Rapid Freezing and Cryo-SEM-EDS Imaging of Foraminifera (Unicellular Eukaryotes) Using a Conductive Viscous Cryogenic Glue

Spatial distribution of water-soluble molecules and ions in living organisms is still challenging to assess. Energy-dispersive X-ray spectroscopy (EDS) via cryogenic scanning electron microscopy (cryo-SEM) is one of the promising methods to study them without loss of dissolved contents. High-resolution cryo-SEM-EDS has challenges in sample preparation, including cross-section exposure and sample drift/charging due to insulative surrounding water. The former becomes problematic for large and inseparable organisms, such as benthic foraminifera, a unicellular eukaryote playing significant roles in marine ecosystems, which often exceed the size limit for the most reliable high-pressure freezing. Here we show graphite oxide dispersed in sucrose solution as a good glue to freeze, expose cross-section by cryo-ultramicrotome, and analyze elemental distribution owing to the glue's high viscosity, adhesion force, and electron conductivity. To demonstrate the effectiveness and applicability of the glue for cryo-SEM-EDS, deep-sea foraminifer Uvigerina akitaensis was sampled during a cruise and plunge frozen directly on the research vessel, where the liquid nitrogen supply is limited. The microstructures were preserved as faithfully in cryo-SEM images as those with the conventional resin-substituted transmission electron micrograph. We found elements colocalized within the cytoplasm originating from water-soluble compounds that can be lost with conventional dehydrative fixation.

The unique fibrilar to platy nano- and microstructure of twinned rotaliid foraminiferal shell calcite

Diversification of biocrystal arrangements, incorporation of biopolymers at many scale levels and hierarchical architectures are keys for biomaterial optimization. The planktonic rotaliid foraminifer Pulleniatina obliquiloculata displays in its shell a new kind of mesocrystal architecture. Shell formation starts with crystallization of a rhizopodial network, the primary organic sheet (POS). On one side of the POS, crystals consist of blocky domains of 1 μm. On the other side of the POS crystals have dendritic-fractal morphologies, interdigitate and reach sizes of tens of micrometers. The dendritic-fractal crystals are twinned. At the site of nucleation, twinned crystals consist of minute fibrils. With distance away from the nucleation-site, fibrils evolve to bundles of crystallographically well co-oriented nanofibrils and to, twinned, platy-blade-shaped crystals that seam outer shell surfaces. The morphological nanofibril axis is the crystallographic c-axis, both are perpendicular to shell vault. The nanofibrillar calcite is polysynthetically twinned according to the 60°/[100] (= m/{001}) twin law. We demonstrate for the twinned, fractal-dendritic, crystals formation at high supersaturation and growth through crystal competition. We show also that c-axis-alignment is already induced by biopolymers of the POS and is not simply a consequence of growth competition. We discuss determinants that lead to rotaliid calcite formation.

Molecular and morphological diversity of monothalamous foraminifera from South Georgia and the Falkland Islands: Description of four new species

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

Investigation of Deep-Sea Ecosystems Using Marker Fatty Acids: Sources of Essential Polyunsaturated Fatty Acids in Abyssal Megafauna

Abyssal seafloor ecosystems cover more than 50% of the Earth's surface. Being formed by mainly heterotrophic organisms, they depend on the flux of particulate organic matter (POM) photosynthetically produced in the surface layer of the ocean. As dead phytoplankton sinks from the euphotic to the abyssal zone, the trophic value of POM and the concentration of essential polyunsaturated fatty acids (PUFA) decrease. This results in pronounced food periodicity and limitations for bottom dwellers. Deep-sea invertebrate seston eaters and surface deposit feeders consume the sinking POM. Other invertebrates utilize different food items that have undergone a trophic upgrade, with PUFA synthesized from saturated and monounsaturated FA. Foraminifera and nematodes can synthesize arachidonic acid (AA), eicosapentaenoic acid (EPA), while some barophylic bacteria produce EPA and/or docosahexaenoic acid. FA analysis of deep-sea invertebrates has shown high levels of PUFA including, in particular, arachidonic acid, bacterial FA, and a vast number of new and uncommon fatty acids such as 21:4(n-7), 22:4(n-8), 23:4(n-9), and 22:5(n-5) characteristic of foraminifera. We suppose that bacteria growing on detritus having a low trophic value provide the first trophic upgrading of organic matter for foraminifera and nematodes. In turn, these metazoans perform the second-stage upgrading for megafauna invertebrates. Deep-sea megafauna, including major members of Echinodermata, Mollusca, and Polychaeta display FA markers characteristic of bacteria, foraminifera, and nematodes and reveal new markers in the food chain.

In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change

Abyssal plains cover more than half of Earth's surface, and the main food source in these ecosystems is phytodetritus, mainly originating from primary producers in the euphotic zone of the ocean. Global climate change is influencing phytoplankton abundance, productivity, and distribution. Increasing importance of picoplankton over diatom as primary producers in surface oceans (especially projected for higher latitudes) is projected and hence altering the quantity of organic carbon supplied to the abyssal seafloor as phytodetritus, consequences of which remain largely unknown. Here, we investigated the in situ responses of abyssal biota from viruses to megafauna to different types of phytoplankton input (diatoms or cyanobacteria which were labeled with stable isotopes) at equatorial (oligotrophic) and temperate (eutrophic) benthic sites in the Pacific Ocean (1°N at 4277 m water depth and 39°N at 5260 m water depth, respectively). Our results show that meiofauna and macrofauna generally preferred diatoms as a food source and played a relatively larger role in the consumption of phytodetritus at higher latitudes (39°N). Contrarily, prokaryotes and viruses showed similar or even stronger responses to cyanobacterial than to diatom supply. Moreover, the response of prokaryotes and viruses was very rapid (within 1-2 days) at both 1°N and 39°N, with quickest responses reported in the case of cyanobacterial supply at higher latitudes. Overall, our results suggest that benthic deep-sea eukaryotes will be negatively affected by the predicted decrease in diatoms in surface oceans, especially at higher latitudes, where benthic prokaryotes and viruses will otherwise likely increase their quantitative role and organic carbon cycling rates. In turn, such changes can contribute to decrease carbon transfer from phytodetritus to higher trophic levels, with strong potential to affect oceanic food webs, their biodiversity and consequently carbon sequestration capacity at the global scale.

Anaerobic metabolism of Foraminifera thriving below the seafloor

Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20–40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.

Potential impact of global climate change on benthic deep-sea microbes

Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.

Biologically agglutinated eukaryotic microfossil from Cryogenian cap carbonates

Cryogenian cap carbonates that overlie Sturtian glacial deposits were formed during a post-glacial transgression. Here, we describe microfossils from the Kakontwe Formation of Zambia and the Taishir Formation of Mongolia-both Cryogenian age, post-Sturtian cap carbonates-and investigate processes involved in their formation and preservation. We compare microfossils from these two localities to an assemblage of well-documented microfossils previously described in the post-Sturtian Rasthof Formation of Namibia. Microfossils from both new localities have 10 ± 1 μm-thick walls composed of carbonaceous matter and aluminosilicate minerals. Those found in the Kakontwe Formation are spherical or ovoid and 90 ± 5 μm to 200 ± 5 μm wide. Structures found in the Taishir Formation are mostly spherical, 50 ± 5 μm to 140 ± 5 μm wide, with distinct features such as blunt or concave edges. Chemical and mineralogical analyses show that the walled structures and the clay fraction extracted from the surrounding sediments are composed of clay minerals, especially muscovite and illite, as well as quartz, iron and titanium oxides, and some dolomite and feldspar. At each locality, the mineralogy of the microfossil walls matched that of the clay fractions of the surrounding sediment. The abundance of these minerals in the walled microfossils relative to the surrounding carbonate matrix and microbial laminae, and the presence of minerals that cannot precipitate from solution (titanium oxide and feldspar), suggests that the composition represents the original mineralogy of the structures. Furthermore, the consistency in mineralogy of both microfossils and sediments across the three basins, and the uniformity of size and shape among mineral grains in the fossil walls indicate that these organisms incorporated these minerals by primary biological agglutination. The discovery of new, mineral-rich microfossil assemblages in microbially laminated and other fine-grained facies of Cryogenian cap carbonates from multiple localities on different palaeocontinents demonstrates that agglutinating eukaryotes were widespread in carbonate-dominated marine environments in the aftermath of the Sturtian glaciation.

Surviving anoxia in marine sediments: The metabolic response of ubiquitous benthic foraminifera (Ammonia tepida)

High input of organic carbon and/or slowly renewing bottom waters frequently create periods with low dissolved oxygen concentrations on continental shelves and in coastal areas; such events can have strong impacts on benthic ecosystems. Among the meiofauna living in these environments, benthic foraminifera are often the most tolerant to low oxygen levels. Indeed, some species are able to survive complete anoxia for weeks to months. One known mechanism for this, observed in several species, is denitrification. For other species, a state of highly reduced metabolism, essentially a state of dormancy, has been proposed but never demonstrated. Here, we combined a 4 weeks feeding experiment, using 13C-enriched diatom biofilm, with correlated TEM and NanoSIMS imaging, plus bulk analysis of concentration and stable carbon isotopic composition of total organic matter and individual fatty acids, to study metabolic differences in the intertidal species Ammonia tepida exposed to oxic and anoxic conditions. Strongly contrasting cellular-level dynamics of ingestion and transfer of the ingested biofilm components were observed between the two conditions. Under oxic conditions, within a few days, intact diatoms were ingested, degraded, and their components assimilated, in part for biosynthesis of different cellular components: 13C-labeled lipid droplets formed after a few days and were subsequently lost (partially) through respiration. In contrast, in anoxia, fewer diatoms were initially ingested and these were not assimilated or metabolized further, but remained visible within the foraminiferal cytoplasm even after 4 weeks. Under oxic conditions, compound specific 13C analyses showed substantial de novo synthesis by the foraminifera of specific polyunsaturated fatty acids (PUFAs), such as 20:4(n-6). Very limited PUFA synthesis was observed under anoxia. Together, our results show that anoxia induced a greatly reduced rate of heterotrophic metabolism in Ammonia tepida on a time scale of less than 24 hours, these observations are consistent with a state of dormancy.

Novel benthic foraminifera are abundant and diverse in an area of the abyssal equatorial Pacific licensed for polymetallic nodule exploration

The benthic biota of the Clarion–Clipperton Zone (CCZ, abyssal eastern equatorial Pacific) is the focus of a major research effort linked to possible future mining of polymetallic nodules. Within the framework of ABYSSLINE, a biological baseline study conducted on behalf of Seabed Resources Development Ltd. in the UK-1 exploration contract area (eastern CCZ, ~4,080 m water depth), we analysed foraminifera (testate protists), including ‘live’ (Rose Bengal stained) and dead tests, in 5 cores (0–1 cm layer, >150-μm fraction) recovered during separate megacorer deployments inside a 30 by 30 km seafloor area. In both categories (live and dead) we distinguished between complete and fragmented specimens. The outstanding feature of these assemblages is the overwhelming predominance of monothalamids, a group often ignored in foraminiferal studies. These single-chambered foraminifera, which include agglutinated tubes, spheres and komokiaceans, represented 79% of 3,607 complete tests, 98% of 1,798 fragments and 76% of the 416 morphospecies (live and dead combined) in our samples. Only 3.1% of monothalamid species and 9.8% of all species in the UK-1 assemblages are scientifically described and many are rare (29% singletons). Our results emphasise how little is known about foraminifera in abyssal areas that may experience major impacts from future mining activities.