Diversity Of Foraminifera Research Articles

Benthic foraminifera as bio-indicators of natural and anthropogenic conditions in Roscoff Aber Bay (Brittany, France).

Living benthic foraminifera, known as environmental bio-indicators of both natural and anthropogenic conditions in marine environments, were investigated in the coastal environment of Roscoff Aber Bay (Brittany, France). Eight sampling sites subject to natural variations (freshwater inputs, tides) and/or anthropogenic impacts (pollution, eutrophication) were studied over four seasons in 2021-2022 (November, February, May, August). We sought to understand the spatial distribution of foraminiferal populations within and between sampling sites over the different seasons and to identify sensitive species and those tolerant to anthropogenic impacts. To this end, sedimentary and biogeochemical characteristics of the sediments were examined by measuring grain size, temperature, oxygen, salinity, pH, environmental pigment concentration (chl a and phaeopigments), total organic carbon (TOC), isotopic ratios of carbon (δ13C), nitrogen (δ15N) and sulfide (δ34S), and chl a fluorescence. Considering these parameters as potential driving factors, four environments were distinguished among the sampling sites: open water, terrestrial, oligotrophic and eutrophic. These showed an increasing gradient of organic supply as well as very different microbial activities, highlighted by carbon and sulfide isotopic ratios. Foraminiferal population study revealed the dominant species characterising these main environments. The lowest abundance but highest diversity of foraminifera was found in the harbour site, associated with the dominance of Haynesina germanica, suggesting this species is tolerant to eutrophic environments and anthropogenic impacts. Open water was dominated by Ammonia beccarii and Elphidium crispum, while Quinqueloculina seminula was the most abundant species in the site with the greatest terrestrial influence. Interestingly, the observed organic enrichment of the harbour due to anthropogenic activities (fisheries, waste deposits, etc.) does not seem to significantly affect foraminiferal diversity. Overall, the benthic foraminiferal species in Roscoff Aber Bay appear to be an excellent proxy for marine environmental conditions under various natural and anthropogenic influences.

Diversity of Foraminifera from the Indian Coast

Foraminifera, members of the class Granuloreticulosa, are marine protozoans distributed across both pelagic and benthic zones of the ocean. After the death of these microscopic organisms, their shells are washed along the intertidal sandy shores along with sand granules. This organism's shell is called a test which is composed of calcium carbonate, silica, or agglutinated materials that characterize the genera of Foraminifera. In the present study, the sand samples were collected along the different sites of the Indian coastline viz. Juhu Beach (Mumbai), Alibaug Beach (Raigad), Palolem Beach (Goa), Kanyakumari Beach (Tamil Nadu), and Puri Beach (Odisha). In this study, samples from Juhu Beach showed the highest foraminiferan diversity (24%) followed by Alibaug (21%) > Kanyakumari = Puri (19%) > Goa (17%). Across all selected study sites, the prevalence of specimens from the Globothalamea class was notable, comprising 39% of the total foraminiferans. This was followed by Monothalamae (26%), Fusulinata (13%), Tubothalamea (11%), and Nodosariata (11%). 13 extinct genera were also documented in the study.

Exploring the underwater life in transitional environments: Benthic foraminifera, ostracods, and dinoflagellate cysts – Biotic trends and EcoQS assessment in the Mar Piccolo of Taranto (Ionian sea, southern Italy)

Coastal areas have historically thrived as centers of human activities due to their resources, economic opportunities, and natural allure. The rapid growth of coastal populations has however brought forth a multitude of challenges to tackle, with pollution emerging as a significant and far-reaching issue. Our study focuses on the Mar Piccolo of Taranto (Ionian Sea, Southern Italy), a lagoon-like coastal basin (separated in two sub-basins) that, since decades, has been heavily affected by human activities and aquaculture, leading to environmental deterioration. Although past studies have looked at environmental conditions in the Mar Piccolo from a chemical perspective, the biological component (e.g., biological indicators) has been mostly neglected. In this study, we firstly aim to examine the distribution and diversity of foraminifera, ostracods, and dinoflagellate cysts in December 2016 and compare our findings with data collected in December 2011. Foraminiferal and ostracod communities exhibit similar patterns in the two sampling campaigns, while the communities of encysted dinoflagellates show differences concerning both densities and diversity. Then, we evaluate the Ecological Quality Status (EcoQS) using ecological indices. While the indices in the inner basin appear to reflect an actual ecological degradation, they yield conflicting results in the outer basin. In the outer basin, indeed, the indices overestimate the EcoQS. This study highlights the potential of these indices for characterizing the EcoQS but emphasizes the need for improvements in their reliability. This research also contributes to a more holistic understanding of environmental condition in the Mar Piccolo and underscores the importance of integrating biological quality elements into ecosystem management and remediation strategies.

A matter of choice: Understanding the interactions between epiphytic foraminifera and their seagrass host Halophila stipulacea

In sub/tropical waters, benthic foraminifera are among the most abundant epiphytic organisms inhabiting seagrass meadows. This study explored the nature of the association between foraminifera and the tropical seagrass species H. stipulacea, aiming to determine whether these interactions are facilitative or random. For this, we performed a "choice" experiment, where foraminifera could colonize H. stipulacea plants or plastic "seagrasses" plants. At the end of the experiment, a microbiome analysis was performed to identify possible variances in the microbial community and diversity of the substrates. Results show that foraminifera prefer to colonize H. stipulacea, which had a higher abundance and diversity of foraminifera than plastic seagrass plants, which increased over time and with shoot age. Moreover, H. stipulacea leaves have higher epiphytic microbial community abundance and diversity. These results demonstrate that seagrass meadows are important hosts of the foraminifera community and suggest the potential facilitative effect of H. stipulacea on epiphytic foraminifera, which might be attributed to a greater diversity of the microbial community inhabiting H. stipulacea.

The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton.

The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.

Benthic foraminifera diversity from the south Atlantic Ocean: Tierra del Fuego and surrounding waters (South America).

The present study provides a detailed record of foraminiferal fauna and their ecological implications from surface sediments from Atlantic shelf of Tierra del Fuego, Argentina. The foraminiferal assemblage is mostly composed by four main hyaline genera, such as Cibicidoides, Cibicides, Globocassidulina and Buccella, which allowed the identification of three environmental zones. Zone 1 (Z1, 37 to 90 m) encompasses the eastern Beagle Channel and San Sebastian Bay. The assemblage reflected well-oxygenated marine inner shelf habitat, adapted to cold temperate waters. Zone 2 (Z2, up to 98.4 m), is located around the southern tip of Tierra del Fuego. The assemblage suggested a deeper marine environment, well oxygenated and with higher energy, probably due to the effect of tides and mainly by the influence of Malvinas Current. Finally, Zone 3 (Z3, up to 195 m) is located furthest from the Atlantic coast and the assemblage suggested an environment characteristic of outer shelf, with well-oxygenated cold waters and high-energy environment, reflected by species adhered to the substrate and coarse sediments. The distribution and abundance of certain species showed the influence of the Malvinas Current, while others evidenced a contribution of the Cape Horn waters.

Impact of submarine karst sulfur springs on benthic foraminiferal assemblage in sediment of northern Adriatic Sea

PurposeThis work highlights the sedimentary characteristics and the role of submarine sulfur-rich karstic springs in the distribution of benthic foraminifera in the northern part of the Adriatic Sea (Bay of Koper). Little is known about how local conditions such as temperature and sulfur bursts may influence sediment properties, benthic habitat variability, and composition of foraminiferal assemblages. Here we compare the distribution of total and living benthic assemblages in surface sediment samples collected from a funnel-shaped depression created by submarine sulfur springs.Materials and methodsSampling was performed at water depths between 24.6 and 32.2 m in fine-grained sandy silt to silty sand (partially washed). Sedimentological, mineralogical, and geochemical analyses of the sediment were carried out and the distribution of benthic foraminifera living around the springs was studied.Results and discussionIn general, sediment characteristics (i.e., mineralogical, geochemical, and organic content) around the sulfur springs do not show prominent deviations from the marine surface sediment of the area; however, some differences exist among depressions of different depths. Deeper depressions in the lower parts probably extend to older continental sediments of Late Pleistocene age with alluvial features, while shallower depressions were formed entirely in Holocene marine sediments typical of a wider area. Only one of the five samples (M05) contained living foraminifera in sufficient abundance for biocenosis research. The benthic foraminiferal assemblages of moderate diversity are composed of opportunistic species. Elphidium translucens, Ammonia ex gr. tepida, Haynesina depressula, and Porosononion granosum dominate, while A. neobeccarii, Reussella spinulosa, and Textularia bocki are subordinate.ConclusionsThe distribution and diversity of foraminifera in the sediment near sulfur springs can be explained by several factors and their interactions. The intensity of the spring discharge affects the mixing/oxygenation of the sediment, the shape of spring depressions, and the granulometry of the coarser sediment around the springs. Sediment characteristics indicate different types of sediment origin. This is related to and can be explained by the depth of spring depressions.

Assessing the spatial distribution of meiofaunal communities in Krossfjord, Svalbard Archipelago: Foraminifera diversity as a key component

The study furnishes an insight into the ecology of meiofauna through an elaborate examination of the living Foraminifera in the Krossfjorden system of the Svalbard Archipelago. Samples collected during the Summer Phase Indian Arctic Expeditions of 2017 and 2018 were analyzed to reveal novel insights into the distribution, abundance and species composition of living Foraminifera in this less studied fjord system. The investigation uncovered a rich and diverse meiofaunal community consisting of ten taxonomic groups, among which living Foraminifera emerged as a prominent component. The spatial patterns of Foraminifera distribution were examined, revealing their preferences for specific habitats and environmental conditions within the Krossfjorden system. The Shannon diversity index (H’) indicates good overall diversity of foraminifera in the Krossfjord region, with H’ ranging from 4.49 to 4.891 in 2017 and from 3.885 to 4.984 in 2018. The research discovered noteworthy inequalities in the distribution of Foraminifera species amid inner and outer stations, as inferred by PERMANOVA analysis (p<0.05). The foraminiferan species Nonionellina labradorica was the dominant species in outer, middle and inner zones in the fjord, while species Lobatula lobatula, Quinqueloculina seminulum, Hormosinella sp., and Procerolagena sp. played significant roles in driving the dissimilarity between outer, middle, and inner zones. Environmental factors accounted for a substantial 83.1% of the variations observed in foraminiferan species distribution across four CCA axes. The fluctuations in potential temperature, sand fraction, chlorophyll-a, C:N ratio, organic matter, and salinity have had a noteworthy effect on the distribution of species. These findings underscore the susceptibility of Foraminifera and the broader meiofaunal community to the impacts of environmental variations in this rapidly changing Arctic ecosystem. The outcomes of this research provide a crucial baseline for understanding the ecological dynamics of meiofaunal communities in the Krossfjorden system, contributing to predicting future changes in benthic habitats, including the potential repercussions for meiobenthic productivity.

Evidence of recent sea-level rise and the formation of a classic Maya canal system inferred from Boca Paila cave sediments, Sian Ka'an biosphere, Mexico

Cave sediments along the eastern coast of the Yucatán Peninsula contain important records of paleoenvironmental change that have not been fully explored. Reconstructing environmental changes in Boca Paila lagoon reveals details about sea level, flooding of the Sian Ka'an Biosphere, and the timeline of occupation at Muyil, an important Classic Maya maritime trading site. Three sediment cores (BP1, BP2, and BP3) were collected from a cave system beneath Boca Paila lagoon in the Sian Ka'an Biosphere. Radiocarbon dating, geochemical (X-Ray Fluorescence Core Scanning, δ13C, C/N), and microfossil (foraminifera, diatoms, pollen) analyses were performed. The combined results show three distinct phases of coastal evolution. Phase 1 (1157 BCE or earlier), an upland area with mangrove associate Conocarpus erectus, grasses, and ferns, is characterized by: organic-rich detrital peat; a relative absence of foraminifera and diatoms; organic geochemistry results within terrestrial ranges (δ13C values of −28‰ to −26‰); and low Sr/Ca, Si/Ti, and Ti/K ratios. These indicate dry conditions at the karst surface. Phase 2 (1157 BCE – 312 CE), a shallow wetland, is represented by: an increase in weathering products (Ti/K) and diatom productivity (Si/Ti); more positive δ13C values (−27‰ to −22‰) and decreasing C/N ratios; and increased marine foraminifera (e.g., Ammodiscus sp.). These indicate more open water conditions. Phase 3 (>312 CE), a wetland/lagoon environment, is characterized by: carbonate-rich marl; a greater diversity of foraminifera (Ammonia spp., Elphidium spp., Rosalina spp., and Bolivina spp.), diatoms (Cyclotella meneghiniana, Craticula spp., Amphora spp., Hyalosynedra laevigata, and Grammatophora spp.) and pollen (from mangroves, ferns, grasses, palms, and pine); increased Si/Ti and Sr/Ca values; and mixed marine and terrestrial organic geochemistry values (δ13C values of −22‰ to −20‰). These indicate increased input of marine organic sediment during sea-level rise. Sea-level and climate records support the interpretation of a dry upper karst environment prior to ∼1157 BCE, with sea-level rise forming shallow (<50 cm) wetlands by ∼312 CE. Previous archaeological analysis estimates that the first settlers arrived at Muyil ∼350 BCE, but that population expansion and construction of most structures occurred during the Postclassic (925–1550 CE). Sea-level rise would have been an important factor in the expansion of coastal settlements and trade routes; continued sea-level rise after ∼312 CE allowed for the formation of deeper lagoons and channels connecting the coast to Muyil and other inland sites which would likely not have been navigable prior to the Early Classic period (250–600 CE) as they would be too shallow. This study highlights the impacts of environment on society, as well as the importance of karst cave systems for obtaining paleoenvironmental records.

Benthic Foraminifera Diversity of the Abyssal Northwest Atlantic

The species diversity of benthic foraminifera at four abyssal working areas in the Labrador Sea, Labrador Basin, and Southwest of the Azores is documented. One hundred and fifty taxa (forty-three not assigned to a species) were found and their diversity was recorded. One hundred and twenty-four taxa (fifteen not assigned to a species) were illustrated with optical and/or SEM (Scanning Electron Microscope) images on twelve plates. The material was sampled during RV Sonne cruise SO286 as part of IceDivA2 (Icelandic marine Animals meets Diversity along latitudinal gradients in the deep sea of the Atlantic Ocean 2). IceDivA2 investigated the biodiversity within key groups of the marine benthic abyssal habitats of the North Atlantic. Thirty-two samples from four sliced and three full cores, from six stations sampled with a MUC (Multiple corer), were analyzed. Given low sedimentation rates in such environments the material is assumed to be of Holocene to late Pleistocene age. Due to the scarcity of living specimens this study was based on total assemblages. Four species-based clusters are identified, which correspond to the four working areas. The samples of each cluster show specific characteristics markedly different from those of the samples of the other clusters. It indicates that abyssal faunas are heterogeneous. Three clusters are dominated by Epistominella exigua (Brady, 1884), which is recorded as not rare to dominant in many abyssal plains worldwide. The faunal differences are manifested in the long tail of less important species and differing abundances of E. exigua.

Ocean kinetic energy and photosynthetic biomass are important drivers of planktonic foraminifera diversity in the Atlantic Ocean

To assess the anthropogenic effect on biodiversity, it is essential to understand the global diversity distribution of the major groups at the base of the food chain, ideally before global warming initiation (1850 Common Era CE). Since organisms in the plankton are highly interconnected and carbonate synthesizing species have a good preservation state in the Atlantic Ocean, the diversity distribution pattern of planktonic foraminifera from 1741 core-top surface sediment samples (expanded ForCenS database) provides a case study to comprehend centennial to decadal time-averaged diversity patterns at pre-1970 CE times, the tempo of the substantial increase in tropospheric warming. In this work, it is hypothesized and tested for the first time, that the large-scale diversity patterns of foraminifera communities are determined by sea surface temperature (SST, representing energy), Chl-a (a surrogate for photosynthetic biomass), and ocean kinetic energy (as EKE). Alpha diversity was estimated using species richness (S), Shannon Wiener index (H), and Simpson evenness (E), and mapped using geostatistical approaches. The three indices are significantly related to SST, Chl-a, and EKE (71-88% of the deviance in the generalized additive mixed model, including a spatial component). Beta diversity was studied through species turnover using gradient forest analysis (59% of the variation). The primary community thresholds of foraminifera species turnover were associated with 5-10 °C and 22-28 °C SST, 0.05-0.15 mg m-3 Chl-a, and 1.2-2.0 cm2 s-2 log10 EKE energy, respectively. Six of the most important foraminifera species identified for the environmental thresholds of beta diversity are also fundamental in transfer functions, further reinforcing the approaches used. The geographic location of the transition between the four main biogeographic zones was redefined based on the results of beta diversity analysis and incorporating the new datasets, identifying the major marine latitudinal gradients, the most important upwelling areas (Benguela Current, Canary Current), the Equatorial divergence, and the subtropical fronts (Gulf Stream-North Atlantic Drift path in the north, and the South Atlantic current in the south). In conclusion, we provide statistical proof that energy (SST), food supply (Chl-a), and currents (EKE) are the main environmental drivers shaping planktonic foraminifera diversity in the Atlantic ocean and define the associated thresholds for species change on those variables.

Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers

The biotic crisis following the end-Cretaceous asteroid impact resulted in a dramatic renewal of pelagic biodiversity. Considering the severe and immediate effect of the asteroid impact on the pelagic environment, it is remarkable that some of the most affected pelagic groups, like the planktonic foraminifera, survived at all. Here we queried a surface ocean metabarcoding dataset to show that calcareous benthic foraminifera of the clade Globothalamea are able to disperse actively in the plankton, and we show using molecular clock phylogeny that the modern planktonic clades originated from different benthic ancestors that colonized the plankton after the end-Cretaceous crisis. We conclude that the diversity of planktonic foraminifera has been the result of a constant leakage of benthic foraminifera diversity into the plankton, continuously refueling the planktonic niche, and challenge the classical interpretation of the fossil record that suggests that Mesozoic planktonic foraminifera gave rise to the modern communities.

Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?

In mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scale.

Radiolarian size and silicification across the Paleocene-Eocene boundary and into the early Eocene

The Paleocene-Eocene Thermal Maximum (PETM) was a major environmental perturbation that drove range shifts, adaptation, and faunal turnover in marine and terrestrial clades. Open ocean planktonic responses—including body size trends—have been characterized for calcareous nannoplankton, dinocysts, and planktonic foraminifera. Relatively little, however, is known about the response of radiolarians, which share life modes and phylogenetic history with planktonic foraminifera but make their tests (i.e., ‘shells’) out of silica rather than calcium carbonate. Here, we compare radiolarian assemblage changes in the Southwest Pacific with assemblages from Atlantic and Indian Ocean sites. We also measured radiolarian test size before, during, and after the PETM in a pelagic sedimentary succession at Mead Stream, South Island, New Zealand. Our results show a substantial positive shift in mean radiolarian test size at Mead Stream at the assemblage level concurrent with the onset of the PETM, primarily due to an increase in the size and relative abundance of spumellarian radiolarians. We investigate oligotrophy, elevated seawater silica concentration, and redeposition as potential drivers for this size shift. Mead Stream radiolarians remain large for 1.3 Myr, long past the recovery of the carbon isotope excursion and a return to baseline in terrigenous sedimentation, bioturbation, and benthic foraminifera diversity, leaving the ultimate cause of the observed changes in test size uncertain. We find little evidence for a uniform morphological response to the event or its aftermath across sites, particularly as relates to the relative extent of silicification of different groups of radiolarians.

Metabarcoding reveals high diversity of benthic foraminifera linked to water masses circulation at coastal Svalbard.

Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega- and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represent a main component of meiofauna in the Arctic. Several studies analyzed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in the Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1384 amplicon sequence variants (ASVs). More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that are strongly influenced by warm and salty Atlantic water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be very useful for inferring present and past environmental conditions in the Arctic.

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

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.

Molecular diversity of foraminiferal eDNA in sediments and their correlations with environmental factors from the Yellow Sea

Foraminiferal environmental DNA (eDNA) is an efficient and reliable indicator of environmental changes. Here, we investigated the foraminiferal diversity of 25 stations (33–36°N) in the Yellow Sea based on eDNA and presented the first assessment on the correlations between foraminifera diversity and environmental conditions in the region. A total of 71 sediment samples were collected and local environmental parameters were measured. The foraminiferal eDNA was extracted from the samples and part of the small subunit (SSU) rRNA gene was amplified from the samples. After high–throughput sequencing, 1,701,899 amplified reads were detected and clustered into 426 operational taxonomic units (OTUs). The benthic foraminiferal eDNA community diversity and group diversity showed significant positive correlations with water depth and total inorganic carbon (TIC) in sediments, and significant negative correlations with temperature and total organic carbon (TOC) in sediments. However, in terms of the correlation between relative abundance and environmental factors, there were wide variations from species to species. In this work, planktic foraminiferal eDNA was detected in the sediments, and its OTUs number could reflect the changes in ocean currents and upper layer water masses to a certain extent. This is the first study on relationship of foraminiferal eDNA and environmental factors in the Yellow Sea shelf region of the western Pacific Ocean, and it demonstrates that community parameters in foraminiferal eDNA could be a valuable proxy for environmental changes in the shelf sea.

Assemblages of Benthic Foraminifera in Pujada Island, Davao Oriental, Philippines

The present study investigated the composition, density, abundance, and diversity of benthic foraminifera, and their relationship with various physico-chemical parameters such as pH, salinity, temperature, and sediment grain size. Foraminifera were collected from the intertidal zone using sediment cores and extracted from the sediments through sieving. The extracted foraminifera were stained with Rose bengal solution and preserved with buffered formalin. A total of 9,459 individuals of foraminifera were identified, consisting of 39 species classified into four orders, 16 families, and 21 genera. The top three most abundant genera were Calcarina, Baculogypsina, and Amphistegina. The comparison (ANOVA) of the abundance of foraminifera among the six stations revealed highly significant differences (P= 0.000; df= 38). Station 1 exhibited the highest diversity of foraminifera on Pujada Island, as indicated by an H’ value of 3.06. Conversely, station 6 displayed the lowest diversity, with an H’ value of 1.59. The pH, salinity, and temperature values are all within acceptable limits for seawater. The decreased diversity observed in some stations are attributed by various factors, like site disturbance (accessibility to many tourists and availability of beach resorts) and the variation in sediment grain size composition. The findings suggest that generally, Pujada Island remains an undisturbed coastal area. As a result, this study provides a baseline for future monitoring of the impacts of natural and human-induced activities in the region, thereby recommending the use of foraminifera's as bioindicators for marine health.&#x0D;

Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses.

Foraminifera include diverse shell-building lineages found in a wide array of aquatic habitats from the deep-sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present a metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera-specific primers that target the hypervariable regions of the foraminifera SSU-rRNA gene (~250-300bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority of which are undetermined taxa that have no closely matching sequences in the reference database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single-chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa-like forms. Our pilot study provides the community with an additional set of newly designed and taxon-specific primers to elucidate foraminiferal diversity across different habitats.

Spatial and Vertical Benthic Foraminifera Diversity in the Oxygen Minimum Zone of Mejillones Bay, Northern Chile

Mejillones Bay is located in northern Chile (23°S) and is influenced by an Oxygen Minimum Zone (OMZ), with oxygen levels below 0.5 ml l–1. This area presents particular ecological characteristics, such as circulation of currents, hotspot, high productivity and industrial activity. This extreme ecosystem generates the need to understand their dynamics and changes across time and space, as well as to identify the main differences with other OMZs. For this reason, we studied the benthic foraminifera to use them as environmental and oxygenation proxies. For this purpose, two sediment cores (ZA and Z1A) were collected, obtaining 14 samples of the first 8 cm (vertical distribution), and 18 samples with a mini boxcore (spatial distribution). When analyzing the foraminifera community, some similarities were found in environmental characteristics of other OMZs, such as the predominance of Bolivina seminuda, Bolivina costata, Epistominella exigua, Fursenkoina sp., and Nonioella stella (species typical of hypoxic conditions). In addition, a high abundance of angular-asymmetric morphologies was observed, indicating eutrophied silty substrates and low current circulation. However, the Mejillones Bay recorded a particular spatial and vertical dynamics respect to others OMZs, due to presence of other species of Bolivinids not reported for this area before, and a high abundance of Buliminella elegantissima, which is not recorded in most of OMZs. Foraminifera with rounded-symmetric morphologies were present and dominant in deeper layers, reflecting a turbulent and high-energy environment. On the basis of depth and conditions of microxia or dysoxia, no significative pattern of spatial and vertical distribution was observed. The latter can be explained by local factors such as cyclonic and anticyclonic whirlpools, wastewater from industrial activity and natural disaster such a Tsunami occurred in 1877. These factors contributed to the mixture of the benthic foraminifera and prevented the formation of spatial and vertical patterns. Finally, an intensification of hypoxia was identified, indicating microxia (0,01 ml l–1) in the superficial layers (0–3 cm from years 1996 to 2012), while the deeper layers (4–8 cm from years 1985 to 1877) presented foraminiferal species that indicated dysoxia conditions (0,07 ml l–1). The latter differs from other OMZs, which show greater oxygenation in the most superficial layers and microxia in deeper layers. This study represents the first ecological reconstruction using benthic foraminifera proxies for the Mejillones Bay, which results indicate an OMZ with ecological and environmental features that differ from other OMZs.