Taxonomic revision of freshwater foraminifera with the description of two new agglutinated species and genera

Novel contributions to the molecular and morphological diversity of freshwater monothalamid foraminifera: Description of six new species

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.

COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Monitoring community composition of Foraminifera (single-celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) metabarcoding to assess the presence of multiple taxa, this has not been straightforward for Foraminifera partially due to the high genetic variability in widely used ribosomal markers. Here, we test the correctness in retrieving foraminiferal communities by metabarcoding of mock communities, bulk-DNA from coral reef sediment samples, and eDNA from their associated ethanol preservative using the recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we compared our results with large benthic foraminiferal communities previously reported from the same sampling sites. Results from our mock communities demonstrate that all species were detected in two mock communities and all but one in the remaining four. Technical replicates were highly similar in number of reads for each assigned ASV in both the mock communities and bulk-DNA samples. Bulk-DNA showed a significantly higher species richness than their associated eDNA samples, and also detected additional species to what was already reported at the specific sites. Our study confirms that metabarcoding using the foraminiferal COI marker adequately retrieves the diversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nuclear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool to assess foraminiferal community composition under the condition that the reference database is adequate to the target taxa.

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.

Taxon-rich transcriptomics supports higher-level phylogeny and major evolutionary trends in Foraminifera

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.

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 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 are undetermined taxa that have no closely-matching sequences in the 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.

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

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.

Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera

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.

Testate Amoebae in Karst Caves of the Dinaric Arc (South-Eastern Europe) with a Description of Centropyxis bipilata sp. nov

Karst freshwater caves are subterranean habitats characterized by the constant absence of light and relatively small variations of temperature and air humidity. They are mostly food deprived environments, with the exception if large bat colonies are present or if they are intensively supplied with organic matter by sinking rivers. Even though these habitats are often described as harsh, they have enabled the evolution of highly specialized and often endemic animals. The cave eukaryotic micro-organisms, on the other hand, are scarcely researched. The results of research of testate amoebae in the caves of the Dinaric arc detected 23 species, 12 of which were first found in caves. Also, a description of Centropyxis bipilata sp. nov. is presented. This species is clearly distinguished from other described species based on shell size, the presence of two struts and the usually dark ring around the aperture. Testate amoebae were registered on aquatic and terrestrial cave sediments and transitional habitats (like hygropetric and wet walls). The most frequent species within the samples were: Trinema lineare, Cryptodifflugia oviformis and Centropyxis bipilata sp. nov. Maximum diversity of testate amoebae was registered in Ponor Kovači with twenty species. In 24.4 % of the investigated samples microphototrophs were found, implying good surface-subsurface connectivity that could also affect testate amoebae diversity. This research showed that caves are underestimated habitats that can provide us with new data about the testate amoebae biogeography and diversity.