Preliminary identification of dehalogenation specificities exhibited by dehalorespiring bacteria from a marine microbial community

The ability of a previously PCB-enriched microbial culture from Venice Lagoon marine sediments to dechlorinate pentachlorophenol (PCP) and 2,3,5-trichlorophenol (2,3,5-TCP) was confirmed under anaerobic conditions in microcosms consisting of site water and sediment. Dechlorination activities against Aroclor 1254 PCB mixture were also confirmed as control. Pentachlorophenol was degraded to 2,4,6-TCP (75.92±0.85 mol%), 3,5-DCP (6.40±0.75 mol%), and phenol (15.40±0.87 mol%). From the distribution of the different dechlorination products accumulated in the PCP-spiked cultures over time, two dechlorination pathways for PCP were proposed: (i) PCP to 2,3,4,6-TeCP, then to 2,4,6-TCP through the removal of both meta double-flanked chlorine substituents (main pathway); (ii) alternately, PCP to 2,3,5,6-TeCP, 2,3,5-TCP, 3,5-DCP, then phenol, through the removal of the para double-flanked chlorine, followed by ortho single-flanked chlorines, and finally meta unflanked chlorines (minor pathway). Removal of meta double-flanked chlorines is thus preferred over all other substituents. 2,3,5-TCP, that completely lacks double-flanked chlorines, was degraded to 3,5-DCP through removal of the ortho single-flanked chlorine, with a 99.6% reduction in initial concentration of 2,3,5-TCP by week 14. 16S rRNA PCR-DGGE using Chloroflexi-specific primers revealed a different role of the two microorganisms VLD-1 and VLD-2, previously identified as dechlorinators in the Aroclor 1254 PCB-enriched community, in the dehalogenation of chlorophenols. VLD-1 was observed both in PCP- and TCP-dechlorinating communities, whereas VLD-2 only in TCP-dechlorinating communities. This indicates that VLD-1 and VLD-2 may both dechlorinate ortho single-flanked chlorines, but only VLD-1 is able to remove double-flanked meta or para chlorines.

Microphytobenthos composition in Heron Reef, Australia, by High Performance Liquid Chromatography (HPLC) (July 2012)

We quantified pigment biomarkers by high performance liquid chromatography (HPLC) to obtain a broad taxonomic classification of microphytobenthos (MPB) (i.e. identification of dominant taxa). Three replicate sediment cores were collected at 0, 50 and 100 m along transects 5-9 in Heron Reef lagoon (n=15) (Fig. 1). Transects 1-4 could not be processed because the means to have the samples analysed by HPLC were not available at the time of field data collection. Cores were stored frozen and scrapes taken from the top of each one and placed in cryovials immersed in dry ice. Samples were sent to the laboratory (CSIRO Marine and Atmospheric Research, Hobart, Australia) where pigments were extracted with 100% acetone during fifteen hours at 4°C after vortex mixing (30 seconds) and sonication (15 minutes). Samples were then centrifuged and filtered prior to the analysis of pigment composition with a Waters - Alliance HPLC system equipped with a photo-diode array detector. Pigments were separated using a Zorbax Eclipse XDB-C8 stainless steel 150 mm x 4.6 mm ID column with 3.5 µm particle size (Agilent Technologies) and a binary gradient system with an elevated column temperature following a modified version of the Van Heukelem and Thomas (2001) method. The separated pigments were detected at 436 nm and identified against standard spectra using Waters Empower software. Standards for HPLC system calibration were obtained from Sigma (USA) and DHI (Denmark).

Benthic and substrate cover data derived from photo-transect surveys in Lizard Island, Great Barrier Reef conducted on October 3-7, 2012

Underwater georeferenced photo-transect surveys were conducted on October 3-7, 2012 at various sections of the reef and lagoon at Lizard Island, Great Barrier Reef. For this survey a snorkeler swam while taking photos of the benthos at a set distance from the benthos using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A Canon G12 digital camera was placed in a Canon underwater housing and photos were taken at 1 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry bag and logged the position at the surface while being towed by the photographer (Roelfsema, 2009). A total of 1,265 benthic photos were taken. Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 79 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Habitat Map for Lizard Island reef, Australia derived from a photo-transect survey field data collected in December 2011 and September/October 2012

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Location and ages of terrestrial peatlands located on continental shelves and in coastal sediments

This synthesis dataset contains records of freshwater peat and lake sediments from continental shelves and coastal areas. Information included is site location (when available), thickness and description of terrestrial sediments as well as underlying and overlying sediments, dates (when available), and references.

Sources, Fate and Transformation of Organic Matter in Wetlands and Estuaries

Dissolved organic matter (DOM) is a complex mixture of organic compounds and represents the largest reservoirs of carbon (C) on earth. Particulate organic matter (POM) is another important carbon component in C cycling and controls a variety of biogeochemical processes. Estuaries, as important interfaces between land and ocean, play important roles in retaining and transforming such organic matter (OM) and serve as both sources and sinks of DOM and POM. There is a diverse array of both autochthonous and allochthonous OM sources in wetland/estuarine ecosystems. A comprehensive study on the sources, transformation and fate of OM in such ecosystems is essential in advancing our understanding of C cycling and better constraining the global C budget. In this work, DOM characteristics were investigated in different estuaries. Dissolved organic matter source strengths and dynamics were assessed in a seagrass-dominated subtropical estuarine lagoon. DOM dynamics controlled by hydrology and seagrass primary productivity were confirmed, and the primary source of DOM was quantified using the combination of excitation emission matrix fluorescence with parallel factor analysis (EEM-PARAFAC) and stable C isotope analysis. Seagrass can contribute up to 72% of the DOM in the study area. The spatial and temporal variation of DOM dynamics was also studied in a freshwated dominated estuary fringed with extensive salt marshes. The data showed that DOM was primarily derived from freshwater marshes and controlled by hydrology while salt marsh plants play a significant role in structuring the distribution patterns of DOM quality and quantity. The OM dynamics was also investigated in a mangrove-dominate estuary and a comparative study was conducted between the DOM and POM pools. The results revealed both similarity and dissimilarity in DOM and POM composition. The dynamics of both OM pools are largely uncoupled as a result of source differences. Fringe mangrove swamps are suggested to export similar amounts of DOM and POM and should be considered as an important source in coastal C budgets. Lastly, chemical characterizations were conducted on the featured fluorescence component in OM in an attempt to better understand the composition and origins of the specific PARAFAC component. The traditionally defined ‘protein-like’ fluorescence was found to contain both proteinaceous and phenolic compounds, suggesting that the application of this parameter as a proxy for amino acid content and bioavailability may be limited.

Fidelity bias in mollusk assemblages from coastal lagoons of Southern Brazil

The South America southern coast exhibits many outcrops with abundant shell beds, from the Pleistocene through the Recent. How much biological information is preserved within these shell beds? Or, what is the actual probability a living community has to leave a fossil record corresponding to these shell deposits? Although ecological and biogeographical aspects might had been pointed, considering these temporal scales, up to the moment there is no taphonomically-oriented studies available. Quantitative comparisons between living (LAs), death (DAs) and fossil assemblages (FAs) are important not only in strictly taphonomic studies, but have grown a leading tool for conservation paleobiology analysis. Comparing LAs, DAs and FAs from estuaries and lagoons in the Rio Grande do Sul Coastal Plain makes possible to quantitatively understand the nature and quantity of biological information preserved in fossil associations in Holocene lagoon facies. As already noted by several authors, spatial scale parts the analysis, but we detected that the FAs refl ects live ones, rather than dead ones, as previously not realized. The results herein obtained illustrates that species present in DA are not as good preserved in recent (Holocene) fossil record as originally thought. Strictly lagoon species are most prone to leave fossil record. The authors consider that the fi delity pattern here observed for estuarine mollusks to be driven by (i) high temporal and spatial variability in the LAs, (ii) spatial mixing in the DA and (iii) differential preservation of shells, due to long residence times in the taphonomically active zone.

Grain size distribution of the lagoonal deposits within the South Malé Atoll, Maldives, Indian Ocean

Seismic and multibeam data, as well as sediment samples were acquired in the South Malé Atoll in the Maldives archipelago in 2011 to unravel the stratigraphy and facies of the lagoonal deposits. Multichannel seismic lines show that the sedimentary succession locally reaches a maximum thickness of 15-20 m above an unconformity interpreted as the emersion surface which developed during the last glacial sea-level lowstand. Such depocenters are located in current-protected areas flanking the reef rim of the atoll or in infillings of karst dolinas. Much of the 50 m deep sea floor in the lagoon interior is current swept, and has no or very minor sediment cover. Erosive current moats line drowned patch reefs, whereas other areas are characterized by nondeposition. Karst sink holes, blue holes and karst valleys occur throughout the lagoon, from its rim to its center. Lagoonal sediments are mostly carbonate rubble and coarse-grained carbonate sands with frequent large benthic foraminifers, Halimeda flakes, red algal nodules, mollusks, bioclasts, and intraclasts, some of them glauconitic, as well as very minor ooids. Finer-grained deposits locally are deposited in current-protected areas behind elongated faros, i.e., small atolls which are part of the rim of South Malé Atoll. The South Malé Atoll is a current-flushed atoll, where water and sediment export with the open sea is facilitated by the multiple passes dissecting the atoll rim. With an elevated reef rim and tower-like reefs in the atoll interior it is an example of a leaky bucket atoll which shares characteristics of incipiently drowned carbonate banks or drowning sequences as known from the geological record.

Geochemistry on manganese crusts from French Polynesia

The Tuamotu Archipelago in French Polynesia is a Co-rich ferromanganese crust province. The NODCO I survey (1986) provided detailed data on Co-rich crusts in this environment through the exploration of a restricted zone in the vicinity of Niau Island on the southern flank of the archipelago. This flat zone is a fossil atoll which, under the action of subsidence and tectonic movements, has collapsed to a water depth of 1000 m. The plateau is partially filled with coralline sediments. Outcrops of ferromanganese crusts, associated with rare nodules and slabs, are located on the inner side of the coral reef which bounds the ancient lagoon. The successive episodes of plateau history have been recorded in the different growth periods of the ferromanganese crusts. The crusts, nodules and slabs belong to the same morphological, mineralogical and geochemical family. Cobalt contents vary from 0.7 to 1.3%. The highest values belong to the thinnest ferromanganese crusts which are located on the flanks of the plateau. Average Ni contents are about 0.5% and Cu contents about 0.1%; Pt contents vary from 0.2 to 1.3 ppm. Platinum and Co are enriched in the outermost oxide zone of the crusts. Poorly crystallized -MnO2 is the dominant mineralogical phase. Cobalt enrichment seems to be related to -MnO2 particle size. The greatest contents are located in the finest material where the particle size is less than 0.1 m. Cobalt-rich crusts of the Niau Zone have the same characteristics as the Co-rich crusts from the Equatorial North Pacific. They differ in original setting: the reefal environment in the Niau Zone is superficial, overlying a volcanic substrate.

Magnetic susceptibility and ice-rafted debris in surface sediments of the Nordic Sea

Magnetic susceptibility and ice-rafted debris of surface sediments in the Nordic Seas were investigated to reconstruct source areas and recent transport pathways of magnetic minerals. From the distribution of magnetic susceptibility and ice-rafted debris and published data on petrographic tracers for iceberg drift, we reconstructed a counter-clockwise iceberg drift pattern during cooler phases in the Holocene, which is similar to conceptual and numerical models for Weichselian iceberg drift. The release of basaltic debris at Scoresby Sund played a significant role for the magnetic signature of stadial/interstadial events during isotope stage 3 recorded in sediment cores of the Nordic Seas.

The Provenance and Geochemical Alteration of Bermudan Eolianites

Large calcareous eolianites cover the remote island of Bermuda, accounting for more than 90% of the limestone bedrock. This study examines the sedimentology and geochemistry of these eolianites to better understand Pleistocene oceanography and the meteoric alteration of subtropical carbonate sediments. Cluster analyses reveal that the eolian carbonate sediments fall into two natural groups that represent lagoonal and reefal end members of marine sediment production. Coral fragments are uncharacteristically absent, possibly destroyed prior to their incorporation into eolian deposits by endolithic microboring organisms or broken up during transport. Sediment assemblages lead to the following interpretations of the Bermudan offshore environment: (1) the Ledge Flats reef system along the southwestern coast has been active since MIS 11, contributing coralline algal-rich sediment to the northern beaches of Sandy’s Parish and acting as an energy barrier in the south, allowing for low energy sedimentation in the quiet back- reef region; (2) on the northeastern coast, the low energy back-reef region landward of the Ledge Flats has thrived since MIS 11; (3) during MIS 5e, slightly warmer water temperatures led to the hindrance of coralline algal growth along the southern coast and in the North Lagoon. These are the first interpretations of Pleistocene marine assemblages on Bermuda. Meteoric fluids progressively transformed the pristine carbonate sediments into hardened limestones in a predictable solubility-dependent manner. The progressive alteration is coincident with: (1) divergence of δ18O and δ13C values from those similar to unaltered sediment towards those of calcrete, due to interaction with CO2-charged meteoric fluids; (2) depletion of elements with low partitioning coefficients and low meteoric concentrations, such as barium, boron, magnesium, potassium, sodium, strontium, and uranium; (3) enrichment of iron from Terra Rossa-hosted iron oxides; (4) enrichment of aluminum via detrital minerals sourced from protosol horizons; and (5) manganese concentrations that remain uncharacteristically low, owing to the lack of a consistent manganese source. Elemental correlations are useful for characterizing meteoric diagenesis, assuming the primary mineralogy is recognized, all components have been fully altered, and inter-particle cements are ubiquitous.

Revisiting the Late Jurassic-Early Cretaceous of the NW South Iberian Basin: new ages and sedimentary environments

The study of the Upper Jurassic-Lower Cretaceous deposits (Higueruelas, Villar del Arzobispo and Aldea de Cortés Formations) of the South Iberian Basin (NW Valencia, Spain) reveals new stratigraphic and sedimentological data, which have significant implications on the stratigraphic framework, depositional environments and age of these units. The Higueruelas Fm was deposited in a mid-inner carbonate platform where oncolitic bars migrated by the action of storms and where oncoid production progressively decreased towards the uppermost part of the unit. The overlying Villar del Arzobispo Fm has been traditionally interpreted as an inner platform-lagoon evolving into a tidal-flat. Here it is interpreted as an inner-carbonate platform affected by storms, where oolitic shoals protected a lagoon, which had siliciclastic inputs from the continent. The Aldea de Cortés Fm has been previously interpreted as a lagoon surrounded by tidal-flats and fluvial-deltaic plains. Here it is reinterpreted as a coastal wetland where siliciclastic muddy deposits interacted with shallow fresh to marine water bodies, aeolian dunes and continental siliciclastic inputs. The contact between the Higueruelas and Villar del Arzobispo Fms, classically defined as gradual, is also interpreted here as rapid. More importantly, the contact between the Villar del Arzobispo and Aldea de Cortés Fms, previously considered as unconformable, is here interpreted as gradual. The presence of Alveosepta in the Villar del Arzobispo Fm suggests that at least part of this unit is Kimmeridgian, unlike the previously assigned Late Tithonian-Middle Berriasian age. Consequently, the underlying Higueruelas Fm, previously considered Tithonian, should not be younger than Kimmeridgian. Accordingly, sedimentation of the Aldea de Cortés Fm, previously considered Valangian-Hauterivian, probably started during the Tithonian and it may be considered part of the regressive trend of the Late Jurassic-Early Cretaceous cycle. This is consistent with the dinosaur faunas, typically Jurassic, described in the Villar del Arzobispo and Aldea de Cortés Fms.

The relationship between vegetation and modern pollen assemblages on Mount Paggeo (NE Greece)

In this study, we investigated the relationship between vegetation and modern-pollen rain along the elevational gradient of Mount Paggeo. We apply multivariate data analysis to assess the relationship between vegetation and modern-pollen rain and quantify the representativeness of forest zones. This study represents the first statistical analysis of pollen-vegetation relationship along an elevational gradient in Greece. Hence, this paper improves confidence in interpretation of palynological records from north-eastern Greece and may refine past climate reconstructions for a more accurate comparison of data and modelling. Numerical classification and ordination were performed on pollen data to assess differences among plant communities that beech (Fagus sylvatica) dominates or co-dominates. The results show a strong relationship between altitude, arboreal cover, human impact and variations in pollen and nonpollen palynomorph taxa percentages.

What is this thing called Historical Archaeology?

Historical archaeology, in its narrow temporal sense -as an archaeology of the emergence and subsequent evolution of the Modern world- is steadily taking pace in Spanish academia. This paper aims at provoking a more robust debate through understanding how Spanish historical archaeology is placed in the international scene and some of its more relevant particularities. In so doing, the paper also stresses the strong links that have united historical and prehistorical archaeology since its inception, both in relation to the ontological, epistemological and methodological definition of the first as to the influence of socio-political issues in the latter. Such reflection is partly a situated reflection from prehistory as one of the paper’s authors has been a prehistorian for most of her professional life.