Variation in sensitivity of large benthic Foraminifera to the combined effects of ocean warming and local impacts

Global diversity patterns of larger benthic foraminifera under future climate change

Global warming threatens the viability of tropical coral reefs and associated marine calcifiers, including symbiont-bearing larger benthic foraminifera (LBF). The impacts of current climate change on LBF are debated because they were particularly diverse and abundant during past warm periods. Studies on the responses of selected LBF species to changing environmental conditions reveal varying results. Based on a comprehensive review of the scientific literature on LBF species occurrences, we applied species distribution modeling using Maxent to estimate present-day and future species richness patterns on a global scale for the time periods 2040-2050 and 2090-2100. For our future projections, we focus on Representative Concentration Pathway 6.0 from the Intergovernmental Panel on Climate Change, which projects mean surface temperature changes of +2.2°C by the year 2100. Our results suggest that species richness in the Central Indo-Pacific is two to three times higher than in the Bahamian ecoregion, which we have identified as the present-day center of LBF diversity in the Atlantic. Our future predictions project a dramatic temperature-driven decline in low-latitude species richness and an increasing widening bimodal latitudinal pattern of species diversity. While the central Indo-Pacific, now the stronghold of LBF diversity, is expected to be most pushed outside of the currently realized niches of most species, refugia may be largely preserved in the Atlantic. LBF species will face large-scale non-analogous climatic conditions compared to currently realized climate space in the near future, as reflected in the extensive areas of extrapolation, particularly in the Indo-Pacific. Our study supports hypotheses that species richness and biogeographic patterns of LBF will fundamentally change under future climate conditions, possibly initiating a faunal turnover by the late 21st century.

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.

Are physiological responses in foraminifera reliable environmental stress bioindicators? A systematic review

Foraminifera are considered good bioindicators of environmental stress based on morphological abnormalities, but physiological responses occur far earlier and have not been evaluated as pollution markers. The aim of this review was to collate all published articles reporting physiological changes in foraminifera after environmental and anthropogenic stressors, to evaluate their reliability as early markers of environmental stress. We reviewed 70 studies, meeting the inclusion criteria, reporting 13 physiological effects classes after exposure to 17 different stressors. Immune functions, bleaching and lifecycle disruptions, were the most reported. Amphistegina and Ammonia showed high proportion of effects with lead and mercury, with a significant relationship between these heavy metals and the number of physiological effects classes in Ammonia, and between bleaching in Amphistegina gibbosa and Amphistegina lobifera with solar light and temperature. This suggests physiological responses are potentially reliable early indicators of environmental stress. It is necessary to increase quantitative physiological measures and standard exposure protocols in order to properly evaluate these organisms as pollution bioindicators.

The combined effects of rising temperature and salinity may halt the future proliferation of symbiont-bearing foraminifera as ecosystem engineers

Rising sea surface temperatures and extreme heat waves are affecting symbiont-bearing tropical calcifiers such as corals and Large Benthic Foraminifera (LBF). In many ecosystems, parallel to warming, global change unleashes a host of additional changes to the marine environment, and the combined effect of such multiple stressors may be far greater than those of temperature alone. One such additional stressor, positively correlated to temperature in evaporation-dominated shallow-water settings is rising salinity. Here we used laboratory culture experiments to evaluate the combined thermohaline tolerance of one of the most common LBF species and carbonate producer, Amphistegina lobifera. The experiments were done under ambient (39 psu) and modified (30, 45, 50 psu) salinities and at optimum (25 °C) and warm temperatures (32 °C). Calcification of the A. lobifera holobiont was evaluated by measuring alkalinity loss in the culturing seawater, as an indication of carbonate ion uptake. The vitality of the symbionts was determined by monitoring pigment loss of the holobiont and their photosynthetic performances by measuring dissolved oxygen. We further evaluated the growth of Peneroplis (P. pertusus and P. planatus), a Rhodophyta bearing LBF, which is known to tolerate high temperatures, under elevated salinities. The results show that the A. lobifera holobiont exhibits optimal performance at 39 psu and 25 °C, and its growth is significantly reduced upon exposure to 30, 45, 50 psu and under all 32 °C treatments. Salinity and temperature exhibit a significant interaction, with synergic effects observed in most treatments. Our results confirm that Peneroplis has a higher tolerance to elevated temperature and salinity compared to A. lobifera, implying that a further increase of salinity and temperatures may result in a regime shift from Amphistegina- to Peneroplis-dominated assemblages.

Potential utility of reflectance spectroscopy in understanding the paleoecology and depositional history of different fossils

The potential of reflectance spectroscopy to infer the paleoecological and depositional evolution of different micro and macro invertebrate fossils has been evaluated by analyzing their reflectance spectra within the spectral domain of 350–2500 nm using the FIELDSPEC3 spectroradiometer. Mineralogical information derived from the rapid and non-destructive spectral analysis has been substantiated using concurrent mineralogical data from conventional geochemical analyses. The diagnostic Fe-crystal field effect induced spectral features are identified on the representative spectra of different benthic foraminifera. These spectral features are resulted due to the incorporation of Fe during the biomineralization process. These features are absent in planktic foraminifera. The encrustation of Fe-oxides is inferred to be responsible for imprinting the Fe-crystal field feature in the spectra of micro and macrofossils at 900–1200 nm. Vibrational spectral features of the Al–OH bond are also identified. Both of these features are an indicator of post-depositional diagenetic history. The presence of Al and Fe in macrofossil shells is also believed to be related to ecological conditions as these elements are biogenically incorporated during shell formation. This study reveals the value of reflectance spectroscopy to infer ecological behavior and post-depositional environment of different organisms.

Behavior of eukaryotic symbionts in large benthic foraminifers Calcarina gaudichaudii and Baculogypsina sphaerulata under exposure to wastewater

Large benthic foraminifers (LBFs) are significant contributors to coral island formation in the Pacific Ocean. In recent years, the population of LBFs has decreased because of the increase in anthropogenic influences, such as wastewater (WW) discharge. To implement efficient mitigation measures, pollution tolerance in LBFs should be understood. However, the effects of WW on LBFs and their symbionts have not yet been demonstrated. This study examined the changes in the photosynthetic efficiency (Y[II]) of Calcarina gaudichaudii and Baculogypsina sphaerulata in response to WW by using a pulse-amplitude-modulation fluorometer. These LBFs were exposed to WW with different dilution levels for 22 days. The Y(II) values of the LBFs were found to deteriorate within 1-2 days. However, the Y(II) values both deteriorated and were enhanced in the experiments, thus indicating that WW contains both harmful and beneficial components. Baculogypsina sphaerulata showed an earlier response and greater sensitivity to WW and a higher epibiont infestation than C. gaudichaudii. This result can be attributed to the differences in the physiological and morphological responses of distinct LBFs. A sequencing analysis of 18S rDNA confirmed that the dominant eukaryotic symbionts in the two LBFs studied were Ochrophyta and Labyrinthulomycetes. These eukaryotic symbionts were released and attached as epibionts onto LBFs that were exposed to WW, thus leading to an increase in inactive LBFs. The Shannon-Weaver and Simpson diversity indices revealed that eukaryotic symbiont communities decreased in biodiversity after exposure to WW because of the abundance of algal symbionts. On the basis of these results, we conclude that WW, even with 10,000 × dilution, causes a decrease in active LBF populations owing to the release of eukaryotic symbionts, the decrease in biodiversity, and the infestation of epibionts even though Y(II) is temporarily enhanced. These responses are more significant in B. sphaerulata than in C. gaudichaudii.

High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef-dwelling calcifier

Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo-West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological-scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.

Foraminifera as bioindicators of water quality: The FoRAM Index revisited

Coral reefs worldwide are degrading at alarming rates due to local and global stressors. There are ongoing needs for bioindicator systems that can be used to assess reef health status, the potential for recovery following destructive events such as tropical storms, and for the success of coral transplants. Benthic foraminiferal shells are ubiquitous components of carbonate sediment in reef environments that can be sampled at minimal cost and environmental impact. Here we review the development and application of the FoRAM Index (FI), which provides a bioindicator metric for water quality that supports reef accretion. We outline the strengths and limitations of the FI, and propose how it can be applied more effectively across different geographical regions.

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.

Strategies in times of crisis-insights into the benthic foraminiferal record of the Palaeocene-Eocene Thermal Maximum

Climate change is predicted to alter temperature, carbonate chemistry and oxygen availability in the oceans, which will affect individuals, populations and ecosystems. We use the fossil record of benthic foraminifers to assess developmental impacts in response to environmental changes during the Palaeocene-Eocene Thermal Maximum (PETM). Using an unprecedented number of µ-computed tomography scans, we determine the size of the proloculus (first chamber), the number of chambers and the final size of two benthic foraminiferal species which survived the extinction at sites 690 (Atlantic sector, Southern Ocean, palaeodepth 1900 m), 1210 (central equatorial Pacific, palaeodepth 2100 m) and 1135 (Indian Ocean sector, Southern Ocean, palaeodepth 600-1000 m). The population at the shallowest site, 1135, does not show a clear response to the PETM, whereas those at the other sites record reductions in diameter or proloculus size. Temperature was similar at all sites, thus it is not likely to be the reason for differences between sites. At site 1210, small size coincided with higher chamber numbers during the peak event, and may have been caused by a combination of low carbonate ion concentrations and low food supply. Dwarfing at site 690 occurred at lower chamber numbers, and may have been caused by decreasing carbonate saturation at sufficient food levels to reproduce. Proloculus size varied strongly between sites and through time, suggesting a large influence of environment on both microspheric and megalospheric forms without clear bimodality. The effect of the environmental changes during the PETM was more pronounced at deeper sites, possibly implicating carbonate saturation.This article is part of a discussion meeting issue 'Hyperthermals: rapid and extreme global warming in our geological past'.

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia

Ocean warming is known to cause detrimental effects in coral reef fauna that rely on photo-symbiosis for survival. Microbial associations can facilitate the success of species across a range of environmental conditions, and play a role in the capacity of organisms to respond to climate change. In 2016, the Great Barrier Reef experienced its third mass bleaching event, with sea surface temperature rising to 1.3°C above long-term monthly summer averages. Here, I investigate the effects of ocean warming on the chlorophyll a (chl a) content and microbiome of the large benthic Foraminifera Amphistegina radiata. Samples were collected in January and April 2016, before and after the mass bleaching event. In total, 71 specimens were collected from two different depths (6- and 18-m) to investigate depth-dependant responses associated with changes in chl a and microbiome. Pigment analysis showed a significant reduction in chl a between time points in specimens collected at both depths. Reduction in pigmentation was accompanied by changes in the microbiome, and a significant interaction of depth and time was observed. Genus-level bacterial community associated with A. radiata was significantly different across depth and time. However, ocean warming affected populations at both depths to a similar extent, and resulted in change from a Betaproteobacteria-dominated assemblage in January to a more diverse bacterial community by April. Analysis of presence/absence and relative abundance of bacterial taxa revealed significant differences between time points at both depths analyzed. OTUs classified as Firmicutes, which were either absent, or present in very low relative abundances (<0.1%) across all sample groups in January, were identified in abundances as high as ∼20% in specimens collected from 18-m depth in April. Class-level shifts were observed in shallow-dwelling specimens, from high abundances of Betaproteobacteria to a high abundance and diversity of Actinobacteria. These results demonstrate the sensitivity of LBF to the effects of ocean warming, for which depth did not provide protection, and highlights the capacity of LBF to re-assemble bacterial communities after a disturbance. This study provides the first molecular-based demonstration of changes in foraminifera-associated bacterial assemblages during a bleaching event on a natural reef system.

Challenges in using CellTracker Green on foraminifers that host algal endosymbionts

The uses of fluorescent microscopy and fluorescent probes, such as the metabolically activated probe CellTracker™  Green CMFDA (CTG), have become common in studies of living Foraminifera. This metabolic requirement, as well as the relatively quick production of the fluorescent reaction products, makes CTG a prime candidate for determining mortality in bioassay and other laboratory experiments. Previous work with the foraminifer Amphistegina gibbosa, which hosts diatom endosymbionts, has shown that the species is capable of surviving both acute chemical exposure and extended periods of total darkness by entering a low-activity dormant state. This paper explores the use of CTG and fluorescent microscopy to determine mortality in such experiments, as well as to explore the physiology of dormant foraminifers. The application of CTG was found to be complicated by the autofluorescence of the diatom symbionts, which masks the signal of the CTG, as well as by interactions between CTG and propylene glycol, a chemical of interest known to cause dormancy. These complications necessitated adapting methods from earlier studies using CTG. Here we present observations on CTG fluorescence and autofluorescence in A. gibbosa following both chemical exposure and periods of total darkness. While CTG can indicate vital activity in dormant foraminifers, complications include underestimates of total survival and recovery, and falsely indicating dead individuals as live due to rapid microbial colonization. Nonetheless, the brightness of the CTG signal in dormant individuals exposed to propylene glycol supports previously published results of survival patterns in A. gibbosa. Observations of CTG fluorescence in individuals kept for extended periods in aphotic conditions indicate uptake of CTG may begin within 30 min of exposure to light, suggesting darkness-induced dormancy and subsequent recovery can occur on short time scales. These results suggest that CTG accurately reflects changes associated with dormancy, and can be useful in laboratory experiments utilizing symbiont-bearing foraminifers.

Reef calcifiers are adapted to episodic heat stress but vulnerable to sustained warming

Shallow marine ecosystems naturally experience fluctuating physicochemical conditions across spatial and temporal scales. Widespread coral-bleaching events, induced by prolonged heat stress, highlight the importance of how the duration and frequency of thermal stress influence the adaptive physiology of photosymbiotic calcifiers. Large benthic foraminifera harboring algal endosymbionts are major tropical carbonate producers and bioindicators of ecosystem health. Like corals, they are sensitive to thermal stress and bleach at temperatures temporarily occurring in their natural habitat and projected to happen more frequently. However, their thermal tolerance has been studied so far only by chronic exposure, so how they respond under more realistic episodic heat-event scenarios remains unknown. Here, we determined the physiological responses of Amphistegina gibbosa, an abundant western Atlantic foraminifera, to four different treatments––control, single, episodic, and chronic exposure to the same thermal stress (32°C)––in controlled laboratory cultures. Exposure to chronic thermal stress reduced motility and growth, while antioxidant capacity was elevated, and photosymbiont variables (coloration, oxygen-production rates, chlorophyll a concentration) indicated extensive bleaching. In contrast, single- and episodic-stress treatments were associated with higher motility and growth, while photosymbiont variables remained stable. The effects of single and episodic heat events were similar, except for the presumable occurrence of reproduction, which seemed to be suppressed by both episodic and chronic stress. The otherwise different responses between treatments with thermal fluctuations and chronic stress indicate adaptation to thermal peaks, but not to chronic exposure expected to ensue when baseline temperatures are elevated by climate change. This firstly implies that marine habitats with a history of fluctuating thermal stress potentially support resilient physiological mechanisms among photosymbiotic organisms. Secondly, there seem to be temporal constraints related to heat events among coral reef environments and reinforces the importance of temporal fluctuations in stress exposure in global-change studies and projections.