Dinoflagellate cyst accumulation rates of ODP Hole 146-893A from Santa Barbara Basin

The dinoflagellate cyst record from Ocean Drilling Program Hole 893A, Santa Barbara Basin, southern California, is examined at millennial-scale resolution for the past 40 kyr. Changes in cyst abundance, composition of cyst assemblages, and their diversity reflect major shifts in climate and ocean circulation in the region over this time interval. Throughout the sequence, dinoflagellate cyst assemblages are dominated by heterotrophic dinoflagellates. Brigantedinium spp. and other upwelling-related taxa such as Echinidinium and Protoperidinium americanum are abundant, indicating the continued influence of coastal upwelling on the basin during the late Quaternary. A significant increase in cyst accumulation rates is seen during the Holocene and, to a lesser extent, during shorter warming events such as Bolling/Allerod and Dansgaard-Oeschger interstadials, implying enhanced marine productivity during these periods. Cyst diversity is high during the Holocene. An increase in abundance of cysts produced by autotrophic dinoflagellates in the late Holocene suggests enhanced input of warm, nutrient-rich waters. In contrast, cyst assemblages from the Last Glacial Maximum exhibit a relatively low diversity and an increase in the cysts of heterotrophic dinoflagellates, in particular Selenopemphix nephroides. The presence of this taxon in association with Brigantedinium spp. implies substantial cooling of surface waters in the Santa Barbara Basin at that time.

Effects of fire on the structure and composition of open eucalypt forests

Fires are integral to the healthy functioning of most ecosystems and are often poorly understood in policy and management, however, the relationship between floristic composition and habitat structure is intrinsically linked, particularly after fire. The aim of this study was to test whether the variability of habitat structure or floristic composition and abundance in forests at a regional scale can be explained in terms of fire frequency using historical data and experimental prescribed burns. We tested this hypothesis in open eucalypt forests of Fraser Island off the east coast of Australia. Fraser Island dunes show progressive stages in plant succession as access to nutrients decreases across the Island. We found that fire frequency was not a good predictor of floristic composition or abundance across dune systems; rather, its affects were dune specific. In contrast, habitat structure was strongly influenced by fire frequency, independent of dune system. A dense understorey occurred in frequently burnt areas, whereas infrequently burnt areas had a more even distribution of plant heights. Plant communities returned to pre-burn levels of composition and abundances within 6 months of a fire and frequently burnt areas were dominated by early successional species of plant. These ecosystems were characterized by low diversity and frequently burnt areas on the east coast were dominated by Pteridium. Greater midstorey canopy cover in low frequency areas reduces light penetration and allows other species to compete more effectively with Pteridium. Our results strongly indicate that frequent fires on the Island have resulted in a decrease in relative diversity through dominance of several species. Prescribed fire represents a powerful management tool to shape habitat structure and complexity of Fraser Island forests.

(Table T2) Relative signal intensity of intact polar lipids in sediments from ODP Sites 207-1257 and 207-1258

We report results from the analysis of intact polar lipids (IPLs) in sediments from Ocean Drilling Program Sites 1257 and 1258. IPLs, constituting the cell membranes of living organisms, were detected in organic-lean sediments but not in underlying organic-rich black shales. Microbial activity in organic-lean sediments is likely due to sulfate-dependent oxidation of methane whereas difficulties detecting IPLs in black shales are interpreted to result from unfavorable signal-to-noise ratios due to low cell concentrations in combination with extremely high analytical noise created by uncharacterized organic matrix. IPLs found are consistent with a low-diversity community of archaea and bacteria. The concentrations of IPLs are more than one order of magnitude lower than those in Neogene deep subsurface sediments at the Peruvian margin, suggestive of significantly lower cell concentrations in Demerara Rise. This finding is consistent with inferred low rates of subsurface microbial activity.

(Table T1) Abundance of radiolarian skeletons in scrape samples of ODP Hole 178-1098B

Palmer Deep is a series of three glacially overdeepened basins on the Antarctic Peninsula shelf, ~20 km southwest of Anvers Island. Site 1098 (64°51.72'S, 64°12.48'W) was drilled in the shallowest basin, Basin I, at 1012 m water depth. The sediment recovered was primarily laminated, siliceous, biogenic, pelagic muds alternating with siliciclastic hemipelagic sediments (Barker, Camerlenghi, Acton, et al., 1999). Sedimentation rates of 0.1725 cm/yr in the upper 25 m and 0.7-0.80 cm/yr in the lower 25 m of the core have been estimated from 14C (Domack et al., 2001). The oldest datable sediments have an age of ~13 ka and were underlain by diamicton sediments of the last glacial maximum (Domack et al., 2001). The large-scale water-mass distribution and circulation in the vicinity of Palmer Deep is dominated by Circumpolar Deep Water (CDW) below 200 m (Hofmann et al., 1996). Palmer Deep is too far from the coast to be influenced by glacial meltwater and cold-tongue generation associated with it (Domack and Williams, 1990; Dixon and Domack, 1991). Circulation patterns in the Palmer Deep area are not well understood, but evidence suggests southward flow across Palmer Deep from Anvers Island to Renaud Island (Kock and Stein, 1978). The water south of Anvers Island is nearly open with loose pack ice from February through May. The area is covered with sea ice beginning in June (Gloersen et al., 1992; Leventer et al., 1996). Micropaleontologic data from the work of Leventer et al. (1996) on a 9-m piston core has revealed circulation and climate patterns for the past 3700 yr in the Palmer Deep. The benthic foraminifer assemblage is dominated by two taxa, Bulimina aculeata and Bolivina pseudopunctata, which are inversely related. High relative abundances of B. aculeata occur cyclically over a period of ~230 yr. The assemblage associated with high abundance of B. aculeata in Palmer Deep resembles that from the Bellingshausen shelf, which is associated with CDW. In addition to the faunal evidence, hydrographic data indicate incursions of CDW into Palmer Deep (Leventer et al., 1996). A distinctive diatom assemblage dominated by a single genus was associated with peaks in B. aculeata, whereas a few different assemblages were associated with lows in B. aculeata. Leventer et al. (1996) interpreted the variability in diatom assemblages as an indication of changes in productivity associated with changes in water column stability. Abelmann and Gowing (1997) studied the horizontal and vertical distributions of radiolarians in the Atlantic sector of the Southern Ocean. They show that the spatial distribution of radiolarian assemblages reflects hydrographic boundaries. In a transect from the subtropical Atlantic to polar Antarctic zones, radiolarians in the upper 1000 m of the water column occurred in distinct surface and deep-living assemblages related to water depth, temperature, salinity, and nutrient content. Living assemblages resembled those preserved in underlying surface sediments (Abelmann and Gowing, 1997). Circumantarctic coastal sediments from neritic environments contained a distinctive assemblage dominated by the Phormacantha hystrix/Plectacantha oikiskos group and Rhizoplegma boreale (Nishimura et al., 1997). Low diversity and species compositions distinguished the coastal sediments from the typical pelagic Antarctic assemblages. Factors that controlled the assemblages were water depth, proximity to the coast, occurrence of sea ice, and steepness of topography, rather than temperature and salinity. Nishimura et al. (1997) found a gradient of sorts from deep-water sites containing diverse assemblages typical of pelagic environments to coastal sites with low diversity assemblages dominated by P. hystrix/P. oikiskos group and R. boreale. In general, sites between these two extremes had increased proportions of the coastal assemblage with decreasing water depth (Nishimura et al., 1997). At a site near Hole 1098 (GC905), they showed that the relative abundance of the coastal assemblage increased downcore (Nishimura et al., 1997). The purpose of the research presented here was to make a cursory investigation into the radiolarian assemblages as possible paleoenvironmental indicators.

Genomic consequences of mating system evolution in the Pacific coastal dune endemic, Abronia umbellata (Nyctaginaceae)

The advent of next-generation sequencing has significantly reduced the cost of obtaining large-scale genetic resources, opening the door for genomic studies of non-model but ecologically interesting species. The shift in mating system, from outcrossing to selfing, has occurred thousands of times in angiosperms and is accompanied by profound changes in the population genetics and ecology of a species. A large body of work has been devoted to understanding why the shift occurs and the impact of the shift on the genetics of the resulting selfing populations, however, the causes and consequences of the transition to selfing involve a complicated interaction of genetic and demographic factors which are difficult to untangle. Abronia umbellata is a Pacific coastal dune endemic which displays a striking shift in mating system across its geographic range, with large-flowered outcrossing populations south of San Francisco and small-flowered selfing populations to the north. Abronia umbellata is an attractive model system for the study of mating system transitions because the shift appears to be recent and therefore less obscured by post-shift processes, it has a near one-dimensional geographic range which simplifies analysis and interpretation, and demographic data has been collected for many of the populations. In this study, we generated transcriptome-level data for 12 plants including individuals from both subspecies, along with a resequencing study of 48 individuals from populations across the range. The genetic analysis revealed a recent transition to selfing involving a drastic reduction in genetic diversity in the selfing lineage, potentially indicative of a recent population bottleneck and a transition to selfing due to reproductive assurance. Interestingly, the genetic structure of the populations was not coincident with the current subspecies demarcation, and two large-flowered populations were classified with the selfing subspecies, suggesting a potential need for re-evaluation of the current subspecies classification. Our finding of low diversity in selfing populations may also have implications for the conservation value of the threatened selfing subspecies.

Comportamento geoquímico do fósforo em sistemas lacustres tropicais

Considerando a multiplicidade dos impactos ambientais associados às albufeiras pretendeu-se verificar a disponibilidade da utilização, como recurso agrícola, dos sedimentos desenvolvidos sob clima tropical. Estudaram-se duas albufeiras, Três Marias e Tucuruí situadas no Brasil, cujos materiais depositados apresentam forte componente siltosa e argilosa. Possuindo valores de matéria orgânica considerados médios, as amostras têm valores de pH (H20) ácidos, elevados teores de Fe203 e Ah03 e baixa diversidade de minerais argilosos (apenas ilite e caulinite). Apesar das quantidades totais de fósforo serem significativas, os valores da forma disponível deste elemento não ultrapassam o 1%. Através da análise de clusters, correlações de Pearson e fraccionamento químico do fósforo inorgânico, concluiu-se que o elemento que influencia a retenção deste elemento nos sedimentos é o ferro. Embora com baixos teores de fósforo sob forma imediatamente disponível, os sedimentos apresentam boa qualidade para fins agrícolas pois, para diferentes variáveis, ultrapassam os valores médios dos solos minerais. ABSTRACT; considering the diversity of environmental impacts related to dam reservoirs, this study aims at verifying the suitability of sediments accumulated in tropical climates, as agricultural resource. We have studied two Brazilian reservoirs, Três Marias and Tucuruí, whose sediments were classified, respectively, as silty clay and clayey silt. The accumulated material has medium contents of organic matter, acid values of pH(H20), high contents of Fe203 and Al203, and low diversity of clay mineral groups (only illite and kaolinite). Although sediments have significant amounts of phosphorus, the available form of this element never exceeds 1%. Data on statistical analysis of clusters, Pearson correlations and chemical fractionation of inorganic phosphorus, indicates that phosphorus adsorption capacity of sediments is predominantly associated with Fe. Even considering the low levels of the readily available form of phosphorus, for most variables, sediments exceed medium values for mineral soils, making this material advantageous for plant nutrition.

Biology of Grapsus grapsus (LINNAEUS, 1758) (Brachyura, Grapsidae) in the Saint Peter and Saint Paul Archipelago, Equatorial Atlantic Ocean

Eleven expeditions were undertaken to the Saint Peter and Saint Paul Archipelago to study the reproductive biology of Grapsus grapsus, providing additional information on limb mutilation and carapace colour. MATURE software was used to estimate morphological maturity, while gonadal analyses were conducted to estimate physiological maturity. The puberty moult took place at larger size in males (51.4 mm of carapace length) than in females (33.8 mm), while physiological maturity occurred at a similar size in males (38.4 mm) and in females (33.4 mm). Above 50 mm, the proportion of red males increased in the population, indicating that functional maturity is also related to colour pattern. Small habitat and high local population density contributed to the high rate of cannibalism. The low diversity of food items, absence of predators of large crabs and high geographic isolation are the determinants of unique behavioural and biological characteristics observed in the G. grapsus population.

Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year

Background: Disease flares of established atopic dermatitis (AD) are generally associated with a low-diversity skin microbiota and Staphylococcus aureus dominance. The temporal transition of the skin microbiome between early infancy and the dysbiosis of established AD is unknown. Methods: We randomly selected 50 children from the Cork Babies After SCOPE: Evaluating the Longitudinal Impact Using Neurological and Nutritional Endpoints (BASELINE) longitudinal birth cohort for microbiome sampling at 3 points in the first 6 months of life at 4 skin sites relevant to AD: the antecubital and popliteal fossae, nasal tip, and cheek. We identified 10 infants with AD and compared them with 10 randomly selected control infants with no AD. We performed bacterial 16S ribosomal RNA sequencing and analysis directly from clinical samples. Results: Bacterial community structures and diversity shifted over time, suggesting that age strongly affects the skin microbiome in infants. Unlike established AD, these patients with infantile AD did not have noticeably dysbiotic communities before or with disease and were not colonized by S aureus. In comparing patients and control subjects, infants who had affected skin at month 12 had statistically significant differences in bacterial communities on the antecubital fossa at month 2 compared with infants who were unaffected at month 12. In particular, commensal staphylococci were significantly less abundant in infants affected at month 12, suggesting that this genus might protect against the later development of AD. Conclusions: This study suggests that 12-month-old infants with AD were not colonized with S aureus before having AD. Additional studies are needed to confirm whether colonization with commensal staphylococci modulates skin immunity and attenuates development of AD.

Diets of the sole Solea vulgaris Quensel, 1806 and Solea senegalensis Kaup, 1858 in the lower estuary of the Guadiana River (Algarve, southern Portugal): Preliminary results

The feeding habits of two major species of sole, the common sole Solea vulgaris Quensel, 1806 and the Senegalese sole Solea senegalensis Kaup, 1858 were studied in the lower estuary of the Guadiana River (Algarve, southern Portugal). An evaluation of the number, weight, and feeding coefficient of prey types showed that S. vulgaris feed on a limited variety of prey (only Polychaeta and Tanaidacea) and present low-intensity feeding activity, with small differences in diet between seasons. S. senegalensis also have a low-diversity diet (with only one more taxa, Amphipoda), but exhibit more intense feeding activity which varies seasonally, although with little seasonal variation in the relative importance of the main preys. The diet composition of these two species suggests feeding specialization.

Low symbiont diversity in southern Great Barrier Reef corals, relative to those of the Caribbean

The specific identity of endosymbiotic dinoflagellates (Symbiodinium spp.) from most zooxanthellate corals is unknown. In a survey of symbiotic cnidarians from the southern Great Barrier Reef (GBR), 23 symbiont types were identified from 86 host species representing 40 genera. A majority (>85%) of these symbionts belong to a single phylogenetic clade or subgenus (C) composed of closely related (as assessed by sequence data from the internal transcribed spacer region and the ribosomal large subunit gene), yet ecologically and physiologically distinct, types. A few prevalent symbiont types, or generalists, dominate the coral community of the southern GBR, whereas many rare and/or specific symbionts, or specialists, are found uniquely within certain host taxa. The comparison of symbiont diversity between southern GBR and Caribbean reefs shows an inverse relationship between coral diversity and symbiont diversity, perhaps as a consequence of more-rapid diversification of Caribbean symbionts. Among clade C types, generalists C1 and C3 are common to both Caribbean and southern GBR symbiont assemblages, whereas the rest are regionally endemic. Possibly because of environmental changes in the Caribbean after geographic isolation through the Quaternary period, a high proportion of Caribbean fauna associate with symbiont taxa from two other distantly related Symbiodinium clades (A and B) that rarely occur in Pacific hosts. The resilience of Porites spp. and the resistance of Montipora digitata to thermal stress and bleaching are partially explained by their association with a thermally tolerant symbiont type, whereas the indiscriminant widespread bleaching and death among certain Pacific corals, during El Nino Southern Oscillation events, are influenced by associations with symbionts possessing higher sensitivity to thermal stress.

Low genetic diversity in Wolbachia-Infected Culex quinquefasciatus (Diptera: Culicidae) from Brazil and Argentina

Culex quinquefasciatus is a vector of human pathogens, including filarial nematodes and several viruses. Although its epidemiological relevance is known to vary across geographical regions, an understanding of its population genetic structure is still incipient. In light of this, we evaluated the genetic diversity of Cx. quinquefasciatus and Cx. pipiens x Cx. quinquefasciatus hybrids collected from nine localities in Brazil and one site in Argentina. We used mitochondrial genes cox1 and nd4, along with the coxA and wsp genes of the maternally-inherited Wolbachia endosymbiont. The nd4 fragment was invariant between samples, whilst cox1 exhibited four haplotypes that separated two types of Cx. quinquefasciatus, one clustered in southern Brazil. Low sequence diversity was generally observed, being discussed. Both Brazilian and Argentinian mosquitoes were infected with a single Wolbachia strain. As reported in previous studies with these populations, cox1 and nd4 diversity is not congruent with the population structure revealed by nuclear markers or alar morphology. Future Cx. quinquefasciatus research should, if possible, evaluate mtDNA diversity in light of other markers.

On high-rate full-diversity 2x2 space-time codes with low-complexity optimum detection

The 2×2 MIMO profiles included in Mobile WiMAX specifications are Alamouti’s space-time code (STC) fortransmit diversity and spatial multiplexing (SM). The former hasfull diversity and the latter has full rate, but neither of them hasboth of these desired features. An alternative 2×2 STC, which is both full rate and full diversity, is the Golden code. It is the best known 2×2 STC, but it has a high decoding complexity. Recently, the attention was turned to the decoder complexity, this issue wasincluded in the STC design criteria, and different STCs wereproposed. In this paper, we first present a full-rate full-diversity2×2 STC design leading to substantially lower complexity ofthe optimum detector compared to the Golden code with only a slight performance loss. We provide the general optimized form of this STC and show that this scheme achieves the diversitymultiplexing frontier for square QAM signal constellations. Then, we present a variant of the proposed STC, which provides a further decrease in the detection complexity with a rate reduction of 25% and show that this provides an interesting trade-off between the Alamouti scheme and SM.

Generalized low-density codes with BCH constituents for full-diversity near-outage performance

A new graph-based construction of generalized low density codes (GLD-Tanner) with binary BCH constituents is described. The proposed family of GLD codes is optimal on block erasure channels and quasi-optimal on block fading channels. Optimality is considered in the outage probability sense. Aclassical GLD code for ergodic channels (e.g., the AWGN channel,the i.i.d. Rayleigh fading channel, and the i.i.d. binary erasure channel) is built by connecting bitnodes and subcode nodes via a unique random edge permutation. In the proposed construction of full-diversity GLD codes (referred to as root GLD), bitnodes are divided into 4 classes, subcodes are divided into 2 classes, and finally both sides of the Tanner graph are linked via 4 random edge permutations. The study focuses on non-ergodic channels with two states and can be easily extended to channels with 3 states or more.

High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are ecologically important root symbionts of most terrestrial plants. Ecological studies of AMF have concentrated on differences between species; largely assuming little variability within AMF species. Although AMF are clonal, they have evolved to contain a surprisingly high within-species genetic variability, and genetically different nuclei can coexist within individual spores. These traits could potentially lead to within-population genetic variation, causing differences in physiology and symbiotic function in AMF populations, a consequence that has been largely neglected. We found highly significant genetic and phenotypic variation among isolates of a population of Glomus intraradices but relatively low total observed genetic diversity. Because we maintained the isolated population in a constant environment, phenotypic variation can be considered as variation in quantitative genetic traits. In view of the large genetic differences among isolates by randomly sampling two individual spores, <50% of the total observed population genetic diversity is represented. Adding an isolate from a distant population did not increase total observed genetic diversity. Genetic variation exceeded variation in quantitative genetic traits, indicating that selection acted on the population to retain similar traits, which might be because of the multigenomic nature of AMF, where considerable genetic redundancy could buffer the effects of changes in the genetic content of phenotypic traits. These results have direct implications for ecological research and for studying AMF genes, improving commercial AMF inoculum, and understanding evolutionary mechanisms in multigenomic organisms.