Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle Findings: Plankton WP2 replicate net hauls (200 µm) were taken at the Western Channel Observatory long-term monitoring station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,042 sequences were obtained for all samples. The sequences clustered in to 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 138 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 75 taxonomic groups. Conclusions: The percentage of OTUs assigned to major eukaryotic taxonomic groups broadly aligns between the metagenetic and morphological analysis and are dominated by Copepoda. However, the metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for estimating diversity and species richness of zooplankton communities.

Planktonic foraminifera in the Maastrichtian of Hor-Hahar

The lengthy warm, stable climate of the Cretaceous terminated in the Campanian with a cooling trend, interrupted in the early and latest Maastrichtian by two events of global warming, at ~70-68 Ma and at 65.78-65.57 Ma. These climatic oscillations had a profound effect on pelagic ecosystems, especially on planktic foraminiferal populations. Here we compare biotic responses in the tropical-subtropical (Tethyan) open ocean and mesotrophic (Zin Valley, Israel) and oligotrophic (Tunisia) slopes, which correlate directly with global warming and cooling. The two warming events coincide with blooms of Guembelitria, an extreme opportunist genus best known as the main survivor of the Cretaceous-Paleogene (K-Pg) catastrophe. In the Maastrichtian, Guembelitria bloomed in the uppermost surface water above shelf and slope environments but failed to reach the open ocean as it did at K-Pg. The coldest interval of the late Maastrichtian (~68-65.78 Ma) is marked by an acme of the otherwise rare species Gansserina gansseri, a deep-dwelling keeled globotruncanid. The G. gansseri acme event can be traced from the deep ocean even onto the Tethyan slope, marking copious production and circulation of cold intermediate water. This acme is abruptly terminated by extinction of the species, a dramatic reversal attributed to a short-term global warming episode. This extinction corresponds precisely with the second bloom of Guembelitria that began ~300 kyr prior to the K-Pg event. The antithetical relationship between blooming of Guembelitria and the G. gansseri acme reflects planktic foraminiferal sensitivity to warm-cool-warm-cool climatic oscillations marking the end of the Cretaceous.

Organic-walled dinoflagellate cysts analysis and statistical analysis of 116 surface sediment samples from the eastern Indian Ocean

Assemblages of organic-walled dinoflagellate cysts (dinocysts) from 116 marine surface samples have been analysed to assess the relationship between the spatial distribution of dinocysts and modern local environmental conditions [e.g. sea surface temperature (SST), sea surface salinity (SSS), productivity] in the eastern Indian Ocean. Results from the percentage analysis and statistical methods such as multivariate ordination analysis and end-member modelling, indicate the existence of three distinct environmental and oceanographic regions in the study area. Region 1 is located in western and eastern Indonesia and controlled by high SSTs and a low nutrient content of the surface waters. The Indonesian Throughflow (ITF) region (Region 2) is dominated by heterotrophic dinocyst species reflecting the region's high productivity. Region 3 is encompassing the area offshore north-west and west Australia which is characterised by the water masses of the Leeuwin Current, a saline and nutrient depleted southward current featuring energetic eddies.

Taxonomic lists and abundances of the Lower Miocene bivalve assemblages of the Vives quarry (Meilhan, SW France)

Biodiversity estimates through geological times are difficult because of taphonomic perturbations that affect sedimentary records. Pristine shell assemblages, however, allow for calibration of past diversity. Diversity structures of two exceptionally preserved Miocene bivalve assemblages are quantitatively determined, compared with recent communities and used as paleoenvironmental proxy. The extremely rich assemblages were collected in Aquitanian (Early Miocene) carbonate sands of the Vives Quarry (Meilhan, SW France). Both paleontological and sedimentological data indicate a coral patch-reef environment, which deposits were affected by transport processes. Among two samples more than 28.000 shells were counted and 135 species identified. Sample Vives 1 is interpreted as a proximal debris flow and Sample Vives 2 as a sandy shoreface/foreshore environment influenced by storms. The two Vives assemblages have a similar diversity structure despite facies differences. Rarefaction curves level off at ~600 shells. The rare species account for more than 80 % of the species pool. The high values of PIE diversity index suggest a relatively high species richness and an even distribution of abundance of the most common species within the assemblages. The fossil data are compared to death shell assemblages (family level) of a modern reefal setting (Touho area, New Caledonia). The shape of the rarefaction curves and PIE indices of Meilhan fossil assemblages compare well to modern data, especially those of deep (>10 m water depth), sandy depositional environments found downward the reef slope (slope and pass settings). In addition to primary ecological signals, the similarity of the Vives samples and the Recent deep samples derives from taphonomic processes. This assumption is supported by sedimentological and paleontological observations. Sediment transports gather allochthonous and in situ materials leading to mixing of various ecological niches. Such taphonomic processes are recorded in the diversity metrics. Environmental mixing and time-averaging of the shell assemblages disturb the preservation of local-scale diversity properties but favour the sampling of the regional-scale diversity.

Avian occupancy probabilities, vegetation structure, and presence of Northern Bobwhite (Colinus virginianus) in eastern and central Oklahoma (2009-2011)

Changes in land use and land cover throughout the eastern half of North America have caused substantial declines in populations of birds that rely on grassland and shrubland vegetation types, including socially and economically important game birds such as the Northern Bobwhite (Colinus virginianus; hereafter bobwhites). As much attention is focused on habitat management and restoration for bobwhites, they may act as an umbrella species for other bird species with similar habitat requirements. We quantified the relationship of bobwhites to the overall bird community and evaluated the potential for bobwhites to act as an umbrella species for grassland and shrubland birds. We monitored bobwhite presence and bird community composition within 31 sample units on selected private lands in the south-central United States from 2009 to 2011. Bobwhites were strongly associated with other grassland and shrubland birds and were a significant positive predictor for 9 species. Seven of these, including Bell's Vireo (Vireo bellii), Dicksissel (Spiza americana), and Grasshopper Sparrow (Ammodramus savannarum), are listed as species of conservation concern. Species richness and occupancy probability of grassland and shrubland birds were higher relative to the overall bird community in sample units occupied by bobwhites. Our results show that bobwhites can act as an umbrella species for grassland and shrubland birds, although the specific species in any given situation will depend on region and management objectives. These results suggest that efficiency in conservation funding can be increased by using public interest in popular game species to leverage resources to meet multiple conservation objectives.

Abundance of mesozooplankton in central Adriatic Sea from 1959 to 1991 at Stoncica Station

The dataset is composed of 50 years of approximately monthly mesozooplankton sampling at station Stoncica. The volume of filtered water was estimated assuming 70% efficiency of the Hensen 330 micrometer mesh size net according to Laevastu (1958). Subsamples amounting to 1/20 of the catch were counted for the most representative groups. The whole catch was examined for rare species.The results in the datatables are recalculated to (#/m**3).

Mesocosm experiment on warming and acidification effects on phytoplankton composition and cell size

While the isolated responses of marine phytoplankton to climate warming and to ocean acidification have been studies intensively, studies on the combined effect of both aspects of Global Change are still scarce. Therefore, we performed a mesocosm experiment with a factorial combination of temperature (9 and 15°C) and pCO2 (560 ppm and 1400 ppm) with a natural autumn plankton community from the western Baltic Sea. Temporal trajectories of total biomass and of the biomass of the most important higher taxa followed similar patterns in all treatments. When averaging over the entire time course, phytoplankton biomass decreased with warming and increased with CO2 under warm conditions. The contribution of the two dominant higher phytoplankton taxa (diatoms and cryptophytes) and of the 4 most important species (3 diatoms, 1 cryptophyte) did not respond to the experimental treatments. Taxonomic composition of phytoplankton showed only responses at the level of subdominant and rare species. Phytoplankton cell sizes increased with CO2 addition and decreased with warming. Both effects were stronger for larger species. Warming effects were stronger than CO2 effects and tended to counteract each other. Phytoplankton communities without calcifying species and exposed to short-term variation of COO2 seem to be rather resistant to ocean acidification.

Coccolithophore abundance and biometry in the South China Sea, 2014

Coccolithophore contributions to the global marine carbon cycle are regulated by the calcite content of their scales (coccoliths), and the relative cellular levels of photosynthesis and calcification. All three of these factors vary between coccolithophore species, and with response to the growth environment. Here, water samples were collected in the northern basin of the South China Sea (SCS) during summer 2014 in order to examine how environmental variability influenced species composition and cellular levels of calcite content. The vertical structure of the coccolithophore community was strongly regulated by mesoscale eddies. All living coccolithophores produced within the euphotic zone (1 % of surface irradiance), and Florisphaera profunda was a substantial coccolithophore and coccolith-calcite producer in the Deep Chlorophyll-a Maximum (DCM), especially in most oligotrophic anti-cyclonic eddy centers. Placolith-bearing coccolithophores, plus F. profunda, and other larger and numerically rare species made almost equal contributions to coccolith-based calcite in the water column. For Emiliania huxleyi biometry measurements, coccolith size positively correlated with nutrients, and it is suggested that coccolith length is influenced by nutrient and light related growth rates. However, larger sized coccoliths were related to low pH and calcite saturation, although it is not a simple cause and effect relationship. Genotypic or ecophenotypic variation may also be linked to coccolith size variation.

(Table 2) Radiolaria species in nodule samples from the Clarion-Clipperton province, Pacific Ocean

Radiolaria were studied in 19 manganese nodules raised from the bottom. The nodules occurred mainly on the surface of thin Quaternary sediments covering Tertiary deposits of various ages (Middle Eocene to Early Miocene). Radiolaria in nodule cores and in inner and surface layers were studied. We found 85 radiolaria species and groups of species. Usually 1-4 to 6-19 radiolaria species were detected in each of the samples. Species belonging to Middle Eocene, Late Miocene to Early Oligocene, and Oligocene to Early Miocene were found. Rare Neogene species were revealed only in fractured surface layers. Age of the nodules is mainly Oligocene. Seismic waves cause sediment vibration, loosening disintegration, and removal of suspension by bottom currents. The vibration effect causes ancient nodules to float up to the surface of Quaternary sediment. This hypothesis suggests the reason for characteristics of the Clarion-Clipperton zone: regional stratigraphic hiatus, accumulation of residual fields of nodules, and the ''floating up'' of nodules to the surface of the Quaternary sediments.

Calcareous nannofossil species richness across the Paleocene-Eocene Thermal Maximum

The Paleocene-Eocene Thermal Maximum (PETM, ~5 million years ago) was an interval of global warming and ocean acidification attributed to rapid release and oxidation of buried carbon. We show that the onset of the PETM coincided with a prominent increase in the origination and extinction of calcareous phytoplankton. Yet major perturbation of the surface-water saturation state across the PETM was not detrimental to the survival of most calcareous nannoplankton taxa and did not impart a calcification or ecological bias to the pattern of evolutionary turnover. Instead, the rate of environmental change appears to have driven turnover, preferentially affecting rare taxa living close to their viable limits.

Major, trace and rare earth elements and minerals at DSDP Legs 69-70 Holes

We obtained major and trace element data on 113 samples from basalts drilled during DSDP Legs 69 and 70 in the Costa Rica Rift area. The majority have major and trace element characteristics typical of ocean-ridge tholeiities. Most of the basalts are relatively MgO rich (MgO > 8 wt.%) and have Mg values (MgO/MgO + 0.85FeO x 100) of about 53, characteristics that clearly indicate that the various magmas underwent only a small amount of crystal fractionation before being erupted onto the seafloor. According to their normative mineralogies, the rocks are olivine tholeiites. A few samples plot close to the diopside-hypersthene join of the projected basalt tetrahedron. Except for basalts from two thin intervals in Hole 504B, which differ significantly from all the other basalts of the hole, practically no chemical downhole variation could be established. In the two exceptional intervals, both TiO2 and P2O5 contents are markedly enriched among the major oxides. The trace elements in these intervals are distinguished by relatively high contents of magmatophile elements and have flat to enriched chondrite-normalized distribution patterns of light rare earth elements (LREE). Most of the rocks outside these intervals are strongly depleted in large-ionlithophile (LIL) elements and LREE. We offer no satisfactory hypothesis for the origin of these basalts at this time. They might have originated within pockets of mantle materials that were more primitive than the LIL-element-depleted magmas that were the source of the other basalts. A significant change with depth in the type of alteration occurs in the 561 meters of basalt cored in Hole 504B. According to the behavior of such alteration-sensitive species as K2O, H2O-, CO2, S, Tl, and the iron oxidation ratio, the alteration is oxidative in the upper part and nonoxidative or even reducing in the lower part. The oxidative alteration may have resulted from low temperature basalt/seawater interaction, whereas hydrothermal solutions may be responsible for the nonoxidative alteration.

Foraminiferal species and dissolution index at DSDP Hole 78-541

The calcite compensation depth (CCD) fluctuates as a result of changes in the water-mass system, thereby producing a distinct dissolution pattern. Differential dissolution changes the composition of the foraminiferal assemblages, reflecting the depositional environment in respect to the fluctuating CCD. The dissolution pattern for the comparatively shallow Site 541 on the Barbados Ridge indicates a depositional environment mostly above the CCD, but below the foraminiferal lysocline during the late Miocene to early Pleistocene. In contrast, sediments of the deeper-water Site 543 indicate a depositional environment above the CCD during the late Pliocene to early Pleistocene only. Furthermore, similarities in the dissolution pattern of corresponding time intervals of Site 541 (represented by superimposed faulted intervals termed Tectonic Units A and B) are recognizable. Sediments deposited clearly above the foraminiferal lysocline are rare

Detection histories for eight species of Amazona parrots in Venezuela during the NeoMaps bird surveys in 2010

Documenting changes in distribution is necessary for understanding species' response to environmental changes, but data on species distributions are heterogeneous in accuracy and resolution. Combining different data sources and methodological approaches can fill gaps in knowledge about the dynamic processes driving changes in species-rich, but data-poor regions. We combined recent bird survey data from the Neotropical Biodiversity Mapping Initiative (NeoMaps) with historical distribution records to estimate potential changes in the distribution of eight species of Amazon parrots in Venezuela. Using environmental covariates and presence-only data from museum collections and the literature, we first used maximum likelihood to fit a species distribution model (SDM) estimating a historical maximum probability of occurrence for each species. We then used recent, NeoMaps survey data to build single-season occupancy models (OM) with the same environmental covariates, as well as with time- and effort-dependent detectability, resulting in estimates of the current probability of occurrence. We finally calculated the disagreement between predictions as a matrix of probability of change in the state of occurrence. Our results suggested negative changes for the only restricted, threatened species, Amazona barbadensis, which has been independently confirmed with field studies. Two of the three remaining widespread species that were detected, Amazona amazonica, Amazona ochrocephala, also had a high probability of negative changes in northern Venezuela, but results were not conclusive for Amazona farinosa. The four remaining species were undetected in recent field surveys; three of these were most probably absent from the survey locations (Amazona autumnalis, Amazona mercenaria and Amazona festiva), while a fourth (Amazona dufresniana) requires more intensive targeted sampling to estimate its current status. Our approach is unique in taking full advantage of available, but limited data, and in detecting a high probability of change even for rare and patchily-distributed species. However, it is presently limited to species meeting the strong assumptions required for maximum-likelihood estimation with presence-only data, including very high detectability and representative sampling of its historical distribution.

Phenotypic evolution in a fossil gastropod species lineage: evidence for adaptive radiation?

Detecting speciation in the fossil record is a particularly challenging matter. Palaeontologists are usually confronted with poor preservation and limited knowledge on the palaeoenvironment. Even in the contrary case of adequate preservation and information, the linkage of pattern to process is often obscured by insufficient temporal resolution. Consequently, reliable documentations of speciation in fossils with discussions on underlying mechanisms are rare. Here we present a well-resolved pattern of morphological evolution in a fossil species lineage of the gastropod Melanopsis in the long-lived Lake Pannon. These developments are related to environmental changes, documented by isotope and stratigraphical data. After a long period of stasis, the ancestral species experiences a phenotypic change expressed as shift and expansion of the morphospace. The appearance of several new phenotypes along with changes in the environment is interpreted as adaptive radiation. Lake-level high stands affect distribution and availability of habitats and, as a result of varied functional demands on shell geometry, the distribution of phenotypes. The on-going divergence of the morphospace into two branches argues for increasing reproductive isolation, consistent with the model of ecological speciation. In the latest phase, however, progressively unstable conditions restrict availability of niches, allowing survival of one branch only.

Presence-absence species/sample matrix for the measured sections at the area of Maghara, North Sinai, Egypt

As age-diagnostic fossils are rare in the Middle to Upper Jurassic sedimentary succession of Gebel Maghara, North Sinai, Egypt, and in order to ensure maximal stratigraphic resolution, chronostratigraphic boundaries were determined based on quantitative biostratigraphy. A data matrix comprising 231 macrofaunal taxa in 93 samples from four sections has been processed with the Unitary Association (UA) Method. This led to construction of a sequence of 29 UAs (maximal sets of actually or virtually coexisting taxa), which have been grouped into 14 laterally reproducible association zones. The UA method allowed an in-depth analysis of the stratigraphically conflicting taxa, enabled the biostratigraphic subdivision of the studied interval, and also provided stratigraphic correlation among the measured sections and with the Tethyan ammonite zones.