Denitrification likely catalyzed by endobionts in an allogromiid foraminifer

Impact of pesticides on marine coral reef foraminifera

Our laboratory study looked into how pesticides affect the foraminifera species Heterostegina depressa and their obligatory algal endosymbionts. We incubated the foraminifera separately with different types of pesticides at varying concentrations (1 %, 0.01 % and 0.0001 %); we included the insecticide Confidor© (active substance: imidacloprid), the fungicide Pronto©Plus (tebuconazole), and the herbicide Roundup© (glyphosate). Our evaluation focused on the symbiont's photosynthetically active area (PA), and the uptake of dissolved inorganic carbon (DIC) and nitrogen (nitrate) to determine the vitality of the foraminifera. Our findings showed that even the lowest doses of the fungicide and herbicide caused irreparable damage to the foraminifera and their symbionts. While the insecticide only deactivated the symbionts (PA = 0) at the highest concentration (1 %), the fungicide, and herbicide caused complete deactivation even at the lowest levels provided (0.0001 %). The fungicide had the strongest toxic effect on the foraminiferal host regarding reduced isotope uptake. In conclusion, all pesticides had a negative impact on the holosymbiont, with the host showing varying degrees of sensitivity towards different types of pesticides.

The change in metabolic activity of a large benthic foraminifera as a function of light supply

We studied metabolic activity of the symbiont-bearing large benthic foraminifer Heterostegina depressa under different light conditions. Besides the overall photosynthetic performance of the photosymbionts estimated by means of variable fluorescence, the isotope uptake (¹³C and ¹⁵N) of the specimens (= holobionts) was measured. Heterostegina depressa was either incubated in darkness over a period of 15 days or exposed to an 16:8 h light:dark cycle mimicking natural light conditions. We found photosynthetic performance to be highly related to light supply. The photosymbionts, however, survived prolonged darkness and could be reactivated after 15 days of darkness. The same pattern was found in the isotope uptake of the holobionts. Based on these results, we propose that ¹³C-carbonate and ¹⁵N-nitrate assimilation is mainly controlled by the photosymbionts, whereas ¹⁵N-ammonium and ¹³C-glucose utilization is regulated by both, the symbiont and the host cells.

Characterizing potential pathogens from intracellular bacterial community of protists in wastewater treatment plants

Protists are a trophically diverse and biogeochemically significant component of water environments and are widely reported as hosts of bacteria. However, the potential role of protists in wastewater treatment plants (WWTPs) as reservoirs for human pathogens does not appear to have received adequate attention. Here, a combination of fluorescence-activated cell sorting and Illumina sequencing was applied to characterize the dynamics of the internalized bacterial community of the enriched protists from the influents and effluents of five WWTPs. The results showed that Proteobacteria (mainly Betaproteobacteria) dominate the intracellular bacterial communities of protists in both influents and effluents of WWTPs, accounting for 72.6% of the total intracellular bacterial communities. The most frequently detected genus was Sulfuricurvum in the influent samples, Chryseobacterium and Pseudomonas were most prevalent in the effluent samples. Compared with the influents, a more diverse and abundant intracellular bacterial community was observed in the effluents. Moreover, the potential intracellular bacterial pathogens were 26 times higher in effluents than in influents, with Pseudomonas fluorescens and Pseudomonas putida significantly enriched in effluents. This work provides insights into the dynamics of bacterial communities and potential pathogens harbored by protists in the influents and effluents from WWTPs, contributing to the improved evaluation of biosafety in WWTPs.

Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria

Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera

Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.

Bacterial and archaeal symbioses with protists

Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.

Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments

Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.

Simulated future conditions of ocean warming and acidification disrupt the microbiome of the calcifying foraminifera Marginopora vertebralis across life stages

Foraminifera host diverse microbial communities that can shift in response to changing environmental conditions. To characterize climate change impacts on the foraminifera microbiome across life stages, we exposed adult Marginopora vertebralis (Large Benthic Foraminifera) to pCO₂ and temperature scenarios representing present-day, 2050 and 2100 levels and raised juveniles under present-day and 2050 conditions. While treatment condition had no significant effect on the seawater microbial communities, exposure to future scenarios significantly altered both adult and juvenile microbiomes. In adults, divergence between present-day and 2050 or 2100 conditions was primarily driven by a reduced relative abundance of Oxyphotobacteria under elevated temperature and pCO₂ . In juveniles, the microbial shift predominantly resulted from changes in the proportion of Proteobacteria. Indicator species analysis identified numerous treatment-specific indicator taxa, most of which were indicative of present-day conditions. Oxyphotobacteria, previously reported as putative symbionts of foraminifera, were indicative of present-day and 2050 conditions in adults, but of present-day conditions only in juveniles. Overall, we show that the sensitivity of the M. vertebralis microbiome to climate change scenarios extends to both life stages and primarily correlates with declines in Oxyphotobacteria and shifts in Proteobacteria under elevated temperature and pCO₂ .

Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole

Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.

Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists

The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.

Lack of denitrification causes a difference in benthic foraminifera living in the oxygen deficient zones of the Bay of Bengal and the Arabian Sea

Despite being located at the same latitudes, the Bay of Bengal oxygen deficient zone (ODZ) is markedly different than the Arabian Sea ODZ. The uptake of oxygen in the Bay of Bengal does not lead to denitrification as in the Arabian Sea. This difference in ODZ of the Bay of Bengal and the Arabian Sea is expected to support different benthic fauna. We report that the living benthic foraminifera in the Bay of Bengal ODZ are markedly different than that in the Arabian Sea ODZ. Only four species (Brizalina spathulata, Eubuliminella exilis, Uvigerina peregrina and Rotaliatinopsis semiinvoluta) dominant in the Bay of Bengal ODZ have also been reported from the Arabian Sea oxygen deficient waters. The difference in living benthic foraminifera dominant in the ODZ of the Bay of Bengal and the Arabian Sea, is attributed to the lack of denitrification and associated processes in the Bay of Bengal.

Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation

Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.

Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis

Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.

Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone

Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors-nitrate (NO₃ ^-) or oxygen (O₂)-makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O₂ respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O₂ respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O₂ respiration than for denitrification, indicating that NO₃ ^- metabolism during denitrification is more efficient than O₂ metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O₂ respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO₃ ^- storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO₃ ^- availability. This suggests that the cell size of denitrifying foraminifera is not limited by O₂ but rather by NO₃ ^- availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO₃ ^- is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO₃ ^- and O₂.

Evolutionary significance of the microbial assemblages of large benthic Foraminifera

Large benthic Foraminifera (LBF) are major carbonate producers on coral reefs, and are hosts to a diverse symbiotic microbial community. During warm episodes in the geological past, these reef-building organisms expanded their geographical ranges as subtropical and tropical belts moved into higher latitudes. During these range-expansion periods, LBF were the most prolific carbonate producers on reefs, dominating shallow carbonate platforms over reef-building corals. Even though the fossil and modern distributions of groups of species that harbour different types of symbionts are known, the nature, mechanisms, and factors that influence their occurrence remain elusive. Furthermore, the presence of a diverse and persistent bacterial community has only recently gained attention. We examined recent advances in molecular identification of prokaryotic (i.e. bacteria) and eukaryotic (i.e. microalgae) associates, and palaeoecology, and place the partnership with bacteria and algae in the context of climate change. In critically reviewing the available fossil and modern data on symbiosis, we reveal a crucial role of microalgae in the response of LBF to ocean warming, and their capacity to colonise a variety of habitats, across both latitudes and broad depth ranges. Symbiont identity is a key factor enabling LBF to expand their geographic ranges when the sea-surface temperature increases. Our analyses showed that over the past 66 million years (My), diatom-bearing species were dominant in reef environments. The modern record shows that these species display a stable, persistent eukaryotic assemblage across their geographic distribution range, and are less dependent on symbiotic photosynthesis for survival. By contrast, dinoflagellate and chlorophytic species, which show a provincial distribution, tend to have a more flexible eukaryotic community throughout their range. This group is more dependent on their symbionts, and flexibility in their symbiosis is likely to be the driving force behind their evolutionary history, as they form a monophyletic group originating from a rhodophyte-bearing ancestor. The study of bacterial assemblages, while still in its infancy, is a promising field of study. Bacterial communities are likely to be shaped by the local environment, although a core bacterial microbiome is found in species with global distributions. Cryptic speciation is also an important factor that must be taken into consideration. As global warming intensifies, genetic divergence in hosts in addition to the range of flexibility/specificity within host-symbiont associations will be important elements in the continued evolutionary success of LBF species in a wide range of environments. Based on fossil and modern data, we conclude that the microbiome, which includes both algal and bacterial partners, is a key factor influencing the evolution of LBF. As a result, the microbiome assists LBF in colonising a wide range of habitats, and allowed them to become the most important calcifiers on shallow platforms worldwide during periods of ocean warming in the geologic past. Since LBF are crucial ecosystem engineers and prolific carbonate producers, the microbiome is a critical component that will play a central role in the responses of LBF to a changing ocean, and ultimately in shaping the future of coral reefs.

Kleptoplastidic benthic foraminifera from aphotic habitats: insights into assimilation of inorganic C, N and S studied with sub-cellular resolution

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 ¹³ C-bicarbonate, ¹⁵ N-ammonium and ³⁴ S-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 ¹³ C 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 ¹⁵ N-ammonium and ³⁴ S-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.

A Novel Eukaryotic Denitrification Pathway in Foraminifera

Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period.

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms

Biological treatment represents a key step in nutrient removal from wastewater. Until now these process has mainly been considered prokaryotic, with the interactions between prokaryotes and eukaryotes not being properly explored. We therefore investigated the co-occurrence of eukaryotes and prokaryotes in biological nitrogen removal biofilms. We found that biofilms in the nitrifying reactor contained the highest diversity and abundance of both prokaryotes and eukaryotes, with nearly three times higher prokaryote species richness than for the denitrifying reactor. The positive associations between eukaryote abundance and prokaryote diversity could potentially be explained by mutualism - and/or predator/prey interactions. Further mechanistic insight, however, is needed to determine the main diversifying mechanisms. In summary, eukaryote and prokaryote interactions seem to play a fundamental yet underexplored role in biological wastewater treatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Eukaryote and prokaryote interactions may play an important role in wastewater treatment. This study found that prokaryote species richness was nearly three times higher in the aerobe nitrification than in an anaerobe denitrification reactor, coinciding with the highest level of eukaryotes. This knowledge can be important in process control, and potentially in the development of novel approaches based on nitrate accumulating denitrifying eukaryotes.

Sinks and Sources of Intracellular Nitrate in Gromiids

A substantial nitrate pool is stored within living cells in various benthic marine environments. The fate of this bioavailable nitrogen differs according to the organisms managing the intracellular nitrate (ICN). While some light has been shed on the nitrate carried by diatoms and foraminiferans, no study has so far followed the nitrate kept by gromiids. Gromiids are large protists and their ICN concentration can exceed 1000x the ambient nitrate concentration. In the present study we investigated gromiids from diverse habitats and showed that they contained nitrate at concentrations ranging from 1 to 370 mM. We used ¹⁵N tracer techniques to investigate the source of this ICN, and found that it originated both from active nitrate uptake from the environment and from intracellular production, most likely through bacterial nitrification. Microsensor measurements showed that part of the ICN was denitrified to N₂ when gromiids were exposed to anoxia. Denitrification seemed to be mediated by endobiotic bacteria because antibiotics inhibited denitrification activity. The active uptake of nitrate suggests that ICN plays a role in gromiid physiology and is not merely a consequence of the gromiid hosting a diverse bacterial community. Measurements of aerobic respiration rates and modeling of oxygen consumption by individual gromiid cells suggested that gromiids may occasionally turn anoxic by their own respiration activity and thus need strategies for coping with this self-inflicted anoxia.

Functional xanthophyll cycle and pigment content of a kleptoplastic benthic foraminifer: Haynesina germanica

Some shallow water benthic foraminifera are able to retain functional chloroplasts (kleptoplasts) from their food source, i.e. diatoms. Here we assessed the functionality of the kleptoplast xanthophyll cycle (XC, i.e. the main diatom short-term photo-regulation mechanism) and we surveyed Haynesina germanica kleptoplast pigment composition over time and at different light regimes. Six common diatom lipophilic pigments were detected, two chlorophylls (Chl a, Chl c) and four carotenoids (fucoxanthin and by-products, diadinoxanthin, diatoxanthin and β-carotene), the same pigment profile as the diatom species frequently isolated at the sampling site. The xanthophyll cycle (XC) was functional with kleptoplast diatoxanthin (DT) content increase with concomitant diadinoxanthin (DD) decrease after short term light exposure. DT/(DT+DD) and DT/DD ratios increased significantly in specimens exposed to low light and high light in comparison to specimens maintained in the dark. Specimens placed in very low light after the light treatments reverted to values close to the initial ones, suggesting that H. germanica XC is functional. A functional XC is an indication of H. germanica kleptoplasts capacity for short-term photo-protection from photo-oxidative damages caused by excess of light. Furthermore, the pigment survey suggests that H. germanica preserved some chloroplasts over a longer time than others and that pigment content is influenced by previous light history. Finally, the current study highlighted seasonal differences, with higher pigment contents in winter specimens (27.35 ± 1.30 ng cell^-1) and lower in summer specimens (6.08 ± 1.21 ng cell^-1), a quantitative and qualitative composition suggesting light acclimation to low or high light availability, according to the season.

Intracellular Isotope Localization in Ammonia sp. (Foraminifera) of Oxygen-Depleted Environments: Results of Nitrate and Sulfate Labeling Experiments

Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much (15)N or (34)S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200-500 nm in diameter and co-occurred with possible endobionts, were labeled with (15)N originated from (15)N-labeled nitrate under anoxia and were labeled with both (15)N and (34)S under dysoxia. The labeling with (15)N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.

Carbon and Nitrogen Uptake of Calcareous Benthic Foraminifera along a Depth-Related Oxygen Gradient in the OMZ of the Arabian Sea

Foraminifera are an important faunal element of the benthos in oxygen-depleted settings such as Oxygen Minimum Zones (OMZs) where they can play a relevant role in the processing of phytodetritus. We investigated the uptake of phytodetritus (labeled with (13)C and (15)N) by calcareous foraminifera in the 0-1 cm sediment horizon under different oxygen concentrations within the OMZ in the eastern Arabian Sea. The in situ tracer experiments were carried out along a depth transect on the Indian margin over a period of 4 to 10 days. The uptake of phytodetrital carbon within 4 days by all investigated species shows that phytodetritus is a relevant food source for foraminifera in OMZ sediments. The decrease of total carbon uptake from 540 to 1100 m suggests a higher demand for carbon by species in the low-oxygen core region of the OMZ or less food competition with macrofauna. Especially Uvigerinids showed high uptake of phytodetrital carbon at the lowest oxygenated site. Variation in the ratio of phytodetrital carbon to nitrogen between species and sites indicates that foraminiferal carbon and nitrogen use can be decoupled and different nutritional demands are found between species. Lower ratio of phytodetrital carbon and nitrogen at 540 m could hint for greater demand or storage of food-based nitrogen, ingestion, or hosting of bacteria under almost anoxic conditions. Shifts in the foraminiferal assemblage structure (controlled by oxygen or food availability) and in the presence of other benthic organisms are likely to account for observed changes in the processing of phytodetritus in the different OMZ habitats. Foraminifera dominate the short-term processing of phytodetritus in the OMZ core but are less important in the lower OMZ boundary region of the Indian margin as biological interactions and species distribution of foraminifera change with depth and oxygen levels.

Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes

The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described. A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations.

Denitrification, anammox, and N₂ production in marine sediments

Fixed nitrogen limits primary productivity in many parts of the global ocean, and it consequently plays a role in controlling the carbon dioxide content of the atmosphere. The concentration of fixed nitrogen is determined by the balance between two processes: the fixation of nitrogen gas into organic forms by diazotrophs, and the reconversion of fixed nitrogen to nitrogen gas by denitrifying organisms. However, current sedimentary denitrification rates are poorly constrained, especially in permeable sediments, which cover the majority of the continental margin. Also, anammox has recently been shown to be an additional pathway for the loss of fixed nitrogen in sediments. This article briefly reviews sedimentary fixed nitrogen loss by sedimentary denitrification and anammox, including in sediments in contact with oxygen-deficient zones. A simple extrapolation of existing rate measurements to the global sedimentary denitrification rate yields a value smaller than many existing measurement-based estimates but still larger than the rate of water column denitrification.

Response of the ubiquitous pelagic diatom Thalassiosira weissflogii to darkness and anoxia

Thalassiosira weissflogii, an abundant, nitrate-storing, bloom-forming diatom in the world's oceans, can use its intracellular nitrate pool for dissimilatory nitrate reduction to ammonium (DNRA) after sudden shifts to darkness and anoxia, most likely as a survival mechanism. T. weissflogii cells that stored 4 mM (15)N-nitrate consumed 1.15 (±0.25) fmol NO3 (-) cell(-1) h(-1) and simultaneously produced 1.57 (±0.21) fmol (15)NH4 (+) cell(-1) h(-1) during the first 2 hours of dark/anoxic conditions. Ammonium produced from intracellular nitrate was excreted by the cells, indicating a dissimilatory rather than assimilatory pathway. Nitrite and the greenhouse gas nitrous oxide were produced at rates 2-3 orders of magnitude lower than the ammonium production rate. While DNRA activity was restricted to the first few hours of darkness and anoxia, the subsequent degradation of photopigments took weeks to months, supporting the earlier finding that diatoms resume photosynthesis even after extended exposure to darkness and anoxia. Considering the high global abundance of T. weissflogii, its production of ammonium and nitrous oxide might be of ecological importance for oceanic oxygen minimum zones and the atmosphere, respectively.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria--anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species--in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca-anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

Microbialites, which are organosedimentary structures formed by microbial communities through binding and trapping and/or in situ precipitation, have a wide array of distinctive morphologies and long geologic record. The origin of morphological variability is hotly debated; elucidating the cause or causes of microfabric differences could provide insights into ecosystem functioning and biogeochemistry during much of Earth's history. Although rare today, morphologically distinct, co-occurring extant microbialites provide the opportunity to examine and compare microbial communities that may be responsible for establishing and modifying microbialite microfabrics. Highborne Cay, Bahamas, has extant laminated (i.e., stromatolites) and clotted (i.e., thrombolites) marine microbialites in close proximity, allowing focused questions about how community composition relates to physical attributes. Considerable knowledge exists about prokaryotic composition of microbialite mats (i.e., stromatolitic and thrombolitic mats), but little is known about their eukaryotic communities, especially regarding heterotrophic taxa. Thus, the heterotrophic eukaryotic communities of Highborne stromatolites and thrombolites were studied. Here, we show that diverse foraminiferal communities inhabit microbialite mat surfaces and subsurfaces; thecate foraminifera are relatively abundant in all microbialite types, especially thrombolitic mats; foraminifera stabilize grains in mats; and thecate reticulopod activities can impact stromatolitic mat lamination. Accordingly, and in light of foraminiferal impacts on modern microbialites, our results indicate that the microbialite fossil record may reflect the impact of the radiation of these protists.

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, and metabolic capacity. However, our ability to understand and quantify phage–host interactions is technique-limited. Here, we introduce phageFISH – a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to > 92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus–gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g. early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage–host system, and debut phageFISH as a much-needed tool for studying phage–host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages.