Benthic foraminifera, shell-bearing protists, are familiar from geological studies. Although many species are well known, undescribed single-chambered forms are common in the deep sea. Coastal and sublittoral species often have restricted distributions, but wide ranges are more frequent among deep-water species, particularly at abyssal depths. This probably reflects the transport of tiny propagules by currents across ocean basins that present few insurmountable barriers to dispersal, combined with slow rates of evolution. Undersampling of the vast deep-sea habitat, however, makes it very difficult to establish the ranges of less common foraminiferal species, and endemism may be more prevalent than currently realized. On continental slopes, some species have restricted distributions, but wide-ranging bathyal species that exhibit considerable morphological variation are more common. This may be linked to the greater heterogeneity of continental slopes compared with oceans basins. Improved knowledge of deep-sea foraminiferal biogeography requires sound morphology-based taxonomy combined with molecular genetic studies.

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18 S -V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.

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

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.