Selective zircon accumulation in a new benthic foraminifer,Psammophaga zirconia,sp. nov.

Benthic foraminifera are single‐celled eukaryotes that make a protective organic, agglutinated or calcareous test. Some agglutinated, single‐chambered taxa, including Psammophaga Arnold, 1982, retain mineral particles in their cytoplasm, but the selective mechanism of accumulation is not clear. Here, we report the ability of a foraminiferal species to select and accumulate zircons and other heavy minerals in their cytoplasm. In particular, the use of Scanning Electron Microscope coupled with an Energy Dispersive X‐ray microanalysis system (SEM–EDS) enabled a representative overview of the mineral diversity and showed that the analysed Psammophaga zirconia sp. nov. individuals contained dominantly crystals of zircon (51%), titanium oxides (27%), and ilmenite (11%) along with minor magnetite and other minerals. The studied specimens occur in the shallow central Adriatic Sea where the sediment has a content of zircon below 1% and of other heavy minerals below 4%. For that reason we hypothesize that: (i) P. zirconia may be able to chemically select minerals, specifically zircon and rutile; (ii) the chemical mechanism allowing the selection is based on electrostatic interaction, and it could work also for agglutinated foraminifera (whether for ingestion, like Xenophyophores, or incorporation in the test as in many other described taxa). In particular, this aptitude for high preferential uptake and differential ingestion or retention of zircon is reported here for the first time, together with the selection of other heavy minerals already described in members of the genus Psammophaga. They are generally counted among early foraminifera, constructing a morphologically simple test with a single chamber. Our molecular phylogenetic study confirms that P. zirconia is a new species, genetically distinctive from other Psammophaga, and occurs in the Adriatic as well as in the Black Sea.     

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.     

Effects of carbon dioxide sequestration on California margin deep-sea foraminiferal assemblages

Deep-sea sequestration of CO₂ is being considered as a possible mitigation tool to decrease atmospheric CO₂ concentrations and its associated negative effects. This study investigated potential effects of liquid carbon dioxide (CO₂) injection on deep-sea foraminiferal assemblages. Foraminifera are ideal for this ecological impact investigation because of differing test composition (calcareous and non-calcareous) and thickness, and diverse epifaunal and infaunal depth preferences. The experiment was conducted on August–September 2003, at 3600 m off the coast of Monterey Bay, California, aboard the R/V Western Flyer using the ROV Tiburon. The pH of the site was monitored throughout the experiment. Sediment push-cores were collected (both from the experimental and control sites) and stained to distinguish live (stained) from dead (unstained) individuals. Effects of CO₂ injection on assemblages have been tracked both vertically (to 10 cm depth below sea floor) and horizontally (up to 10 m from CO₂ injection sites), as well as between live and dead individuals. Within corrals (containing the injected CO₂) and their underlying sediments, severe pH changes (near 4.0 units) were recorded. This compares with a record of small average reductions in ocean pH (− 0.05 units) combined with large episodic excursions (− 1.7 units) over the experimental area due to the injection of CO₂. Exposure to this gradient of low pH caused increased mortality and dissolution of calcareous forms within corrals, as far as 5 m from the injection site, and to at least 10 cm depth in the sediments.This experiment revealed several major effects of CO₂ injection on foraminiferal assemblages in surficial sediments: 1) total number of foraminifera in a sample decreases; 2) foraminiferal species richness decreases in both stained and unstained specimens; and 3) relative percentage of stained (live) forms in the remaining tests increases. Down-core trends (to 10 cm below sea floor) have revealed: 1) percent agglutinated forms decline and calcareous forms increase with depth; 2) agglutinated species richness decreases with depth; and 3) experimental core assemblages become increasingly similar with depth to those in control cores not subjected to CO₂ injection. These results imply almost complete initial mortality and dissolution in the upper 10 cm throughout the corrals following liquid CO₂ injection. Since calcareous foraminifera represent more than 50% of the total assemblages, this clearly indicates that emplacement of CO₂ will result in negative effects to diversity and survivorship of the deep-sea benthic meiofauna.     

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.     

The O2, pH and Ca2+ Microenvironment of Benthic Foraminifera in a High CO2 World

Ocean acidification (OA) can have adverse effects on marine calcifiers. Yet, phototrophic marine calcifiers elevate their external oxygen and pH microenvironment in daylight, through the uptake of dissolved inorganic carbon (DIC) by photosynthesis. We studied to which extent pH elevation within their microenvironments in daylight can counteract ambient seawater pH reductions, i.e. OA conditions. We measured the O₂ and pH microenvironment of four photosymbiotic and two symbiont-free benthic tropical foraminiferal species at three different OA treatments (∼432, 1141 and 2151 µatm pCO₂). The O₂ concentration difference between the seawater and the test surface (ΔO₂) was taken as a measure for the photosynthetic rate. Our results showed that O₂ and pH levels were significantly higher on photosymbiotic foraminiferal surfaces in light than in dark conditions, and than on surfaces of symbiont-free foraminifera. Rates of photosynthesis at saturated light conditions did not change significantly between OA treatments (except in individuals that exhibited symbiont loss, i.e. bleaching, at elevated pCO₂). The pH at the cell surface decreased during incubations at elevated pCO₂, also during light incubations. Photosynthesis increased the surface pH but this increase was insufficient to compensate for ambient seawater pH decreases. We thus conclude that photosynthesis does only partly protect symbiont bearing foraminifera against OA.     

Larger agglutinated foraminifera of McMurdo Sound, Antarctica: Are Astrammina rara and Notodendrodes antarctikos allogromiids incognito?

Explorers Cove, an embayment on the oligotrophic western side of McMurdo Sound, Antarctica, is noted for physical and biological similarities to the deep sea. This locality is an important site for foraminiferal biologists because large, deep-sea-like agglutinated taxa are abundant at depths accessible to divers. Using microdissection methods, we found that many of the giant, single-chambered species from this locality display an allogromiid internal organization (i.e., a monothalamous cell body encased by an organic wall or “theca”). Another characteristic feature of these species is the presence of a distinct space separating the cell body and agglutinated test. We used high voltage transmission electron microscopy of thick sections to examine the theca of Astrammina rara, a dominant Explorers Cove species possessing a simple spherical test morphology, and Notodendrodes antarctikos, a distinctive arborescent species. We found that the simple gross morphology of A. rara's agglutinated test belies the complex ultrastructure of its allogromiid-like theca, and that the complex dendritic morphology of N. antarctikos' agglutinated test contradicts the simple ultrastructure of its theca. Additional field and laboratory observations on A. rara revealed that the agglutinated test can be a transient structure. Our observations raise questions regarding the taxonomy and phylogeny of unilocular agglutinated foraminifera and other primitive granuloreticuloseans. The results are also discussed in terms of test function in larger agglutinated foraminifera and the ecology of this important taxon.     

Rectogerochammina eugubina nov. gen., nov. sp., a new agglutinated foraminifer from the Upper Cretaceous of Gubbio, Italy

We describe the new agglutinated foraminiferal genus and species Rectogerochammina eugubina nov. gen., nov. sp. from the Upper Cretaceous Scaglia Rossa Formation of the Umbria-Marche Basin in Italy. The genus differs from Gerochammina (Neagu, 1990) in the presence of a terminal uniserial part.     

Palaeobathymetric zonation of foraminifera from lower Permian shale deposits of a high-latitude southern interior sea

Foraminifera are documented from the type section of the Quinnanie Shale in order to interpret their bathymetric distributions in a shallow high-latitude interior sea during the Kungurian. The marine setting was a narrow elongate half-graben (Merlinleigh Sub-Basin of the Southern Carnarvon Basin) in the Western Australian portion of eastern Gondwana. The Quinnanie Shale is part of the Byro Group of formations that display pronounced shale–sand cyclicity recording frequent changes in bathymetry. The type section of the Quinnanie Shale shows an overall progradational pattern in lithofacies, and consists of five ‘cycles’, each culminating in a prominent sandstone bed. Foraminifera are abundant in the shale and are almost entirely siliceous (organic-cemented) agglutinated types that probably dominated the original fauna of the interior sea. Hierarchical cluster analysis of samples taken every meter through the 162-m-thick type section is used to distinguish ten biofacies, each defined by a different set of dominant agglutinated species. Although biofacies frequently change up-section, there is an overall trend that is related to the progradational trend suggested by the lithofacies. Based on comparisons between lithofacies and biofacies, a palaeobathymetric zonation is established for the foraminifera. This zonation, the sparse macrofauna, and the lithofacies suggest that the interior sea was stratified in terms of salinity and dissolved oxygen levels, and the water was generally hyposaline. Most of the agglutinated foraminiferal species have analogous morphotypes present in modern confined estuaries and interior seas and this points to great conservatism in the evolutionary and ecological development of this component of interior-sea faunas. Aaptotoichus quinnaniensis sp. nov., an organic-cemented agglutinated foraminifer, is described from the Quinnanie Shale type section.     

Cretaceous Carterina (Foraminifera)

Carterina, the sole generic representative of the foraminiferal order Carterinida, has been reported in the literature only from the Holocene and Late Eocene. Organic test linings of this calcitic genus, with well-preserved spicular molds, have now been found in Campanian and Maastrichtian (and possibly Cenomanian) rocks from the Atlantic Ocean off northeastern Brazil. This finding shows that all extant orders of calcareous Foraminifera were present in the Cretaceous.     

Phylogeny and ultrastructure of Miliammina fusca: evidence for secondary loss of calcification in a Miliolid Foraminifer

The classification of the Foraminifera, a widely distributed group of largely marine protists, has traditionally been based on morphological characters. The most important of these are the composition and structure of the shell or "test." Here, we use both phylogenetic analysis of the genes for small subunit rRNA and beta-tubulin and ultrastructural analysis to document a reversion in wall type from more derived calcareous tests to an agglutinated test. These data indicate that the genus Miliammina, and possibly other members of the Rzehakinidae, should be placed in the Order Miliolida as opposed to their current assignment in Order Textulariida. We also address the effects this reversion may have had on the ability of rzehakinacids to effectively colonize marginal marine environments. Finally, the hypothesis that some multilocular agglutinated foraminiferans descended from calcareous lineages has implications for interpretation of the foraminiferal fossil record.     

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.     

Agglutinierte Foraminiferen aus Graptolithen-Schwarzschiefern des Llanvirnium (Ordovizium) von Plettenberg im Sauerland (Nordrhein-Westfalen,NW-Deutschland)

The Plettenberger Bänderschiefer (Ordovician, Lower Llanvirnian, Zone ofDidymograptus bifidus (Hcall) from the type locality at Plettenberg (Sauerland, NW-Germany) yielded a foraminiferal fauna consisting of primitive agglutinated species (Amphitremoida, Bathysiphon,?Raibosammina, ?Thekammina, Thurammina). Forming one of the stratigraphically oldest European foraminiferal assemblages, these taxa were washed out of an unconsolidated graptolite siltstone and represent a pelagic, oxygen-depleted environment.     

Differential dissolution of upper Cretaceous deep-sea benthonic foraminifers from the Angola Basin,South Atlantic Ocean

Material from the Deep Sea Drilling Project (DSDP) Site 527 from the Angola Basin, South Atlantic Ocean, has been analyzed to determine whether Upper Cretaceous benthonic foraminiferal taxa are differentially sensitive to calcite dissolution, and, if so, to rank their order of susceptibility. Two regimes of dissolution, established on the basis of the degree of planktonic foraminiferal fragmentation, representing stronger and less prominent dissolution within the section studied, were used as a framework for reference. A total of 60 calcareous and eight agglutinated benthonic foraminiferal taxa were identified at the species or genus level; of these, twenty-three calcareous and five agglutinated taxa were selected for the dissolution study. Relative abundance of each of the various taxa was tested statistically, using t-test, between dissolution regimes to assess the significance of the change induced by increased dissolution.Nuttallides truempyi andNeoeponides sp. intermediate form are interpreted as resistant to dissolution.Pullenia spp.,Alabamina sp. a,Anomalina sp. a,Praebulimina sp. fusiform, andNuttallinella sp. a are susceptible to dissolution. The majority of the taxa (16 in number) are unaffected by dissolution because they show no change between dissolution regimes. Among the agglutinated taxaGaudryina pyramidata is resistant to dissolution, whereas the remaining four taxa are unaffected by dissolution. At the level of superfamilies, one calcareous superfamily (Discorbacea) is resistant, two (Orbitoidacea and Cassidulinacea) are unaffected, and two (Nodosariacea and Buliminacea) are susceptible to dissolution.     

A family of titanium (IV) alkoxo complexes with N,O and O,O chelating ligands. Crystal structure of [Ti(O-i-Pr)2{2-(−)-menthoxo-pyridine}2]

In view of the wide applicability and versatility of titanium based Lewis acids in selective organic synthesis including asymmetric synthesis, we have synthesized a family of mono and polyatomic titanium derivatives. The polymetallic complexes prepared are bridged by pyridimine, quinone and triazine based ligands. The synthesis of [{Ti(O-i-Pr)₃(Oddbf)}₂] (1), [Ti(O-i-Pr)₂(Oddbf)₂] (2), [{Ti(O-i-Pr)₂(Oddbf)(OMent)}₂] (3) (ddbfO = 2,3-dihydro-2,2-dimethyl-benzofuranoxo; MentO = (1R,2S,5R)-(−)-menthoxo), [{Ti(O-i-Pr)₃(OMenpy)}₂] (4), [Ti(O-i-Pr)₂(OMenpy)₂] (5) (MenpyO = (1S,2S,5R)-(−)-menthoxo-pyridine); [{(Ti(OR)₃)₂L}_n] (RO = isopropoxo, (1R,2S,5R)-(−)-menthoxo) (6-11) and [{(Ti(O-i-Pr)₃)₃L}_n] (12) was accomplished from a Lewis acid such as Ti(O-i-Pr)₄, [{Ti(O-i-Pr)₃(OMent)}₂] or [Ti(OMent)₄] and chelating ligands (ddbfOH = 2,3-dihydro-2,2-dimethyl-benzofuranol; MenpyOH = (1R,2S,5R)-(−)-5-methyl-2-isopropyl-1-(2′-pyridinyl)cyclohexan-1-ol; LH₂ = 4,6-dihydroxy-2,5-diphenyl-pyrimidine, 2,4-dihydroxy-5,6-dimethyl-pyrimidine, 5,8-dihydroxy-1,4-napthoquinone, 2,5-dihydroxy-1,4-benzoquinone and LH₃ = cyanuric acid) that provide a rigid framework for the metal centre. The molecular structure of 5 has been determined by single crystal X-ray diffraction studies.     

Ecology of the Ogun River estuary,Nigeria

The distribution of benthonic communities (particularly Foraminifera) were studied from fourteen samples obtained from the Ogun River estuary and environs. Ten species of benthonic Foraminifera were identified; two of these constitute over 90% of the total foraminiferal population.Two broad biofacies are recognisable, namely the upper estuarine facies of Ammobaculites and the lower estuarine facies comprising arenaceous and calcereous forms with a preponderance of Ammonia beccarii (Linnaeus).Large populations of few species occur in the lower estuary, an area of weakly saline water with marked salinity fluctuations. The upper estuary on the other hand is sparsely populated and contains tests mainly of arenaeous Foraminifera. A few species are distinctive of particular facies but some are distributed throughout the estuary. Substrate is not a causal ecological factor, because sediments are similar in physical attributes throughout the estuary. Salinity and rate of sedimentation are among the more important factors affecting the distribution of all species. The low-energy nature of the environment is established by the abundance of faecal pellets and the fragility of the tests of the arenaceous Foraminifera.     

New organic-walled Foraminifera (Protista) from the ocean's deepest point, the Challenger Deep (western Pacific Ocean)

We describe four new species and a new genus of very small (< 500 µm) Foraminifera from the Challenger Deep, the deepest point in the world's oceans (10 896 m water depth). All have transparent, mainly organic test walls that incorporate some minute agglutinated mineral particles of various shapes and compositions. Nodellum aculeata sp. nov. has an elongate proloculus with a pointed proximal end followed by a long, tubular section. The genus Resigella is represented by two species: in R. laevis sp. nov. , the test comprises 3–4 elongate, oval to cylindrical chambers while R. bilocularis sp. nov. has an oval proloculus followed by a second, larger globular chamber. The fourth species, Conicotheca nigrans gen. et sp. nov. , is characterized by a tiny, elongate, conical test filled with dark stercomata. Except in C. nigrans, the test wall has a brownish tinge; energy-dispersive spectroscopy (EDS) suggests the presence of organically bound Fe in all species including C. nigrans. Scanning electron microscopy (SEM) combined with EDS reveals distinctive wall structures. In N. aculeata, the proloculus is strewn with tiny (< 0.7 µm), elongate grains. In this species and in R. laevis, the test surface (except for the proloculus) is covered with a carpet of minute (∼0.1 µm) finger-like projections, rather similar to the organic cement of agglutinated Foraminifera. In R. bilocularis, the larger second chamber often has a partial veneer of fine mineral grains of varying composition, as well as organic areas consisting of meshed strands. SEM images of these three species reveal flat, plate-like features that we interpret as clay particles. In C. nigrans, the wall is relatively featureless except where the surface is raised into hummocky mounds and scale-like features, again probably clay particles. We suggest that these species represent a distinctive group of ‘agglutinated’ Foraminifera in which the test is predominately organic. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 399–423.     

Chemical implantation of Group 4 cations on silica via cyclopentadienyl- and N,N-dialkylcarbamato derivatives

Chemical implantation of Group 4 cations [Ti(III), Ti(IV), Zr(IV), Hf(IV)] has been carried out under mild conditions by the reaction of polycyclopentadienyl- (MCp_n; M = Ti, n = 3, 4; M = Zr, Hf, n = 4), mixed cyclopentadienyl/N,N-dialkylcarbamato (ML_x(O₂CNEt₂)_y; M = Ti, L = Cp, C₅Me₅ (Cp*), x = 2, y = 1; M = Hf, L = Cp, x = 1, y = 3), and N,N-dialkylcarbamato (M(O₂CNR₂)_n, M = Ti, n = 3, R = ⁱPr; M = Ti, Hf, n = 4, R = Et; M = Zr, n = 4, R = ⁱPr) derivatives, with the silanol groups of amorphous silica. Cyclopentadiene/pentamethylcyclopentadiene and/or carbon dioxide and the secondary amine are released in the process. The amount of implanted cations depends on the metal and on the ligands, the pentamethylcyclopentadienyl complex being less reactive than the unsubstituted congener. The starting complexes and the final products have been characterized by EPR or by ¹³C CP-MAS NMR spectroscopy.     

Effect of salinity and seawater calcite saturation state on Mg and Sr incorporation in cultured planktonic foraminifera

Trace elements incorporated in planktonic foraminiferal test carbonate are commonly used as paleoproxies. For instance, Mg/Ca ratios are frequently used for reconstructing sea surface temperature and, together with the foraminiferal stable oxygen isotope ratios, are also used as paleosalinity proxy. Foraminiferal Sr/Ca ratios constitute another example of the application of trace elements in paleostudies since they may reflect the Sr/Ca values of seawater. However, over the past few decades it has been proven that the incorporation of trace elements in foraminiferal calcite is controlled by more than one environmental parameter. To quantify the effect of salinity on Mg and Sr incorporation planktonic foraminifera Globigerinoides sacculifer (sensu stricto) were grown in the laboratory under different environmental conditions. Laboratory experiments allowed us to separate a direct salinity effect from a possible independent impact through differences in the calcite saturation state of the seawater (Ω). Although the temperature effect is more important than the salinity effect, a change of 4 salinity units is equivalent to a 1 °C bias on Mg/Ca-based temperatures. This effect of salinity on Mg incorporation is minor. However, when using Mg/Ca-based temperatures in combination with foraminiferal δ¹⁸O to calculate salinity, it cannot be neglected. The present study shows salinity as the overriding control on Mg incorporation within the range of Ω studied (Ω between 5.25 and 6.50; [CO₃²⁻] between 218 and 270 μmol/kg) at a constant temperature of 26 °C. In contrast, Ω appears to be the main control on foraminiferal Sr incorporation (0.10 mmol/mol per 100 µmol/kg rise in [CO₃²⁻]), whereas salinity has a non significant influence on Sr/Ca.     

Sediment oxygen demand and benthic foraminiferal faunas in the Arabian Gulf: A test of the method on a siliciclastic substrate

In this study, we investigated the relationship between environmental parameters (water and sediment) and benthic foraminiferal assemblages found in nearshore siliciclastic sediment in the Arabian Gulf. Nearshore marine water and sediment samples were collected from a beach on the Gulf of Bahrain located south of Al Khobar, Saudi Arabia. The water samples were analyzed for biochemical oxygen demand (BOD₅) and other chemical analyses. The sediment samples were tested for sediment oxygen demand (SOD) and heavy metal analysis. Results showed the BOD₅ levels were below the detection limit (<1 ppm), while the mean SOD value was 0.97 ± 0.08 g/m²·day. The water and sediments were unpolluted and free of eutrophic enrichment, while the sediment was anoxic. The two most common genera in the benthic foraminiferal assemblage, Ammonia and Elphidium, are typical of shallow water sandy substrates. This is the first reported comparison between SOD and benthic foraminiferal assemblages.     

The evolutionary landscape of the Mycobacterium tuberculosis genome

Mycobacterium tuberculosis is one of the most deadly human pathogens. The major mechanism for the adaptations of M. tuberculosis is nucleotide substitution. Previous studies have relied on the nonsynonymous-to-synonymous substitution rate (d_N/d_S) ratio as a measurement of selective constraint based on the assumed selective neutrality of synonymous substitutions. However, this assumption has been shown to be untrue in many cases. In this study, we used the substitution rate in intergenic regions (d_i) of the M. tuberculosis genome as the neutral reference, and conducted a genome-wide profiling for d_i, d_S, and the rate of insertions/deletions (indel rate) as compared with the genome of M. canettii using a 50 kb sliding window. We demonstrate significant variations in all of the three evolutionary measurements across the M. tuberculosis genome, even for regions in close vicinity. Furthermore, we identified a total of 233 genes with their d_S deviating significantly from d_i within the same window. Interestingly, d_S also varies significantly in some of the windows, indicating drastic changes in mutation rate and/or selection pressure within relatively short distances in the M. tuberculosis genome. Importantly, our results indicate that selection on synonymous substitutions is common in the M. tuberculosis genome. Therefore, the d_N/d_S ratio test must be applied carefully for measuring selection pressure on M. tuberculosis genes.