A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup

Ubiquitin is a 76 amino acid protein with a remarkable degree of evolutionary conservation. Ubiquitin plays an essential role in a large number of eukaryotic cellular processes by targeting proteins for proteasome-mediated degradation. Most ubiquitin genes are found as head-to-tail polymers whose products are posttranslationally processed to ubiquitin monomers. We have characterized polyubuiquitin genes from the photosynthetic amoeboflagellate Chlorarachnion sp. CCMP 621 (also known as Bigelowiella natans) and found that they deviate from the canonical polyubiquitin structure in having an amino acid insertion at the junction between each monomer, suggesting that polyubiquitin processing in this organism is unique among eukaryotes. The gene structure indicates that processing likely cleaves monomers at the amino terminus of the insertion. We examined the phylogenetic distribution of the insertion by sequencing polyubiquitin genes from several other eukaryotic groups and found it to be confined to Cercozoa (including Chlorarachnion, Lotharella, Cercomonas, and Euglypha) and Foraminifera (including Reticulomyxa and Haynesina). This character strongly suggests that Cercozoa and Foraminifera are close relatives and form a new "supergroup" of eukaryotes.     

Evolutionary implications of swimming behaviour in meiobenthic copepods

Body morphology is said to be the all important factor in determining swimming prowess in copepods. Fusion and differentiation of the body (tagmosis) is coupled with advance into the pelagic realm of the Gymnoplea and is thought, by the provision of a rigid thoracic tagma, to promote swimming efficiency. Thus pelagic copepods are believed to be secondarily derived from bottom dwelling predecessors. Experimental evidence is presented to show that the majority of bottom dwelling harpacticoid families, including the most primitive and the most advanced, have representatives that undergo active sustained swimming movements. Such a widespread occurrence is indicative of a conservative evolutionary trait. This primitive behaviour is linked to precopulatory association which takes place necessarily in the water column; it is a feature retained by representatives of all copepod orders. The implication of cephalic appendage vibration (feeding currents) is the essential feature in the swimming success of the Gymnoplea; planktonic efficiency in these is suggested to have evolved coincident with, rather than because of increased tagmosis.     

Taxonomic position of the superorder Fusulinoida Fursenko in the Foraminifera system

Comparative morphological analysis of the test and apertural structures in lower and higher members of the superorder Fusulinoida and class Miliolata has shown that they are similar in test, developmental trends from primitive forms with a tubular chamber to complex supermultichamber tests of the fusulinoid shape. As series of sections were compared, supplementary inner deposits at the bottom of chambers of endothyrids (tubercles, rostra, chomata) showed homology with the teeth of Miliolata. The high magnesium composition of the test wall and some ultrastructural features shared by the two groups support their affinity and suggest the assignment of the superorder Fusulinoida to the class Miliolata as an early phylogenetic lineage.     

Foraminifera in the diet of coral reef fish from the lagoon of New Caledonia: Predation, digestion, dispersion

Marine benthic Foraminifera are abundant and thus represent a potential food source for fish. Previous studies of Foraminifera in fish diets have examined only small samples, with significant input reported only for a single surface-feeding species of fish. The present study is the first based on a significant sample (247 fish belonging to 83 species, 291 species of Foraminifera identified from more than 20,000 specimens examined). It provides new information on the contribution of Foraminifera to fish diets, and on the impact of fish predation on Foraminifera. The planktonic Tretomphalus phases, selectively ingested by Pomacentrus amboinensis, were the only significant nutritional input from Foraminifera. Herbivorous fish accidentally ingested living epiphytic Foraminifera, which were still living after digestion, and were defecated, with a significant effect on their dispersion. Carnivorous fish ingested a small number of tests, which were generally altered by the acidic phase of digestion and had no impact on foraminiferal assemblages. Sediment feeders ingested large quantities of empty tests that were released elsewhere, suggesting a possible bias in paleontological interpretations by mixing the thanatocoenoses. Observations on gut contents showed that the fish sometimes fed on a wide range of food, changing with food availability and individual preferences of fish.     

Photosynthetic plasticity of endosymbionts in larger benthic coral reef Foraminifera

Larger benthic Foraminifera (LBF) are ecologically important coral reef protists that harbour a large diversity of symbionts from at least four algal phyla. In this study the photosynthetic plasticity of different endosymbiontic algae found within LBF was investigated using pulse amplitude modulated (PAM) fluorometry. Maximum quantum efficiencies of photosystem II (F_v/F_m) obtained from foraminiferal specimens directly after field collection indicated several pronounced differences between species containing endosymbionts from different algal phyla and, to a lesser extent, also varied between species that contain the same phyla of endosymbiontic algae. Foraminiferal species retaining functional chloroplasts and rhodophyte-bearing species had distinctly lower F_v/F_m, than LBF with dinoflagellates, diatoms or chlorophytes. A laboratory experiment was conducted over 48 h exposing species occurring in high- (photophilic), medium- and low-light (sciaphilic) environments to three manipulated light levels. Photophysiological responses were monitored by measuring F_v/F_m at regular intervals and rapid light curves (RLCs) at the end of the experiment. This experiment demonstrated oscillation of maximum quantum efficiencies according to the light-dark cycle. Changes in the shape of the RLCs (e.g., higher α and lower E_k under low light conditions) indicated that photosynthetic plasticity allows LBF to acclimatise rapidly (< 48 h) to different light conditions.     

The Foraminifera of the Pitcairn Islands

Foraminifera were recovered from 18 samples collected in the Pitcairn Islands, 12 from Henderson Island (including the best and most comprehensive collections) and three each from Oeno Atoll and Pitcairn Island itself. Although both algae and sediment samples were collected, the living Foraminifera came, almost exclusively, from phytal (attached or clinging) habitats. Foraminifera in the sediment samples are mainly thanatocoenoses. The fauna is an exclusively calcareous, relatively low diversity assemblage, dominated by large soritids [Marginopora, Amphisorus, Sorites) and Amphistegina , all of which are ubiquitous throughout the tropical Pacific. These larger Foraminifera are usually accompanied by small miliolids in particular, as well as by small attached Foraminifera (discorbids and the like). Typical reefal Foraminifera are generally under-represented. So far, no endemic species have been found. Of more significance, perhaps, is the apparent absence of Calcarina , small rotaliids, elphidiids and agglutinating species, so common in the western Pacific islands. One sample of fossil Foraminifera was analysed, from a shelly sand (c. 30 m above present sea-level) on Henderson Island. Though, for the most part, like the Recent assemblages, this was characterized by Archaias , a soritid which was not found in any of the modern collections made by the 1991– 92 Expedition. This could either be a sampling artifact or refer to a real environmental change since the Pleistocene.     

Middle-Upper Jurassic Foraminifera from Jumara Hills, Kutch, India

A prolific foraminiferal assemblage comprising 51 species is reported from Jurassic sediments of the Chari Formation, Jumara Hills, Kutch, India. The assemblage is dominated by the families Vaginulinidae and Nodosariidae. Sixteen species are reported for the first time from the Indian region including one new species. The foraminiferal assemblage suggests a Callovian to Oxfordian age for the studied sequence. The depositional environment of the studied sequence is interpreted based on foraminiferal evidence combined with lithology and megafauna which indicates that the sediments of the Chari formation exposed at Jumara Hills were deposited in a shallow-water, near shore, environment with fluctuating shoreline in a tectonically unstable shelf zone. The Jumara Hills foraminiferal assemblage exhibits close affinity with certain other Jurassic assemblages of the Tethyan Realm and helped in drawing palaeogeographic conclusions, suggesting that during the Middle and Late Jurassic epochs Kutch had close sea connections with Central Arabia, Afghanistan and Rajasthan on the one hand and Somalia and Malagasy on the other.     

Bryozoans as substratum of fossil fistulose Foraminifera (Fam. Polymorphinidae)

In the Upper Cretaceous-Lower Tertiary sections exposed in the Curfs quarries at Berg (munic. Berg en Terblijt - also known as Geulhem, southern Netherlands) and some other localities, numerous foraminifers of the family Polymorphinidae with complete fistulose apertures have been found. These apertures, which are equipped with circular openings and auxiliary apertural chambers, branching and numerous narrow projecting tubes or stolons, have been widely reported, but their role has been the subject of controversy. The Dutch material shows the foraminifers attached with the apertural tubes to fragments of bryozoan colonies or molluscan shells, suggesting that the tubes could perhaps act as holdfast organs. Most specimens were found in calcarenites of the nearshore facies. The foraminifers cannot be treated as symbiotic organisms nor parasites but as epifauna in search of protection from mechanical destruction by waves and current action. The present case may be best explained as an adaptation of sessile foraminifers with fragile hyaline tests to live in highly disadvantageous, high-energy conditions.     

Palaeozoic Foraminifera: Systematics, palaeoecology and responses to global changes

Because the Foraminifera are very sensitive to various environmental parameters (e.g., water temperature, salinity, light, etc.), there are important proxies used for palaeoenvironmental and palaeogeographic reconstructions. The evolution of the structure, shape and size of the mineralized tests of Foraminifera can directly reflect the variation of these parameters through geological time. Furthermore, their biostratigraphic value has been widely demonstrated. In this context, the systematics, evolution and ecological behaviour of the first mineralized Palaeozoic Foraminifera are important to discuss in order to have a clearer picture of former shallow marine environments, and finally understand their distribution through space and time. The systematics of the fossil group of Foraminifera that first developed a mineralized test remains under discussion. These early foraminifers are considered as Textulariata (as generally admitted), recrystallized Fusulinata or an independent group, sometimes called Astrorhizata. In this paper, we argue to assign the early foraminifers to the Fusulinata, and to subdivide this class into six orders: Parathuramminida, Archaediscida and Earlandiida (forming together the subclass Afusulinana n. subcl.), and Tournayellida, Endothyrida and Fusulinida (subclass Fusulinana nom. translat.). These subdivisions are discussed and linked to the first occurrences of the later classes: Miliolata, Nodosariata and Textulariata. The environmental living conditions of the first fossilized foraminifers remain enigmatic during the Early Palaeozoic (Cambrian-Silurian). During the Late Silurian, the unilocular Parathuramminida started to colonize the inner parts of ramps and platforms. The first plurilocular microgranular foraminifers (Semitextulariidae, Nanicellidae, and Eonodosariidae) developed in back-reefal systems and in deeper-water environments (“griottes”-type nodular limestone) from the late Early Devonian to the early Late Devonian. The Moravamminida, another group of possible Protista, are typical markers of Devonian inner ramp systems. The Semitextulariidae, Nanicellidae, and Eonodosariidae did not survive the Frasnian/Famennian crisis. From the Tournaisian to the Serpukhovian (Mississippian subsystem or Early Carboniferous), numerous new genera and species of Archaediscida, Tournayellida and Endothyrida flourished but remained confined to inner ramp environments. In deeper water depositional systems (i.e. coral thrombolite microbialites and/or nodular limestones), a few opportunistic Foraminifera were living up to the disphotic zone. During the Pennsylvanian (Bashkirian to Gzhelian), the habitats extended to more confined, shallower areas of the inner ramp (with Staffelloidea). During the Late Carboniferous and Permian, the larger Fusulinida (Schwagerinoidea) reached the outer platform as they have been commonly reworked in calciturbidites. During the Late Permian, some taxa were even able to live in hypersaline environments such as sabkhas and hypersaline lagoons. Two major biotic crises occurred during the Permian (post-Middle and post-Late Permian crisis), but the number of survivors after the PTE (Permian/Triassic Extinction) is probably higher than previously admitted. From the Cambrian to the Serpukhovian, the Foraminifera were probably all infaunal or living at the sediment/seawater interface. The TROX and TROX-2 models are consequently applicable. Anoxia, often suggested as triggering environmental crises, was likely not systematically lethal for many infaunal foraminifers. The late Tournaisian-Changhsingian Tetrataxis genus was probably the first epiphyte foraminifer, because of its conical, limpet-like test. The Tetrataxidae (e.g., Tetrataxis, Pseudotaxis and Abadehella) constituted the unique trochospirally coiled plurilocular foraminiferal family of the Palaeozoic. The Bradyinoidea, Ozawainelloidea, Staffelloidea, and the Pseudoschwagerinidae (Schwagerinoidea) are other examples of Pennsylvanian-Permian epiphytes but cannot be considered as planktonic taxa. All the other Schwagerinoidea are related to high-energy environments and coarse-grained substrates. Their history, as well as that of the Neoschwagerinoidea, was likely subject to the vicissitudes of their endosymbiotic algae.     

Distribution of live benthic Foraminifera at three oceanographically dissimilar sites in the northeast Atlantic: preliminary results

Live (i.e. rose Bengal stained) benthic foraminiferal assemblages in the 0–1 cm layer of multiple core samples were examined at three contrasting sites in the northeast Atlantic as part of the Natural Environment Research Council Deep Ocean Benthic Boundary Layer (BENBO) Thematic Programme. Sites A (3600 m water depth) and C (1900 m) were located in the Rockall Trough while Site B (1100 m) was in the Hatton–Rockall Basin. Wet-sorting sediment residues (>125 m fraction) revealed more abundant (98–190 individuals/10 cm²) and diverse (71–99 species /27 cm²) assemblages than found previously in studies employing dry-sorting techniques. At all three sites, the assemblages were numerically dominated by delicate soft-bodied and agglutinated species, most of which are undescribed. Calcareous taxa formed a relatively small proportion of the assemblages (23% of individuals at Site B, 13% at Site C and 7% at Site A). Conversely, the agglutinated hormosinaceans (mainly Reophax species) became more prominent with increasing depth and accounted for 8% of the assemblage at Site B, 33% at Site C and 51% at Site A. Foraminifera represented 67–81% of the fauna in the samples and greatly outnumbered the metazoans. The assemblage at Site A has similarities with abyssal assemblages, while those at Sites B and C contain characteristic bathyal species. At Site B, Uvigerina peregrina and Melonis barleeanum are abundant, suggesting that there are high organic carbon inputs at this site. Reduced species diversity was observed at Site A following the spring phytodetritus bloom due to the presence of large numbers of juvenile Hoeglundina elegans, although it is not clear whether this species is responding to phytodetritus inputs.     

Biotic relations affecting species structure in zooplankton communities

Mathematical modelling and laboratory experiments were used to study how exploitative competition and predation influence the species structure in cladoceran community. For five species of Cladocera (Sida crystallina, Daphnia magna, Simocephalus vetulus, Daphnia longispina, and Diaphanosoma brachyurum), representing a gradient of body size, population characteristics were described as functions of food concentration. Abundance dynamics were simulated in mixed species cultures and invasion experiments under different levels of food supply corresponding to oligo-, meso-, and eutrophic conditions. Separate simulations were also run including and excluding (fish) predation. The competitive ability of each species was estimated as the values of the population equilibrium food concentration. Simulation results showed that for the no-predator scenario, increases in the level of food supply promoted species coexistence while under lower food concentrations only one species remained at the end of the simulation runs. When predation was allowed, the number of species that coexisted at the end of the simulations increased up to four species, indicating that predator pressure facilitated species coexistence because it shortened periods of food depletion. Simulation results were verified in laboratory experiments which suggested that population equilibrium food concentration can be used as an estimate of competitive ability. Finally, species structure and relative abundance in Lake Naroch (Belarus) during the summer of 2004 was found to be consistent with our results from computer simulation and laboratory experiments with regard to competition and predation impacts on zooplankton community. Handling editor: S. I. Dodson     

Tempo and Mode of Spliceosomal Intron Evolution in Actin of Foraminifera

Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Bhattacharya]     

New endothyrids (Foraminifera) from the Upper Visean of the northern Ural Mountains

New endothyrids from the Upper Visean of the western slope of the northern Ural Mountains are described and assigned to the new species Eoendothyranopsis (Ninella) extremus and E. (N.) poststaffelliformis.     

Deep-sea meiobenthic communities underneath the marginal ice zone off Eastern Greenland

Marginal ice zones (MIZ) are known to be the most highly productive systems in the Arctic Ocean with large amounts of primary production reaching the deep seafloor. This study characterizes the effect of the ice-edge related primary production and subsequent phytodetritus sedimentation on deep-sea meiobenthic communities, particularly nematodes, along the Eastern Greenland continental margin in July 2000. Results were based on data from six stations along a depth transect crossing the MIZ with the shallowest stations under the ice-cover (656 and 1,198 m), intermediate stations at the ice-edge (1,560 and 2,129 m), and deepest stations in ice-free areas (2,735 and 3,033 m). The presence of the ice-cover significantly affected the availability of organic matter on the deep seafloor. The present results confirm a close bentho-pelagic coupling in the area of investigation. Enhanced flux of phytodetritus from primary production to the benthic system appears at stations underneath or close to the ice-edge and at the sampling sites in ice-free areas. The availability of phytodetritus at these stations enhanced bacterial activities, meiofauna abundances, and the number of nematodes species. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Late Jurassic (Kimmeridgian) larger benthic Foraminifera from Santiago Coatepec, SE Puebla, Mexico

A micropaleontologic study was carried out from samples collected along a section that crops out in the Santiago Coatepec Stream, located in the southeast of the state of Puebla, Mexico. The sedimentary sequence begins with a reddish conglomerate. Above, thick and thin layers of grey-greenish sandstones that continue in fine-grained, calcareous sandstones, and, finally, in limestones. The reddish conglomerate may represent a continental environment, and the marine transgression began with the sandstone deposit that contains a marine association of Invertebrates such as Trigonids (Myophorella sp.), and other Mollusks such as Trichites sp., Ostreids and Gastropods, Echinoderms, and Sponges as Cladocoropsis mirabilis. This sequence also provides a rich assemblage of larger Foraminifera as well as Algae, which is reported for the first time in this site. The larger agglutinated Foraminiferal assemblage is composed of Alveosepta jaccardi, Pseudocyclammina lituus, Everticyclammina virguliana, Rectocyclammina chouberti, Choffatella cf. Ch. tingitana, Mesoendothyra croatica, Nautiloculina oolithica, Freixialina planispiralis, Audienusina fourcadei, Placopsilina sp., Pseudocyclammina sp., Meandrospira sp. and Lenticulina sp. All those taxa were adapted to special paleoecological conditions, such as a continuous terrigenous input. The Algae are Marinella lugeoni, Pseudoepimastopora jurassica, Permocalculus sp., and Halimeda sp. The stratigraphic distribution of the larger benthic Foraminifera allow us to propose a Kimmeridgian age for the studied sequence. The opening of the Atlantic Ocean permitted the colonization of its margins by the larger Foraminifera during this time. The data provided by the larger Foraminifera, the Algae, and the lithology may suggest an internal platform environment of warm shallow water. This foraminiferal association is constituted by cosmopolitan species which are frequent in the Tethyan Realm.     

Small stonefly predators affect microbenthic and meiobenthic communities in stream leaf packs

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Copepod communities in karstic mediterranean lakes along the eastern Adriatic coast

The copepod communities of karstic lakes along the eastern Adriatic coast were studied. Lakes were divided in several groups according to their morphology (deep, shallow, barrage and reservoirs), production (oligotrophic, mesotophic and eutrophic), and salinity of water: freshwater and brackish. Copidodiaptomus steueri, Eucyclops serrulatusand Macrocyclops albidus belong to the group that inhabited most of the lakes under the study, regardless of lake type. The shallow karstic lakes are usually inhabited by Thermocyclops dybowskii, T. oithonoides, Cyclops vicinus and Eudiaptomus padanus etruscus in freshwater biotopes, and Calanipedia aquaedulcis and Copidodiaptomus steueri in brackish biotopes. The last two species can also be found in deep karstic lakes with brackish water (Bacina lakes in the Neretva River delta). Species like Cyclops abyssorumcan be found in most deep freshwater lakes. Some Calanoida were recorded in only one lake, like Eudiaptomus transsylvanicusin the deep Lake Vrana on the island of Cres, or Eudiaptomus hadzici in the barrage Lake Visovac. Production of the lakes, expressed as copepod biomass, depends on lake trophy, and in some lakes also on hydrology and salinity. Most of the meso-eutrophic lakes in the study area had Calanoida dominating, while Cyclopoida dominated in some oligotrophic and eutrophic lakes as well.     

Perception,pattern, chance and the structure of reef fish communities

The recent history of attempts to understand the ecology of fish on coral reefs is surveyed as an example of the way in which science progresses. Scientists are trapped, both by their sensory equipment and by their preconceptions, into viewing the world in certain ways. Paradigms fall only slowly. Scientists are trained to seek pattern in their data, yet in some cases the largely stochastic variation of a system around its mean condition is the more important key to understanding its ecology. The reef fish assemblage provides such a case. It is unlikely that our present understanding of the nature of reef fish communities will survive unchanged by future research. And it is also unlikely that reef fish ecologists are the only ecologists who have difficulty discovering truth! Editorial     

Attachment of Foraminifera to vestimentiferan tubeworms at cold seeps: Refuge from seafloor hypoxia and sulfide toxicity

A survey of foraminiferal microhabitats at several Gulf of Mexico bathyal/abyssal hydrocarbon seeps reveals that many epibenthic species live not on the sediment, but attached to vestimentiferan tubeworms – centimeters to decimeters above the seafloor – thus avoiding the oxygen depletion and H₂S toxicity at the sediment–water interface. This observation explains how certain species with a relatively high oxygen requirement (e.g., Cibicides spp.) may become components of foraminiferal death assemblages in seep sediments. Thus, when the sedimentary record of Foraminifera is used to interpret the history of past methane venting, the species from elevated microhabitats cannot be ignored, but they need to be considered separately from the sediment dwellers.