ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2004
Harrie T. Besselink
Abstract In the Fourth National Policy Document on Water Management in the Netherlands [1], it is defined that in 2003, in addition to the assessment of chemical substances, special guidelines for the assessment of dredged material should be recorded. The assessment of dredged material is based on integrated chemical and biological effect measurements. Among others, the DR CALUX® (dioxin responsive,chemically activated luciferase expression) bioassay has tentatively been recommended for inclusion in the dredged material assessment. To ensure the reliability of this bioassay, an intra- and interlaboratory validation study, or ring test, was performed, organized by the Dutch National Institute for Coastal and Marine Management (RIKZ) in cooperation with BioDetection Systems BV (BDS). The intralaboratory repeatability and reproducibility and the limit of detection (LOD) and quantification (LOQ) of the DR CALUX bioassay were determined by analyzing sediment extracts and dimethyl sulfoxide (DMSO) blanks. The highest observed repeatability was found to be 24.1%, whereas the highest observed reproducibility was calculated to be 19.9%. Based on the obtained results, the LOD and LOQ to be applied for the bioassay are 0.3 and 1.0 pM, respectively. The interlaboratory calibration study was divided into three phases, starting with analyzing pure chemicals. During the second phase, sediment extracts were analyzed, whereas in the third phase, whole sediments had to be extracted, cleaned, and analyzed. The average interlaboratory repeatability increased from 14.6% for the analysis of pure compound to 26.1% for the analysis of whole matrix. A similar increase in reproducibility with increasing complexity of handlings was observed with the interlaboratory reproducibility of 6.5% for pure compound and 27.9% for whole matrix. The results of this study are intended as a starting point for implementing the integrated chemical,biological assessment strategy and for systematic monitoring of dredged materials and related materials in the coming years. [source]

Linking spatial pattern of bottom fish assemblages with water masses in the North Sea

FISHERIES OCEANOGRAPHY, Issue 1 2009
SIEGFRIED EHRICH
Abstract Understanding the links between large scale spatial structuring of fish assemblages and shaping factors is essential to develop comprehensive ecosystem-based fisheries management. In this study, we investigated spatial patterns of bottom fish assemblages in the North Sea in relation to prevailing water masses in the region. We based our analysis on catch data from the German Small-Scale Bottom Trawl Survey conducted between 1987 and 2005 and used both ordination techniques and Mantel tests. Spatial variability of bottom fish assemblages was larger than inter-annual variability. Five significantly different bottom fish assemblages were associated with the following prevailing hydrographical regimes: i) the English Channel, ii) Continental Coastal, iii) central North Sea, iv) northern North Sea, and v) northern Atlantic water masses. Associations were generated by gradients in relative proportions of abundant species such as grey gurnard (Eutrigla gurnardus), dab (Limanda limanda), whiting (Merlangius merlangus), haddock (Melanogrammus aeglefinus) and Norway pout (Trisopterus esmarki). Taking into account large scale spatial structuring of catch data Mantel tests confirmed significant correlation between the fish assemblages and hydrographical variables. In summary, our results strongly support the hypotheses that hydrographical features such as water masses, fronts, and residual currents could shape bottom fish associations in the North Sea. Spatial demarcations of bottom fish assemblages indicated by this study can be used to support ecosystem-based fisheries management strategies. [source]

Coastal and ancient harbour geoarchaeology

GEOLOGY TODAY, Issue 1 2010
N. Marriner
What roles have human impacts and natural processes had in shaping the evolution of Mediterranean coastlines during the Holocene? Where, when and how did societies transform the coastal zone? At what scales and rhythms did these changes take place? What can ancient harbour sediments tell us about human-environment interactions? During the past 20 years, geoarchaeological research in the Mediterranean has attempted to understand the interplay between culture and nature, and more particularly how environments and processes have played a role in Holocene human occupation of the coastal zone. This approach has drawn on the multidisciplinary study of sediments, as archives of information, to attempt to differentiate between anthropogenic and natural factors, the latter, we argue, having played an increasingly secondary role with time. Three important spatial scales of analysis have emerged, local, regional and Mediterranean, all of which are outlined here. [source]

A Signal for Independent Coastal and Continental histories among North American wolves

MOLECULAR ECOLOGY, Issue 4 2005
BYRON V. WECKWORTH
Abstract Relatively little genetic variation has been uncovered in surveys across North American wolf populations. Pacific Northwest coastal wolves, in particular, have never been analysed. With an emphasis on coastal Alaska wolf populations, variation at 11 microsatellite loci was assessed. Coastal wolf populations were distinctive from continental wolves and high levels of diversity were found within this isolated and relatively small geographical region. Significant genetic structure within southeast Alaska relative to other populations in the Pacific Northwest, and lack of significant correlation between genetic and geographical distances suggest that differentiation of southeast Alaska wolves may be caused by barriers to gene flow, rather than isolation by distance. Morphological research also suggests that coastal wolves differ from continental populations. A series of studies of other mammals in the region also has uncovered distinctive evolutionary histories and high levels of endemism along the Pacific coast. Divergence of these coastal wolves is consistent with the unique phylogeographical history of the biota of this region and re-emphasizes the need for continued exploration of this biota to lay a framework for thoughtful management of southeast Alaska. [source]

Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America

MOLECULAR ECOLOGY, Issue 5 2001
John R. Demboski
Abstract Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanusandS.pacificus) were poorly differentiated. SorexornatusandS.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south-east Alaska, including S. bairdiandS. pacificus); (iii) the semiaquatic species (S. bendiriiandS. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5,6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America. [source]

Presence of Rhodopsin and Porphyropsin in the Eyes of 164 Fishes, Representing Marine, Diadromous, Coastal and Freshwater Species,A Qualitative and Comparative Study,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008
Mina Toyama
There are two types of visual pigments in fish eyes; most marine fishes have rhodopsin, while most freshwater fishes have porphyropsin. The biochemical basis for this dichotomy is the nature of the chromophores, retinal (A1) and 3-dehydroretinal (A2), each of which is bound by an opsin. In order to study the regional distribution of these visual pigments, we performed a new survey of the visual pigment chromophores in the eyes of many species of fish. Fish eyes from 164 species were used to examine their chromophores by high-performance liquid chromatography,44 species of freshwater fish, 20 of peripheral freshwater fish (coastal species), 10 of diadromous fish and 90 of seawater fish (marine species) were studied. The eyes of freshwater fish, limb freshwater fish and diadromous fish had both A1 and A2 chromophores, whereas those of marine fish possessed only A1 chromophores. Our results are similar to those of previous studies; however, we made a new finding that fish which live in freshwater possessed A1 if living near the sea and A2 if living far from the sea if they possessed only one type of chromophore. [source]

Coastal and marine governance in the United Kingdom Editorial

THE GEOGRAPHICAL JOURNAL, Issue 4 2008
STEPHEN FLETCHER
First page of article [source]

Coastal and marine spatial planning: a policy waiting to happen

AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 4 2010
G. Carleton Ray
No abstract is available for this article. [source]

Pacific Salmon Extinctions: Quantifying Lost and Remaining Diversity

CONSERVATION BIOLOGY, Issue 4 2007
RICHARD G. GUSTAFSON
biodiversidad; diversidad de salmones; extinción de poblaciones; historia de vida de salmones Abstract:,Widespread population extirpations and the consequent loss of ecological, genetic, and life-history diversity can lead to extinction of evolutionarily significant units (ESUs) and species. We attempted to systematically enumerate extinct Pacific salmon populations and characterize lost ecological, life history, and genetic diversity types among six species of Pacific salmon (Chinook [Oncorhynchus tshawytscha], sockeye [O. nerka], coho [O. kisutch], chum [O. keta], and pink salmon [O. gorbuscha] and steelhead trout [O. mykiss]) from the western contiguous United States. We estimated that, collectively, 29% of nearly 1400 historical populations of these six species have been lost from the Pacific Northwest and California since Euro-American contact. Across all species there was a highly significant difference in the proportion of population extinctions between coastal (0.14 extinct) and interior (0.55 extinct) regions. Sockeye salmon (which typically rely on lacustrine habitats for rearing) and stream-maturing Chinook salmon (which stay in freshwater for many months prior to spawning) had significantly higher proportional population losses than other species and maturation types. Aggregate losses of major ecological, life-history, and genetic biodiversity components across all species were estimated at 33%, 15%, and 27%, respectively. Collectively, we believe these population extirpations represent a loss of between 16% and 30% of all historical ESUs in the study area. On the other hand, over two-thirds of historical Pacific salmon populations in this area persist, and considerable diversity remains at all scales. Because over one-third of the remaining populations belong to threatened or endangered species listed under the U.S. Endangered Species Act, it is apparent that a critical juncture has been reached in efforts to preserve what remains of Pacific salmon diversity. It is also evident that persistence of existing, and evolution of future, diversity will depend on the ability of Pacific salmon to adapt to anthropogenically altered habitats. Resumen:,Las extirpaciones generalizadas de poblaciones y la consecuente pérdida de diversidad ecológica, genética y de historia natural puede llevar a la extinción de unidades evolutivamente significativas (UES) y especies. Intentamos enumerar sistemáticamente a las poblaciones extintas de salmón del Pacífico y caracterizar a los tipos de diversidad ecológica, de historia natural y genética de seis especies de salmón del Pacífico Oncorhynchus tshawytscha, O. nerka, O. kisutch, O. keta, y O. gorbuscha; y trucha O. mykiss en el occidente de Estados Unidos. Estimamos que, colectivamente, se ha perdido a 29% de casi 1400 poblaciones históricas de estas seis especies en el Pacífico Noroeste y California desde la colonización europea. En todas las especies hubo una diferencia altamente significativa en la proporción de extinción de poblaciones entre regiones costeras (0.14 extintas) e interiores (0.55 extintas). O. nerka (que típicamente cría en hábitats lacustres) y O. tshawytscha (que permanece en agua dulce por muchos meses antes del desove) tuvieron pérdidas poblacionales significativamente mayores que las otras especies y tipos de maduración. Se estimó que las pérdidas agregadas de componentes mayores de la biodiversidad ecológica, de historia natural y genética en todas las especies fueron de 33%, 15% y 27%, respectivamente. Colectivamente, consideramos que estas extirpaciones de poblaciones representan una pérdida entre 16% y 30% de todas las UES históricas en el área de estudio. Por otro lado, más de dos tercios de las poblaciones históricas de salmón del Pacífico persisten en esta área, y aun hay considerable diversidad en todas las escalas. Debido a que más de un tercio de las poblaciones restantes pertenecen a especies enlistadas como amenazadas o en peligro en el Acta de Especies en Peligro de E. U. A., es evidente que se ha llegado a una disyuntiva crítica en los esfuerzos para preservar lo que queda de la diversidad de salmón del Pacífico. También es evidente que la persistencia de la diversidad existente, y su futura evolución, dependerá de la habilidad del salmón del Pacífico para adaptarse a hábitats alterados antropogénicamente. [source]

Extinction-Rate Estimates for a Modern Neotropical Flora

CONSERVATION BIOLOGY, Issue 5 2002
Nigel C. A. Pitman
We present the first quantitative estimates of extinction rate in a complete Neotropical flora based on historical plant-collection records, quantitative measurements of forest loss and plant diversity, and the conservation status of endemic plant species in Ecuador. Our analyses suggest that 19,46 endemic plant species have gone extinct in Ecuador over the last 250 years, mostly because of habitat loss, and therefore are now globally extinct. An additional 282 species, nearly 7% of Ecuador's endemic flora, qualify as critically endangered. We found evidence of impending large-scale plant extinctions in the country's coastal and Andean forests, but little extinction and low potential for extinction in the Amazonian lowlands. Resumen: Las preocupaciones sobre las elevadas tasas de extinción en los trópicos son una característica común en la literatura sobre conservación, pero las mediciones directas son escasas. Presentamos las primeras estimaciones cuantitativas de la tasa de extinción en una flora neotropical completa basada en los expedientes históricos de colecciones de plantas, las mediciones cuantitativas de la pérdida de bosque y de diversidad y el estado de conservación de especies de plantas endémicas en Ecuador. Nuestro análisis sugiere que 19,46 especies de plantas se han extinguido en el Ecuador a lo largo de los últimos 250 años, debido principalmente a la pérdida de hábitat y por lo tanto son ahora extintas a nivel mundial. Además 282 especies, cerca del 7% de la flora endémica del Ecuador califica como críticamente amenazada. Encontramos indicaciones de inminentes extinciones de gran escala en el país, tanto en los bosques costeros como en los bosques de los Andes, pero poca extinción y bajo potencial de extinción en las tierras bajas del Amazonas. [source]

Cyclone disaster vulnerability and response experiences in coastal Bangladesh

DISASTERS, Issue 4 2010
Edris Alam
For generations, cyclones and tidal surges have frequently devastated lives and property in coastal and island Bangladesh. This study explores vulnerability to cyclone hazards using first-hand coping recollections from prior to, during and after these events. Qualitative field data suggest that, beyond extreme cyclone forces, localised vulnerability is defined in terms of response processes, infrastructure, socially uneven exposure, settlement development patterns, and livelihoods. Prior to cyclones, religious activities increase and people try to save food and valuable possessions. Those in dispersed settlements who fail to reach cyclone shelters take refuge in thatched-roof houses and big-branch trees. However, women and children are affected more despite the modification of traditional hierarchies during cyclone periods. Instinctive survival strategies and intra-community cooperation improve coping post cyclone. This study recommends that disaster reduction programmes encourage cyclone mitigation while being aware of localised realities, endogenous risk analyses, and coping and adaptation of affected communities (as active survivors rather than helpless victims). [source]

Integrating species life-history traits and patterns of deforestation in amphibian conservation planning

DIVERSITY AND DISTRIBUTIONS, Issue 1 2010
C. G. Becker
Abstract Aim, To identify priority areas for amphibian conservation in southeastern Brazil, by integrating species life-history traits and patterns of deforestation. Location, State of São Paulo, Brazil. Methods, We used the software Marxan to evaluate different scenarios of amphibian conservation planning. Our approach differs from previous methods by explicitly including two different landscape metrics; habitat split for species with aquatic larvae, and habitat loss for species with terrestrial development. We evaluated the effect of habitat requirements by classifying species breeding habitats in five categories (flowing water, still water permanent, still water temporary, bromeliad or bamboo, and terrestrial). We performed analyses using two scales, grid cells and watersheds and also considered nature preserves as protected areas. Results, We found contrasting patterns of deforestation between coastal and inland regions. Seventy-six grid cells and 14 watersheds are capable of representing each species at least once. When accounting for grid cells already protected in state and national parks and considering species habitat requirements we found 16 high-priority grid cells for species with one or two reproductive habitats, and only one cell representing species with four habitat requirements. Key areas for the conservation of species breeding in flowing and permanent still waters are concentrated in southern state, while those for amphibians breeding in temporary ponds are concentrated in central to eastern zones. Eastern highland zones are key areas for preserving species breeding terrestrially by direct or indirect development. Species breeding in bromeliads and bamboos are already well represented in protected areas. Main conclusions, Our results emphasize the need to integrate information on landscape configuration and species life-history traits to produce more ecologically relevant conservation strategies. [source]

Tafoni development in a cryotic environment: an example from Northern Victoria Land, Antarctica

EARTH SURFACE PROCESSES AND LANDFORMS, Issue 10 2008
Andrea Strini
Abstract Tafoni are a type of cavernous weathering widespread around the world. Despite the extensive distribution of the tafoni, their genesis is not clear and is still a matter of debate, also because they occur in such different climatic conditions and on so many different types of substrate. Geomorphological characterization of more than 60 tafoni in three different Antarctic sites (two coastal and one inland) between 74 and 76° S with sampling of weathering products and salt occurrences are described together with thermal data (on different surfaces) and wind speed recorded in different periods of the year in a selected tafone close to the Italian Antarctic station. The aim of this present study is to provide further information to help understand the processes involved in the growth of tafoni in a cryotic environment, and the relationship of these processes to climate, with particular attention to the thermal regime and the role of wind. The new data presented in this paper suggest that there is no single key factor that drives the tafoni development, although thermal stress seems the most efficient process, particularly if we consider the short-term fluctuations. The data also confirm that other thermal processes, such as freezing,thawing cycles and thermal shock, are not really effective for the development of tafoni in this area. The wind speed measured within the tafoni is half that recorded outside, thus favouring snow accumulation within the tafoni and therefore promoting salt crystallization. On the other hand, the wind effect on the thermal regime within the tafoni seems negligible. While both salt weathering and thermal stress appear active in this cryotic environment, these are azonal processes and are therefore active in other climatic areas where tafoni are widespread (such as the Mediterranean region). Copyright © 2007 John Wiley & Sons, Ltd. [source]

A sediment budget for a cultivated floodplain in tropical North Queensland, Australia

EARTH SURFACE PROCESSES AND LANDFORMS, Issue 10 2007
Fleur Visser
Abstract Sugarcane is grown on the floodplains of northern Queensland adjacent to the Great Barrier Reef lagoon. Sediment and nutrient loss from these sugarcane areas is considered a potential threat to coastal and marine ecosystems. To enable sugarcane cultivation, farmers have structured the landscape into different elements, comprising fields, water furrows, ,headlands' and drains. In order to apply appropriate management of the landscape and reduce export of sediment, it is important to identify which of these elements act as sediment sources or sinks. In this study erosion and deposition rates were measured for the different landscape elements in a subcatchment of the Herbert River and used to create a sediment budget. Despite large uncertainties, the budget shows that the floodplain area is a net source of sediment. Estimated sediment export varies between 2 and 5 t ha,1 y,1. The relative importance of the landscape elements as sediment sources could also be determined. Plant cane is identified as the most important sediment source. Water furrows generate most sediment, but are a less important source of exported sediment due to their low connectivity. Headlands and minor drains act as sediment traps. Copyright © 2007 John Wiley & Sons, Ltd. [source]

The termination of the last major phase of aeolian sand movement, coastal dunefields, Denmark

EARTH SURFACE PROCESSES AND LANDFORMS, Issue 7 2006
Lars B. Clemmensen
Abstract Optically stimulated luminescence (OSL) dating of sand samples from stabilized (or inactive) coastal dunes in Denmark provides information on the age of the termination phase of the last major aeolian activity period. A total of 26 sand samples were taken from four different coastal dunefields around the North Sea, Skagerrak and Kattegat coasts of Denmark. The OSL dates indicate that the last major phase of aeolian activity terminated between ad 1860 and 1905. Most of the dunes examined in this study were active around 1820, during a period documented to have been very stormy. A dune management scheme started around 1792, and this no doubt was a major cause of dunefield stabilization, but an overall decline of storminess, particularly spring and summer storminess, around the end of the 19th century must also have contributed to the increasing inactivity of coastal dunes. The new OSL dates on aeolian sand movement agree well with historical data and data from topographic maps on dune movement. This agreement supports the observation from earlier work that OSL dating of recent aeolian sand movement is accurate over the last few decades to centuries. Copyright © 2005 John Wiley & Sons, Ltd. [source]

A geomatics data integration technique for coastal change monitoring

EARTH SURFACE PROCESSES AND LANDFORMS, Issue 6 2005
J. P. Mills
Abstract This paper reports research carried out to develop a novel method of monitoring coastal change, using an approach based on digital elevation models (DEMs). In recent years change monitoring has become an increasingly important issue, particularly for landforms and areas that are potentially hazardous to human life and assets. The coastal zone is currently a sensitive policy area for those involved with its management, as phenomena such as erosion and landslides affect the stability of both the natural and the built environment. With legal and financial implications of failing to predict and react to such geomorphological change, the provision of accurate and effective monitoring is essential. Long coastlines and dynamic processes make the application of traditional surveying difficult, but recent advances made in the geomatics discipline allow for more effective methodologies to be investigated. A solution is presented, based on two component technologies , the Global Positioning System (GPS) and digital small format aerial photogrammetry , using data fusion to elim-inate the disadvantages associated with each technique individually. A sparse but highly accurate DEM, created using kinematic GPS, was used as control to orientate surfaces derived from the relative orientation stage of photogrammetric processing. A least squares surface matching algorithm was developed to perform the orientation, reducing the need for costly and inefficient ground control point survey. Change detection was then carried out between temporal data epochs for a rapidly eroding coastline (Filey Bay, North Yorkshire). The surface matching algorithm was employed to register the datasets and determine dif-ferences between the DEM series. Large areas of change were identified during the lifetime of the study. Results of this methodology were encouraging, the flexibility, redundancy and automation potential allowing an efficient approach to landform monitoring. Copyright © 2005 John Wiley & Sons, Ltd. [source]

Late Quaternary vadose carbonate diagenesis in coastal and desert dune and beach sands: is there a palaeoclimatic signal?

EARTH SURFACE PROCESSES AND LANDFORMS, Issue 12 2004
Sue McLaren
Abstract A study of the variation in cement amounts in aeolianite and sandy beach calcarenites that range in age from Holocene to Last Interglacial is used to assess whether a palaeoclimatic control on vadose diagenesis can be identi,ed. Examples are taken from modern-day arid to subhumid settings and represent a geographical distribution ranging from Libya and Oman, to the Mediterranean, the Caribbean and Mexico. The results indicate that a palaeoclimatic signal can be identi,ed in some deposits. However, in other sediments there is substantial variability in mean cement abundance within deposits as well as between these sand bodies. Moreover, many of the better cemented sediments are located in areas where there is accelerated diagenesis, such as in the sea spray zone, close to the groundwater table or near to a palaeosurface, rather than in climatically wet regions. The inference is that palaeoclimatic interpretations are substantially complicated by other factors that affect diagenetic processes and change. Therefore caution is needed when studying the role of climate in vadose diagenesis in the light of the effects of other intrinsic and extrinsic controls. This paper does not aim to provide a de,nitive comparison of sites from different climatic zones. The approach taken here is: (a) to see if there is an overall palaeoclimatic signal in the samples studied; (b) to use examples to illustrate how explanations/controls other than those relating to climate can account for the variabilities observed; and (c) if there is a climatic effect, to see if it is the main over-riding control on vadose diagenesis. The conclusions drawn from this research highlight that it is possible to misinterpret evidence if the study is approached with preconceived notions of simplistic relationships between diagenesis and climate. Copyright © 2004 John Wiley & Sons, Ltd. [source]

Direct Simultaneous Determination of Cu, Ni and V in Seawater Using Adsorptive Cathodic Stripping Voltammetry with Mixed Ligands

ELECTROANALYSIS, Issue 10 2005
A. Cobelo-García
Abstract An analytical procedure is proposed for the direct simultaneous determination in a single scan of Cu, Ni and V in seawater by means of adsorptive cathodic stripping voltammetry (ACSV) with mixed ligands (DMG and catechol). Optimum conditions for the determination of these three elements were studied. Detection limits of the technique depended upon the reproducibility of the procedura blank, and were found to be 0.5,nM for Cu, 0.4,nM for Ni and 0.3,nM for V. The method is suitable for the analysis of estuarine, coastal and open-ocean waters, and especially to study the metal contamination in areas subject to oil spill events. [source]

Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre

ENVIRONMENTAL MICROBIOLOGY, Issue 9 2008
Vinh D. Pham
Summary High-throughput identification of rRNA gene-containing clones in large insert metagenomic libraries is difficult, because of the high background of host ribosomal RNA (rRNA) and rRNA genes. To address this challenge, a membrane hybridization method was developed to identify all bacterial small subunit rRNA-containing fosmid clones of microbial community DNA from seven different depths in the North Pacific Subtropical Gyre. Out of 101,376 clones screened, 751 rDNA-containing clones were identified that grouped in ,60 different clades. Several rare sequences only remotely related to known groups were detected, including a Wolbachia -related sequence containing a putative intron or intervening sequence, as well as seven sequences from Order Myxococcales not previously detected in pelagic habitats. Stratified, depth-specific population structure was evident within both cultured and uncultured lineages. Conversely, some eurybathyal members of the genera Alcanivorax and Rhizobium shared identical small subunit ribosomal DNA sequences that were distributed from surface waters to the 4000 m depth. Comparison with similar analyses in Monterey Bay microbial communities revealed previously recognized, as well as some distinctive, depth-stratified partitioning that distinguished coastal from open ocean bacterioplankton populations. While some bias was evident in fosmid clone recovery in a few particular lineages, the overall phylogenetic group recovery and distributions were consistent with previous studies, as well as with direct shotgun sequence data from the same source DNA. [source]

Prevalence of highly host-specific cyanophages in the estuarine environment

ENVIRONMENTAL MICROBIOLOGY, Issue 2 2008
Kui Wang
Summary Cyanophages that infect coastal and oceanic Synechococcus have been studied extensively. However, no cyanophages infecting estuarine Synechococcus have been reported. In this study, seven cyanophages (three podoviruses, three siphoviruses and one myovirus) isolated from four estuarine Synechococcus strains were characterized in terms of their morphology, host range, growth and genetic features. All the podoviruses and siphoviruses were highly host specific. For the first time, the photosynthesis gene (psbA) was found in two podoviruses infecting estuarine Synechococcus. However, the psbA gene was not detected in the three siphoviruses. The psbA sequences from the two Synechococcus podoviruses clustered with some environmental psbA sequences, forming a unique cluster distantly related to previous known psbA clusters. Our results suggest that the psbA among Synechococcus podoviruses may evolve independently from the psbA of Synechococcus myoviruses. All three estuarine Synechococcus podoviruses contained the DNA polymerase (pol) gene, and clustered with other podoviruses that infect oceanic Synechococcus and Prochlorococcus, suggesting that the DNA pol is conserved among marine picocyanobacterial podoviruses. Prevalence of host-specific cyanophages in the estuary suggests that Synechococcus and their phages in the estuarine ecosystem may develop a host,phage relationship different from what have been found in the open ocean. [source]

Detection of bacteria associated with harmful algal blooms from coastal and microcosm environments using electronic microarrays

ENVIRONMENTAL MICROBIOLOGY, Issue 3 2007
Edward A. Barlaan
Summary With the global expansion of harmful algal blooms (HABs), several measures, including molecular approaches, have been undertaken to monitor its occurrence. Many reports have indicated the significant roles of bacteria in controlling algal bloom dynamics. Attempts have been made to utilize the bacteria/harmful algae relationship in HAB monitoring. In this study, bacterial assemblages monitored during coastal HABs and bacterial communities in induced microcosm blooms were investigated. Samples were analysed using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene. DGGE bands with peculiar patterns before, during, and after algal blooms were isolated and identified. Probes for six ribotypes representing organisms associated with Chatonella spp., Heterocapsa circularisquama, or Heterosigma akashiwo were used for analysis on NanoChip electronic microarray. In addition, a new approach using cultured bacteria species was developed to detect longer (533 bp) polymerase chain reaction-amplified products on the electronic microarray. The use of fluorescently labelled primers allowed the detection of individual species in single or mixed DNA conditions. The developed approach enabled the detection of the presence or absence and relative abundance of the HAB-related ribotypes in coastal and microcosm blooms. This study indicates the ability of electronic microarray platform to detect or monitor bacteria in natural and induced environments. [source]

The use of peepers to sample pore water in acid sulphate soils

EUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2008
P. VanOploo
Summary Serious environmental impacts of acidic drainage from acid sulphate soils in coastal areas are the result of the interactions between the hydrologic cycle, land use and drainage management, and pore water chemistry. In this study, in situ, diffusion-controlled dialysis profile samplers, or peepers, were used to examine pore water chemistry of acid sulphate soils in a coastal, sugarcane-producing area in Eastern Australia. The peepers sampled pore water at 20-mm intervals over a 1.0-m length, permitting excellent resolution of the sharp transitions in pore water chemistry that occur around a soil profile's iron sulphide oxidation front. Comparison of peeper profiles with soil water profiles extracted from soil samples by centrifuging, illustrated the advantages of peepers over conventional soil water sampling techniques in unconsolidated, sulphidic soils. For conventional sampling, the low permeability, gel-like, unoxidized soil samples had to be frozen then thawed before water could be extracted by centrifuging. Peeper profiles of species not involved in redox reactions agreed well with those from centrifuged soil extracts. Redox sensitive species, however, were in poorer agreement because of the lengthy soil sample preparation and extraction procedures required for extraction by centrifuging. The approximately 6-day equilibration time required for peeper sampling allows them to follow monthly or seasonal changes in pore water chemistry in acid sulphate soils due to variations in climate, and land use and management. [source]

Diversity and distribution of pigmented heterotrophic bacteria in marine environments

FEMS MICROBIOLOGY ECOLOGY, Issue 1 2006
Hailian Du
Abstract A systematic investigation of marine pigmented heterotrophic bacteria (PHB) based on the cultivation method and sequencing analysis of 16S rRNA genes was conducted in Chinese coastal and shelf waters and the Pacific Ocean. Both the abundance of PHB and the ratio of PHB to CFU decreased along trophic gradients from coastal to oceanic waters, with the highest values of 9.9 × 103 cell mL,1 and 39.6%, respectively, in the Yangtze River Estuary. In contrast to the total heterotrophic bacteria (TB) and CFU, which were present in the whole water column, PHB were primarily confined to the euphotic zone, with the highest abundance of PHB and ratio of PHB to CFU occurring in surface water. In total, 247 pigmented isolates were obtained during this study, and the phylogenetic analysis showed a wide genetic diversity covering 25 genera of six phylogenetic classes: Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacilli, Flavobacteria and Sphingobacteria. PHB belonging to Alphaproteobacteria, Flavobacteria and Sphingobacteria were obtained mainly from the South China Sea and East China Sea; PHB from the Pacific Ocean water were predominantly affiliated with Gammaproteobacteria, and most isolates from the Yangtze River Estuary fell into the classes Actinobacteria and Bacilli. The isolates exhibited various colours (e.g. golden, yellow, red, pink and orange), with genus or species specificity. Furthermore, the pigment of PHB cells absorbed light mainly in the wavelength range between 450 and 550 nm. In conclusion, our work has revealed that PHB with broad genetic diversity are widely distributed in the marine environment, and may account for up to 39.6% of culturable bacteria, equivalent to 1.4% of the total microbial community. This value might even be underestimated because it is probable that not all pigmented bacteria were isolated. Their abundance and genetic distribution are heavily influenced by environmental properties, such as light and nutrition, suggesting that they have important roles in the marine ecosystem, especially in the absorption of visible light. [source]

Visualisation of standardized life-history patterns

FISH AND FISHERIES, Issue 4 2001
Dirk Zeller
Abstract The life-history patterns of fish and invertebrate species are complex. But much of this complexity can be captured in simple diagrams of coastal transects, where juveniles usually occur in larger numbers in shallow waters, while adults generally inhabit deeper, offshore waters. Iconographic representations of generalized life-history patterns and depth profiles, with specific key life-history parameters can capture much of these standardized patterns, including spawning areas, nursery/juvenile distributions, adult distributions and spawning migrations. Several examples presented here from a wide range of habitats and ecosystems (temperate and tropical waters, demersal, deep water, pelagic and coral reefs), including an example of different stocks of the same species, illustrate some general patterns with regard to water depth and distance from shore. The present approach should be viewed as a first step towards obtaining standardized patterns about key life-history parameters, and will hopefully lead to incorporation into management of life-history interconnectivity between different fishery sectors or gears. This may contribute to sustainable, ecosystem-based approaches to management by informing policy options when faced with decisions to rationalize overcapitalized fisheries. [source]

Integrating remote sensing in fisheries control

FISHERIES MANAGEMENT & ECOLOGY, Issue 5 2005
N. KOURTI
Abstract, To complement existing fishery control measures, in particular the Vessel Monitoring System (VMS), a pilot operational system to find fishing vessels in satellite images was set up. Radar is the mainstay of the system, which furthermore includes fully automated image processing and communication protocols with the authorities. Different image types are used to match different fisheries , oceanic, shelf and coastal. Vessel detection rates were 75,100% depending on image type and vessel size. Output of the system, in the form of an overview of vessel positions in the area highlighting any discrepancies with otherwise reported positions, can be at the authorities within 30 min of the satellite image being taken , fast enough to task airborne inspection for follow up. [source]

Thermal habitat of striped bass (Morone saxatilis) in coastal waters of northern Massachusetts, USA, during summer

FISHERIES OCEANOGRAPHY, Issue 5 2010
GARY A. NELSON
Abstract Striped bass, Morone saxatilis, were captured and released with temperature-measuring data storage tags in Salem Sound, Massachusetts, to collect data on their thermal preferences in coastal and marine waters and to identify environmental factors that may influence temperatures experienced during their summer residence. Striped bass recaptured during summer of 2006 (21 of 151 releases) experienced a wide range of temperatures (6.5,28.0°C) while at-large for 1,53 days. Overall mean temperature and standard deviation selected by striped bass recaptured in Salem Sound during the longest commonly-shared duration of time (3,12 July) were 17.8 and 3.57°C, respectively. Comparison of temperature data between fish and 13 vertical arrays in Salem Sound revealed that striped bass experienced higher and more variable temperatures, and that daily changes in temperature actually experienced were unrelated to daily changes in surrounding ambient temperature. Regular cyclical changes in temperature of all striped bass and vertical arrays were identified as influences of the local tide, which contributed about a 2°C change in temperature, on average, over the complete cycle. Most striped bass appeared to limit their activities to depths shallower than the lower limit of the thermocline, above which temperatures generally exceed 9.0°C in Salem Sound. Therefore, it is likely that the vertical distribution of striped bass is restricted by the low temperatures below this depth. An implication of this finding is that the spatial distribution of striped bass may be defined coarsely by knowledge of the distribution of temperature in coastal areas. [source]

Variation in virulence among isolates of Armillaria ostoyae

FOREST PATHOLOGY, Issue 2 2002
D. J. MORRISON
The virulence of Armillaria ostoyae isolates from coastal (16) and interior (33) British Columbia, elsewhere in North America (eight) and Europe (six) was assessed on 2-year-old Douglas-fir seedlings in pots during a 3-year trial. Isolates from most geographical locations infected similar proportions of seedlings, had similar average damage scores and killed a similar percentage of diseased seedlings. Isolates from the coastal region had a significantly higher probability than interior isolates that a diseased seedling received a damage score > 3 on a 1,5 scale, and coastal isolates killed a higher proportion of diseased seedlings than interior isolates. The mean damage score for isolates that had been in culture for 20,25 years was about 25% lower than that for recently collected isolates. The results indicate that the higher incidence and longer duration of mortality in the southern interior of British Columbia compared to the coast can not be attributed to greater virulence of interior isolates of A. ostoyae. Variations de virulence chez des isolats de Armillaria ostoyae Des isolats de Armillaria ostoyae provenant de la côte (16 isolats) ou de l'intérieur (33) de la Colombie Britannique, ainsi que d'Amérique du Nord (8) et d'Europe (6), ont été comparés pour leur virulence sur des semis de 2 ans en pot de Pseudotsuga menziesii, suivis pendant 3 ans. Le taux d'infection, le taux moyen de dommages et la mortalitéétaient semblables avec les isolats de la plupart des origines. Sur une échelle de dommages allant de 1 à 5, la probabilité de dépasser la note 3 était significativement plus forte chez les semis infectés par les isolats de la région côtière que par ceux de l'intérieur; les isolats de la région côtière tuaient aussi plus de semis que ceux de l'intérieur. Les isolats en culture depuis 20,25 ans occasionnaient des dommages d'environ 25% inférieurs à ceux occasionnés par des isolats d'obtention récente. Les résultats montrent que la plus grande incidence et la plus grande persistance des mortalités dans le sud de la région intérieure de la Colombie Britannique, ne peuvent pas être attribuées à une plus grande virulence des isolats d' A. ostoyae de cette région. Variation der Virulenz zwischen Isolaten von Armillaria ostoyae Die Virulenz verschiedener Armillaria ostoyae -Isolate vom Küstengebiet (n=16) und dem Inneren von British Columbia (33) sowie aus anderen Gebieten Nordamerikas (8) und Europas (6) wurde an zweijährigen Douglasiensämlingen in Töpfen während drei Jahren untersucht. Die Isolate der meisten geographischen Herkünfte infizierten die Sämlinge in ähnlichem Umfang, führten zu ähnlichen durchschnittlichen Schadensklassen und töteten erkrankte Sämlinge in ähnlichem Ausmass ab. Isolate aus dem Küstengebiet hatten im Vergleich mit Isolaten aus dem Inland British Columbias aber eine signifikant höhere Wahrscheinlichkeit, dass ein erkrankter Sämling eine Schadensklasse > 3 auf einer Skala von 1,5 erreichte, und sie töteten auch mehr erkrankte Sämlinge ab. Bei Isolaten, die 20,25 Jahre in Kultur gehalten worden waren, lag das durchschnittliche Schadensausmass ca. 25% tiefer als bei Isolaten, die in letzter Zeit gesammelt worden waren. Diese Ergebnisse zeigen, dass das häufigere Auftreten und das über einen längeren Zeitraum anhaltende Absterben im südlichen Inland von British Columbia verglichen mit der Küstenregion nicht mit einer höheren Virulenz der Isolate von A. ostoyae aus diesem Gebiet erklärt werden kann. [source]

The Tendaguru Formation (Late Jurassic to Early Cretaceous, southern Tanzania): definition, palaeoenvironments, and sequence stratigraphy

FOSSIL RECORD-MITTEILUNGEN AUS DEM MUSEUM FUER NATURKUNDE, Issue 2 2009
Robert Bussert
Abstract The well-known Late Jurassic to Early Cretaceous Tendaguru Beds of southern Tanzania have yielded fossil plant remains, invertebrates and vertebrates, notably dinosaurs, of exceptional scientific importance. Based on data of the German-Tanzanian Tendaguru Expedition 2000 and previous studies, and in accordance with the international stratigraphic guide, we raise the Tendaguru Beds to formational rank and recognise six members (from bottom to top): Lower Dinosaur Member, Nerinella Member, Middle Dinosaur Member, Indotrigonia africana Member, Upper Dinosaur Member, and Rutitrigonia bornhardti-schwarzi Member. We characterise and discuss each member in detail in terms of derivation of name, definition of a type section, distribution, thickness, lithofacies, boundaries, palaeontology, and age. The age of the whole formation apparently ranges at least from the middle Oxfordian to the Valanginian through Hauterivian or possibly Aptian. The Tendaguru Formation constitutes a cyclic sedimentary succession, consisting of three marginal marine, sandstone-dominated depositional units and three predominantly coastal to tidal plain, fine-grained depositional units with dinosaur remains. It represents four third-order sequences, which are composed of transgressive and highstand systems tracts. Sequence boundaries are represented by transgressive ravinement surfaces and maximum flooding surfaces. In a more simple way, the depositional sequences can be subdivided into transgressive and regressive sequences/systems tracts. Whereas the transgressive systems tracts are mainly represented by shallow marine shoreface, tidal channel and sand bar sandstones, the regressive systems tracts predominantly consist of shallow tidal channel, tidal flat, and marginal lagoonal to supratidal deposits. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Triassic metasedimentary successions across the boundary between the southern Apennines and the Calabrian Arc (northern Calabria, Italy)

GEOLOGICAL JOURNAL, Issue 2 2005
A. Iannace
Abstract The boundary area between the Apenninic fold-and-thrust belt and the crystalline Calabrian Arc, located around Sangineto in northern Calabria, has been investigated. New geological mapping in the Sant'Agata area has been performed on the Triassic successions traditionally attributed to the metasedimentary San Donato Unit. This, coupled with a reappraisal of the stratigraphy and tectonics of coeval successions present more to the south in the Cetraro Unit, results in a new reconstruction of the Triassic evolution of all the metasedimentary successions found in the region. Four informal stratigraphic units have been distinguished in the S. Agata area. The lowest one (Unit A) consists of well-bedded metalimestones and bioturbated marly limestones that correlate with Ladinian,Carnian carbonates in nearby areas. A second unit (Unit B), never recognized before, contains a complex alternation of dolomites, phyllites and some meta-arenites containing several beds of Cavernoso facies, attributed to the Carnian. They grade upward to platform and platform-margin dolomites of Norian,Rhaetian age (Unit C) that in turn are replaced upward and laterally by a fourth unit (Unit D) consisting of well-bedded, dark dolomites and metalimestones with marly interlayers locally found as resedimented large blocks in slope conglomerates. Unit D correlates with Rhaetian,Liassic beds in nearby areas. Several pieces of evidence of post-metamorphic contractional tectonics, with 140°N and 30°N trends, are found together with evidence of SW-directed extension. The siliciclastic Carnian beds of Unit B are correlated with the phyllites of Cetraro, formerly believed to be Middle Triassic; moreover, it is suggested that in the Cetraro area Unit C is almost totally replaced by Unit D. This demonstrates that the former distinction between the two tectonic units in the whole area has to be discarded. We have made a general palaeoenvironmental reconstruction which progresses laterally, during Ladinian,Carnian times, from (i) a coastal, mixed siliciclastic,carbonate,evaporitic area at Cetraro to (ii) a transitional carbonate shelf where siliciclastic input was only episodic, and finally to (iii) a bioconstructed margin which was later replaced by a steepened margin created by tectonic instability. Starting from the Norian, subsidence shifted toward the former coastal area where an intraplatform, restricted basin developed. The proposed stratigraphy corresponds closely to the Alpujarride units of the Betic Cordillera, Spain. Moreover, it is shown that strong affinities also exist, in terms of the structural framework, with the metamorphic units of Tuscany and Liguria. Copyright © 2005 John Wiley & Sons, Ltd. [source]

Lagoon,tidal flat sedimentation in an epeiric sea: Proterozoic Bhander Group, Son Valley, India

GEOLOGICAL JOURNAL, Issue 2 2001
Chandan Chakraborty
Abstract The Bhander Group, the uppermost stratigraphic unit of the Proterozoic Vindhyan Supergroup in Son Valley, exhibits in its upper part a 550,m thick, muddy siliciclastic succession characterized by features indicative of deposition in a wave-affected coastal, lagoon,tidal flat environment suffering repeated submergence and emergence. The basic architecture of the deposit is alternation of centimetre- to decimetre-thick sheet-like interbeds of coarser clastics (mainly sandstone) and decimetre-thick mudstones. The coarser interlayers are dominated by a variety of ripple-formed laminations. The preserved ripple forms on bed-top surfaces and their internal lamination style suggest both oscillatory and combined flows for their formation. Interference, superimposed, ladder-back and flat-topped ripples are also common. Synsedimentary cracks, wrinkle marks, features resembling rain prints and adhesion structures occur in profusion on bed-top surfaces. Salt pseudomorphs are also present at the bases of beds. The mudstone intervals represent suspension settlement and show partings with interfaces characterized by synsedimentary cracks. It is inferred that the sediments were deposited on a coastal plain characterized by a peritidal (supratidal,intertidal) flat and evaporative lagoon suffering repeated submergence and emergence due to storm-induced coastal setup and setdown in addition to tidal fluctuations. The 550,m thick coastal flat succession is surprisingly devoid of any barrier bar deposits and also lacks shoreface and shelfal strata. The large areal extent of the coastal flat succession (c. 100,000,km2) and its great thickness indicate an extremely low-gradient epeiric basin characterized by an extensive coastal flat sheltered from the deeper marine domain. It is inferred that the Bhander coastal flat was protected from the open sea by the Bundelkhand basement arch to the north of the Vindhyan basin, instead of barrier bars. Such a setting favoured accumulation of a high proportion of terrigenous mud in the coastal plain, in contrast to many described examples from the Proterozoic. Copyright © 2001 John Wiley & Sons, Ltd. [source]