletons to be held together at their abbasal surfaces, including a zig-zag design of the basal ring achieved via apical structure, strut attachment and pike rotation (in Distephanus and Dictyocha), and the presence of organic material binding the generally planar basal rings (in Octactis). Contrary to what is generally understood, the siblings are not mirror images of one another. Instead, the triple junctions formed by the skeletal elements of each apical structure are transposed across the middle of the dividing cell to produce a copy with the same rotation. Thus, two dome-shaped skeletons represent halves of a more spherical design, which suggests that the role of the silicoflagellate basal ring is to enable double skeleton formation, but the full implications of this have yet to be explored. Although the purpose of double skeleton formation in silicoflagellates remains unclear, observations from the fossil record indicate that differences in the relative alignment of doublet members can have a high significance for phylogeny. Differences in the doublet structure of living silicoflagellates call for a combined biological and geological perspective of the utility of maintaining Dictyocha, Distephanus and Octactis as separate genera.

This work was funded by the Natural Environment Research Council (NERC) of the United Kingdom (grant NE/G020310/1 to K.D., W.E.N.A. and M.S.) and the Carnegie Trust for the Universities of Scotland. M.S. was supported by the Swiss National Science Foundation (SNSF, fellowships for advanced researchers PA00P2_126226 and PA00P2_142065). Genetic characterisation (SSU rRNA genotyping) and Scanning Electron Microscope (SEM) imaging of individual tests were used in tandem to determine the modern species richness of the foraminiferal family Elphidiidae (Elphidium, Haynesina and related genera) across the Northeast Atlantic shelf biomes. Specimens were collected at 25 locations from the High Arctic to Iberia, and a total of 1013 individual specimens were successfully SEM imaged and genotyped. Phylogenetic analyses were carried out in combination with 28 other elphidiid sequences from GenBank and seventeen distinct elphidiid genetic types were identified within the sample set, seven being sequenced for the first time. Genetic types cluster into seven main clades which largely represent their general morphological character. Differences between genetic types at the genetic, morphological and biogeographic levels are indicative of species level distinction. Their biogeographic distributions, in combination with elphidiid SSU sequences from GenBank and high resolution images from the literature show that each of them exhibits species-specific rather than clade-specific biogeographies. Due to taxonomic uncertainty and divergent taxonomic concepts between schools, we believe that morphospecies names should not be placed onto molecular phylogenies unless both the morphology and genetic type have been linked to the formally named holotype, or equivalent. Based on strict morphological criteria, we advocate using only a three-stage approach to taxonomy for practical application in micropalaeontological studies. It comprises genotyping, the production of a formal morphological description of the SEM images associated with the genetic type and then the allocation of the most appropriate taxonomic name by comparison with the formal type description. Using this approach, we were able to apply taxonomic names to fifteen genetic types. One of the remaining two may be potentially cryptic, and one is undescribed in the literature. In general, the phylogeographic distribution is in agreement with our knowledge of the ecology and biogeographical distribution of the corresponding morphospecies, highlighting the generally robust taxonomic framework of the Elphidiidae in time and space. Publisher PDF

International audience; Benthic foraminiferal pores are considered to play an important role in facilitating the gas exchange between the organism and the environment, with pore size and density supposed to be related to gas exchange intensity. Recent studies have therefore attempted to establish relationships between pore patterns and redox conditions, such as bottom water oxygen and nitrate concentrations. However, a prerequisite for such an attempt is the development of a practical and reliable methodology for measuring pore patterns. The aim of this study is to present a semi-automated pore measurement method for Ammonia, a dominant taxon of temperate coastal environments that are increasingly affected by seasonal hypoxia (bottom water oxygen concentration

International audience; Benthic foraminiferal pores are considered to play an important role in facilitating the gas exchange between the organism and the environment, with pore size and density supposed to be related to gas exchange intensity. Recent studies have therefore attempted to establish relationships between pore patterns and redox conditions, such as bottom water oxygen and nitrate concentrations. However, a prerequisite for such an attempt is the development of a practical and reliable methodology for measuring pore patterns. The aim of this study is to present a semi-automated pore measurement method for Ammonia, a dominant taxon of temperate coastal environments that are increasingly affected by seasonal hypoxia (bottom water oxygen concentrationIn order to demonstrate the efficiency of the method, we applied it in two case studies. Firstly, a study of living Ammonia in Lake Grevelingen (Netherlands) revealed a clear difference in pore patterns between three studied stations characterised by different seasonal bottom water oxygenation patterns. Secondly, a sediment core from the same site clearly showed the presence of two morphotypes of Ammonia; one with numerous, small pores and the other with fewer but much larger pores, resulting in a higher porosity (larger part of the test covered by pores). Since the man-made closure of Lake Grevelingen in 1971, the latter morphotype has progressively replaced the former one. Finally, a summary of the measurements on 870 specimens with both pore patterns shows a strong relationship between pore density and pore surface area, suggesting a physical control of the interaction between these two parameters.

Shallow water Antarctic cibicidids are traditionally identified as Cibicides refulgens or Cibicidoides lobatulus . However, a recent phylogenetic study based on SSU rDNA sequence data has demonstrated that these Antarctic cibicidids form a well-supported clade that branches sister to Mediterranean C. refulgens and is only distantly related to C. lobatulus . Based on these DNA sequences, and a detailed scanning electron microscopic examination of material from Explorers Cove (McMurdo Sound), we place Antarctic cibicidids in a separate species Cibicides antarcticus (Saidova, 1975), which is emended here with molecular, morphological, and ecological features.

Cibicidoides dispars and Cibicidoides variabilis are two neritic cibicidids commonly found on the Patagonian coasts. Phylogenetic analyses of partial SSU rDNA sequences show that they both belong to the genus Cibicidoides. Cibicidoides dispars branches close to Cibicidoides wuellerstorfi, whereas C. variabilis clusters with Cibicidoides pachyderma. In both cases, species clustering together are well separated morphologically and ecologically but close genetically. Molecular data indicate clearly that C. dispars and C. variabilis are well separated genetically from Cibicidoides lobatulus, another shallow water cibicidid sharing a similar ecology and morphology. Moreover, our molecular results show that neritic and bathyal or abyssal species are found together in different clades, suggesting multiple colonization events from shallow to deep water or vice versa. The analysis of more variable ITS rDNA region, on the other hand, reveals small differences between individuals of C. variabilis sampled in the south and north of Chilean Patagonia, which could indicate a cryptic speciation undergoing in this species.

Molecular phylogenetics gives new insights into the taxonomy of foraminifera, independent of their morphology. After a survey of the present knowledge on how molecular phylogeny can contribute to foraminiferal taxonomy, we present an applied example. The comparison of ribosomal DNA (rDNA) sequences belonging to the SSU (Small Subunit) and LSU (Large Subunit) genes of Pseudoeponides falsobeccarii with other similar sequences of rotaliids available in GenBank shows that this species actually belongs to the genus Ammonia, because it groups inside the other Ammonia sequences instead of forming a distinct clade. Moreover, Ammonia falsobeccarii forms a clade well separated from other Ammonia phylotypes, meaning that it can be considered as a distinct species, and not as an ecophenotype of one of the other Ammonia species.

Ammonia and Elphidium collected in the Kiel Fjord for the present study were first identified on morphological bases as Ammonia beccarii (Linne´, 1758) and Elphidium excavatum (Terquem, 1876). Phylogenetic analyses based on partial SSU rDNA and LSU rDNA sequences show that Ammonia specimens sampled in the Kiel Fjord belong to the phylotype T6, which has a disjunct distribution (Wadden and Baltic Seas/China and Japan) and has been identified as Ammonia aomoriensis (Asano, 1951). Partial SSU rDNA sequence analyses indicate that Elphidium specimens from the Kiel Fjord belong to the clade E. excavatum, confirming the morphological identification. This clade can be further divided in three subclades. Kiel Fjord Elphidium belong to two of these subclades and were identified morphologically as the subspecies E. excavatum excavatum (Terquem, 1876) and E. e. clavatum Cushman, 1930.

To infer the phylogenetic relationships of cibicidids, we obtained small subunit ribosomal DNA (SSU rDNA) sequences of six common cibicidid morphospecies. In view of our results, the placement of cibicidids in different superfamilies, the distinction between planoconvex Cibicides and biconvex Cibicidoides , and the erection of genera such as Fontbotia and Lobatula are unjustified. Moreover, the superfamily Planorbulinacea, in which cibicidids are often placed, is polyphyletic and coiling mode cannot be used as a major taxonomic criterion. Our data suggest that all cibicidids examined here could be classified in one unique family, the Cibicididae, that includes Melonis , Hanzawaia , Cibicides (for C. refulgens ), and Cibicidoides for the other five morphospecies studied ( C. kullenbergi , C. lobatulus , C. pachyderma , C. ungerianus , and C. wuellerstorfi ). Among the six sampled morphospecies, Cibicides refulgens is least closely related to any of the other cibicidids and forms a clade consisting of two different species, Cibicides sp. and C. refulgens clearly separated by geography (Antarctic and Mediterranean, respectively). The morphospecies Cibicidoides kullenbergi and C. pachyderma form a single clade representing the same species. The three other species, Cibicidoides lobatulus , C. ungerianus , and C. wuellerstorfi are closely related. Cibicidoides lobatulus possibly comprises two genetically distinct populations, one in the Mediterranean and the other in the North Atlantic.

The traditional morphology-based classification of Rotaliida was recently challenged by molecular phylogenetic studies based on partial small subunit (SSU) rDNA sequences. These studies revealed some unexpected groupings of rotaliid genera. However, the support for the new clades was rather weak, mainly because of the limited length of the analysed fragment. In order to improve the resolution of the phylogeny of the rotaliids, 26 new complete SSU rDNA sequences have been obtained. Phylogenetic analyses of these data, together with seven sequences obtained previously, confirm with stronger statistical support the presence of three major clades among the Rotaliida. The first clade comprises members of the families Uvigerinidae, Cassidulinidae and Bolivinidae. The second clade includes all analysed Discorbidae, Rosalinidae, Planulinidae, Planorbulinidae, Rotaliidae, Elphidiidae, Nummulitidae and one of the Nonionidae. Finally, the third clade comprises the Cibicididae, Pseudoparreliidae, Oridorsalidae, Stainforthiidae, Buliminidae and part of the Nonionidae. The clades 1 and 3 are strongly supported by analyses of the complete SSU rDNA, while the monophyly of clade 2 is less certain, probably due to the rapid evolutionary rates of some lineages included in this clade. These results clearly contradict the classical separation of rotaliid foraminifera into two orders: Rotaliida and Buliminida. Relatively good agreement has been found between molecular data and the morphological definition of the families for which more than one genus was sequenced. However, larger taxon sampling will be necessary for a better definition of the three major clades.

Getting DNA from foraminifers is a difficult task, but it can greatly help the identification of species and the phylogeny of the group (e.g. Pawlowski, 2000; Schweizer et al., 2008; Pawlowski & Holzmann, 2014) which are still mainly based on test morphol- ogy. Therefore, it is crucial to document the test morphology of the sampled specimens and extract DNA from them separately from each other (Pawlowski & Holzmann, 2014). To increase the chances of recovering DNA from a single individual, it is best to pick live foraminifers. However, a major question is how long DNA can outlast an organism after its death in natural conditions (e.g. Lindahl, 1993). This question may seem trivial to biologists but many foraminiferologists with a geological background ques- tion the length of time of decay for DNA in situ. The preservation of DNA when storing foraminifers after sampling has been dis- cussed previously (Holzmann & Pawlowski, 1996), but not its preservation in situ in intertidal conditions. The present experi- ment is designed to test how long after death DNA can still be obtained with routine DNA amplifications when picking dead for- aminifers instead of living ones in intertidal environments., Journal of Micropalaeontology, 34, ISSN:0262-821X

Uvigerina is a common genus of benthic foraminifera, often used as a proxy for paleoclimate and paleoenvironment reconstructions. Better understanding of the phylogeny of Uvigerina would improve its proxy value and would allow us to check whether its different morphospecies are real species or ecophenotypes only. Here, we used partial small-subunit ribosomal DNA (SSU rDNA) sequences to examine the phylogenetic relationships within Uvigerina and between this genus and other rotaliids. Our analyses show that the family Uvigerinidae forms a well supported clade branching as a sister group to Bolivinidae and Cassidulinidae. Studied individuals of Uvigerinidae include three species described as Uvigerina – U. mediterranea , U. elongatastriata and U. peregrina – as well as Rectuvigerina phlegeri and Trifarina earlandi . As U. peregrina is more closely related to R. phlegeri and T. earlandi than to the other two Uvigerina , the taxonomic status of these species needs to be revised. At the intraspecific level, we studied a morphologically highly variable population of U. peregrina from the Oslo Fjord. For the sequences obtained from this population of U. peregrina , we found almost no divergence inside the internal transcribed spacer (ITS), which is the most variable part of ribosomal DNA. This indicates a high morphological plasticity of Uvigerina species, which should be taken into consideration when using this genus as a proxy in paleoecological reconstructions.

Bentiske foraminifers bebor en bred vifte af vandmiljøer, herunder åbne hav-, brakvand, og ferskvandsområder. Her viser vi, at flere forskellige og forskellige foramini grupper (miliolids, rotaliids, textulariids) og Gromia, en anden taksonomisk gruppe også tilhørerende Rhizaria, akkumulere og respirere nitrat via denitrifikation. Den udbredte forekomst blandt fjernt disse beslægtede organismer, tyder på en gammel oprindelse af disse træk. De forskellige metaboliske kapacitet i disse organismer, som gør dem i stand til at aande med ilt og nitrat og fastholde respiratoriske aktivitet, selv når elektronacceptorer er fraværende fra miljøet, kan være en af grundene til deres succesfulde kolonisering af forskellige marine sedimenter miljøer. Bidraget fra eukaryoter, til fjernelse af kvælstof gennem respiration kan være lige så betydningsfuldt som bakteriel denitrifikation i oceanernes sedimenter. Udgivelsesdato: 19-1-10 Benthic foraminifers inhabit a wide range of aquatic environments including open marine, brackish, and freshwater environments. Here we show that several different and diverse foraminiferal groups (miliolids, rotaliids, textulariids) and Gromia, another taxon also belonging to Rhizaria, accumulate and respire nitrates through denitrification. The widespread occurrence among distantly related organisms suggests an ancient origin of the trait. The diverse metabolic capacity of these organisms, which enables them to respire with oxygen and nitrate and to sustain respiratory activity even when electron acceptors are absent from the environment, may be one of the reasons for their successful colonization of diverse marine sediment environments. The contribution of eukaryotes to the removal of fixed nitrogen by respiration may equal the importance of bacterial denitrification in ocean sediments.

The high morphological variability observed in the genus Ammonia, together with its global distribution, led to the description of a plethora of species, subspecies, and varieties. Until now, many researchers used a limited number of (morpho-)species, and considered the numerous varieties as ecophenotypes. Recently, molecular studies show that these putative ecophenotypes are, in reality, well-separated genetically and should rather be considered as separate species. This study aims to investigate the morphological characteristics of three phylotypes (T1, T2, and T6) belonging to the genus Ammonia, encountered along European coasts. For this purpose, Ammonia specimens were sampled at 22 locations between 2014 and 2016 and were imaged using an environmental SEM (Scanning Electron Microscope). For 96 specimens, images of the spiral, umbilical, and peripheral sides were obtained and pore features were investigated using 1000x magnified images of the penultimate chamber on the spiral side. Sixty-one morphometric parameters were measured for each individual. To assign specimens to their respective phylotypes, we employed molecular analyses using SSU (Small Sub-Unit) rDNA fragments. A multivariate approach (Factorial Analysis of Mixed Data, FAMD), allowing the joint analysis of quantitative and qualitative measurements, was used to determine the most reliable morphometric parameters to discriminate the three phylotypes. Our results show that the use of only two morphological characteristics is sufficient to differentiate the three pseudocryptic species: the raised or flush character of the sutures on the central part of the spiral side and the mean pore diameter. These two criteria, which can be observed with a standard stereomicroscope, provide an efficient method to discriminate T1, T2, and T6 with at least 90% accuracy. We consider that there is still insufficient information to reliably assign previously defined formal scientific names to the three phylotypes, and therefore we recommend the continued use of phylotype designations T1, T2, and T6. Our results make it possible to study the distribution of these three pseudocryptic species (T1, T2, and T6) on the basis of stereomicroscope examination alone, which means these species can also be more easily recognized in dead/fossil assemblages. Among other things, this will allow verification in sediment cores of the putative recent introduction in European coastal areas of T6, which is often considered an exotic species originating from East Asia.