Seismic characteristics and accretion history of Halimeda bioherms on Kalukalukuang Bank,eastern Java Sea (Indonesia)

Extensive areas of Halimeda bioherms similar to those described by Orme et al. (1978), Orme (1985), Davies and Marshall (1985), and Phipps et al. (1985) from Australia's Great Barrier Reef have formed on Kalukalukuang Bank (K-Bank) 50 km east of the Sunda Shelf margin in the easter Java Sea. K-Bank is an isolated limestone platform whose top slopes southward from a water depth of about 20 m at the north to about 100 m at the south (30 km). It occurs in a bidirectional monsoonal wind regime and a predominantly southerly flowing current from Makassar Strait. The water column around K-Bank has a well developed shallow thermocline (50 m to 150 m). K-Bank has a relatively flat top with marginal banks of suspected Pleistocene origin as interpreted from seismic relationships. A reconnaissancelevel survey grid of high-resolution seismic profiles indicates that Halimeda bioherms are restricted to the bank margins with the exception of the eastern margin. Bioherms either extend to the steep margin of the platforms or are separated from the platform edge by banks of coral and coralline algae. The morphology of the Halimeda bioherms varies from steep-sided, elongate ridges in the northern bank area, through coalescing symmetrical mounds with partly infilled valleys, to broad undulating areas similar to those described by Orme (1985) from the Great Barrier Reef. High-resolution seismic records indicate erosional episodes in the high-relief areas, an interpretation that seems to be supported by accumulation rates calculated from C¹⁴ dates of cores. Thicknesses of Halimeda accumulation above a prominent reflector considered as Pleitocene, vary from around 20 m in the north to a maximum of over 50 m in the southwest. Accumulation rates obtained from dating of two cores to-ward the north of K-Bank, average 0.294 m/100 yr for core VC4 and a maximum of 0.59 m/100 yr in a part of core PC12. Dating of material from the top 30 cm of a deep bioherm (100 m) in the southwest of K-Bank, indicates that the growth rate of these bioherms has slowed markedly, presumably because of increasing water depth (decreasing light) over the Holocene transgression.     

Bioerosion along a bathymetric gradient in a cold-temperate setting (Kosterfjord, SW Sweden): an experimental study

In the cold-temperate setting of the Swedish Kosterfjord, a 2-year experiment was launched in order to assess bioerosion rates and to investigate the endolithic borer communities in relation to light availability (relative bathymetry), hydrography and exposure time. The inventory of microendolithic traces, studied by SEM analysis of epoxy resin casts of planted bivalve shells, yields diverse ichnocoenoses comprising a total of 21 traces produced by boring cyanobacteria (7), chlorophytes (4), fungi (6) and traces of uncertain affinity (4). The link between the endoliths (biotaxa) and the traces they leave (ichnotaxa) is evaluated by the study of the boring organisms in situ by transmission light microscopy of planted Iceland spar and bivalve shells. Additionally, the activity of various macroborers (foraminiferans, polychaetes, echinoids, gastropods and sponges) is documented, adding to a distinct diversity maximum at 7 m water depth. A highly condensed photic zonation, due to the high latitude (59°) and eutrophic conditions, is recorded by the measurement of the Photosynthetically Active Radiation (PAR) and is confirmed by the bathymetric range of the photic related ichnocoenoses. At 1 m water depth, a mature shallow euphotic ichnocoenosis dominated by cyanobacteria and at 7 m, a deep euphotic ichnocoenosis dominated by chlorophytes, respectively, is developed after as little as 12 months exposure. With the vanishing light availability from 15 m downwards, the ichnocoenoses development is significantly slowed and only immature dysphotic and aphotic borer communities (dominated by fungi) are encountered. Strong fluctuations of salinity (down to 8%) and temperature (0–20°C) in the euphotic zone indicate most phototrophs present to be considerably euryhaline and eurytherm, while most endolithic fungi appear preferentially in the deeper, more stable marine waters.     

Aquatic biodiversity under anthropogenic stress: an insight from the Archipelago Sea (SW Finland)

The Archipelago Sea in the northern Baltic has been subjected to large-scale cultural, economic and ecological changes, especially during the last three decades. Environmental threats originate from both basin-wide sources, affecting the whole Baltic Sea, and from local sources, such as nutrient loading from nearby river outflows, intense agriculture, fish farming, ships' traffic, boating, and man's physical impacts on the landscape and seascape. Both the Åland archipelago and the Archipelago Sea have been listed as hot-spots by HELCOM, Baltic Marine Environment Protection Commission, eutrophication being the main threat to the aquatic environment. In this study we review how biological communities have reacted to an increase in man-induced multisource stresses. Changes in plankton, benthic animals, macroalgal assemblages and fish communities have been documented in most parts of the Baltic Sea since the 1970s. What remains to be understood is the importance of these structural changes for the functioning of the Archipelago Sea ecosystem under various levels of human impact.     

Seasonal oxygen,nitrogen and phosphorus benthic cycling along an impacted Baltic Sea estuary: regulation and spatial patterns

The regulatory roles of temperature, eutrophication and oxygen availability on benthic nitrogen (N) cycling and the stoichiometry of regenerated nitrogen and phosphorus (P) were explored along a Baltic Sea estuary affected by treated sewage discharge. Rates of sediment denitrification, anammox, dissimilatory nitrate reduction to ammonium (DNRA), nutrient exchange, oxygen (O₂) uptake and penetration were measured seasonally. Sediments not affected by the nutrient plume released by the sewage treatment plant (STP) showed a strong seasonality in rates of O₂ uptake and coupled nitrification–denitrification, with anammox never accounting for more than 20 % of the total dinitrogen (N₂) production. N cycling in sediments close to the STP was highly dependent on oxygen availability, which masked temperature-related effects. These sediments switched from low N loss and high ammonium (NH₄ ⁺) efflux under hypoxic conditions in the fall, to a major N loss system in the winter when the sediment surface was oxidized. In the fall DNRA outcompeted denitrification as the main nitrate (NO₃ ^?) reduction pathway, resulting in N recycling and potential spreading of eutrophication. A comparison with historical records of nutrient discharge and denitrification indicated that the total N loss in the estuary has been tightly coupled to the total amount of nutrient discharge from the STP. Changes in dissolved inorganic nitrogen (DIN) released from the STP agreed well with variations in sedimentary N₂ removal. This indicates that denitrification and anammox efficiently counterbalance N loading in the estuary across the range of historical and present-day anthropogenic nutrient discharge. Overall low N/P ratios of the regenerated nutrient fluxes impose strong N limitation for the pelagic system and generate a high potential for nuisance cyanobacterial blooms.     

Temporal variability of abundance and reproductive traits of Centropages kroyeri (Calanoida; Copepoda) in Bizerte Channel (SW Mediterranean Sea, Tunisia)

Abundance and reproductive traits (spawning female, egg production, egg hatching success) and naupliar survival of the dominant calanoid copepod Centropages kroyeri were investigated in relation to biotic (chlorophyll a, phytoplankton and microplankton) and abiotic (temperature and salinity) parameters at a monitoring station located in Bizerte Channel, northern Tunisia. The monitoring was carried out between July 2004 and December 2004, according to two temporal sampling strategies. First, during July, the supposed maximum abundance period of C. kroyeri, daily sampling was conducted. Thereafter, sampling was carried out weekly until the end of the sampling period.The temporal variability of the environmental factors in relation to the reproductive traits of C. kroyeri revealed, first, that temperature is important in controlling the reproduction and dynamics of this species, and second, that the quantity and quality of food available in the field also strongly influence its reproduction. On several sampling dates, the output of certain reproductive traits such as hatching success after 24 h was very weak. It is possible that C. kroyeri produced resting eggs during the study period. Nerveless, the analysis of the phytoplankton during these periods showed that low reproductive activity may have been caused by low phytoplankton quantity and/or by the dominant presence of certain diatom species that are supposed to have an inhibitory effect on the reproductive traits of C. kroyeri, especially on egg hatching success.Among the considered external parameters, temperature and food quality and availability seem to be the most important factors for the reproduction and dynamics of C. kroyeri. Under these biotic and abiotic field conditions, this copepod seems able to modulate the abundance of its population while controlling its reproduction.     

BioImageXD: an open, general-purpose and high-throughput image-processing platform

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.     

Cenozoic deep-sea ostracods from Maud Rise, Weddell Sea, Antarctica (ODP Site 689): a palaeoceanographical perspective

Cenozoic palaeoceanography of the Maude Rise, Weddell Sea, Antarctica, has been investigated using Palaeocene to Quaternary deep-sea ostracod faunas from 23 samples of ODP Site 689. The abundance of ostracods is high enough only during the Palaeogene (Palaeocene-Oligocene) to allow palaeoceanographical inferences based on changes in diversity, dominance, endemism and faunal turnover (first and last occurrences). The abundance is particularly high throughout the Palaeocene and Eocene, but declines irreversibly near the Eocene/Oligocene boundary. The diversity increases more or less continuously from the Early Palaeocene to the Middle Eocene, and then it generally decreases throughout the remaining part of the Palaeogene (Middle Eocene-Oligocene); an exception is a positive peak in the Shannon-Weaver index in a single sample in the Late Oligocene. No positive peaks in diversity and taxa originations (first occurrences) at c. 40-38 Ma, occurs at Site 689; so the site provides no evidence for the establishment of the psychrosphere at this time. This corroborates similar regional results from an earlier study of benthonic foraminifera. Explanations for this may be related to Late Eocene-Early Oligocene changes in sedimentology and clay-mineralogy (associated with the progressive cooling of the Antarctica) which could have negatively affected abundance and diversity locally at Site 689. Alternatively, by this time, the ostracod fauna could also have been subjected to selective removal (with possible local extinction) of taxa (due to increased ventilation) or to thanatocoenosis dissolution (due to a decrease in temperature and availability of CaCO₃). A further possibility may be related to the fact that Site 689 was at intermediate water depths and may have remained within older water masses near the Eocene/Oligocene boundary. Failing these explanations, the results could indicate that the Late Eocene-Early Oligocene palaeoenvironmental changes in the world oceans were more gradual and occurred over a longer time interval than the global ostracod data show, at least at southern high latitudes.     

A Vulnerability Assessment of 300 Species in Florida: Threats from Sea Level Rise,Land Use,and Climate Change

Species face many threats, including accelerated climate change, sea level rise, and conversion and degradation of habitat from human land uses. Vulnerability assessments and prioritization protocols have been proposed to assess these threats, often in combination with information such as species rarity; ecological, evolutionary or economic value; and likelihood of success. Nevertheless, few vulnerability assessments or prioritization protocols simultaneously account for multiple threats or conservation values. We applied a novel vulnerability assessment tool, the Standardized Index of Vulnerability and Value, to assess the conservation priority of 300 species of plants and animals in Florida given projections of climate change, human land-use patterns, and sea level rise by the year 2100. We account for multiple sources of uncertainty and prioritize species under five different systems of value, ranging from a primary emphasis on vulnerability to threats to an emphasis on metrics of conservation value such as phylogenetic distinctiveness. Our results reveal remarkable consistency in the prioritization of species across different conservation value systems. Species of high priority include the Miami blue butterfly (Cyclargus thomasi bethunebakeri), Key tree cactus (Pilosocereus robinii), Florida duskywing butterfly (Ephyriades brunnea floridensis), and Key deer (Odocoileus virginianus clavium). We also identify sources of uncertainty and the types of life history information consistently missing across taxonomic groups. This study characterizes the vulnerabilities to major threats of a broad swath of Florida’s biodiversity and provides a system for prioritizing conservation efforts that is quantitative, flexible, and free from hidden value judgments.     

The Spines of the Channel Catfish, Ictalurus punctatus, as an Anti-Predator Adaptation: an Experimental Study

Although experimental evidence is lacking, the stout pectoral spine of catfishes has been interpreted as a defensive adaptation. The spine can be rigidly locked and abducted to produce stridulation sounds, which have been hypothesized to serve a warning function. We studied spine function in channel catfish (Ictalurus punctatus) as a deterrent to predation by largemouth bass (Micropterus salmoides) by presenting individuals with pairs of catfish, one with its pectoral spines clipped and the other intact. The number of initial attacks on clipped and intact fish was similar, suggesting that bass do not recognize the spine visually. Bass showed evidence of learning across trials, striking clipped fish fewer times and consuming them. Conversely, intact fish were attacked more than clipped ones because intact fish were repeatedly disgorged and attacked again, suggesting that bass become sensitized to the spine. Ingestion times were longer for intact than clipped fish, and fewer intact fish were eaten. Eighty‐eight percent of intact fish survived in the mouth of a bass one or more times. Catfish did not stridulate or use their spines to deter initial attacks, refuting the warning hypothesis. Locking and stridulation motions, only observed when catfish were held inside the mouth of a bass, did not deter subsequent attacks indicating that neither the spine nor stridulation carry a warning function. It is possible, therefore, that stridulation sounds function as a distress call. The spine functions against a gape‐limited predator by increasing the difficulty of ingestion but not capture.     

Vertical distribution, population structure and life history of Thysanoessa longipes (Crustacea: Euphausiacea) around Yamato Rise, central Japan Sea

The diel vertical migration, growth and spawning season of theeuphausiid, Thysanoessa longipes, were investigated using seasonalsamples collected from waters around the Yamato Rise, centralJapan Sea, during the period 1987 to 1999. Thysanoessa longipeswas present throughout a broad bathymetric layer extending downas deep as 1000 m. There was a clear trend for larger specimensto occur at deeper depths. The peak of abundance of the totalpopulation occurred at depths of 30–300 m at night, and150–500 m during the day, and the distance of the dielvertical migrations of the total population was estimated tobe between 100 and 150 m. Population structure analysis revealedthe occurrence of three cohorts aged 0+, 1+ and 2+ years, withfemales attaining a larger body size than males. Growth as determinedby body length was found to fit well to the von Bertalanffygrowth equation. The estimated life span for males and femalesis 3 years, and females reach maturity in 2 years. Based onthe occurrence of calyptopis larvae, spawning of T. longipeswas estimated to occur over only a limited period of the yearbetween April and May.     

Dinoflagellate cyst distribution along a shelf to slope transect of an oligotrophic tropical sea (Sunda Shelf, South China Sea)

From 51 surface samples collected along a shelf to slope transect of the Sunda Shelf, South China Sea, 36 taxa of organic‐walled dinoflagellate cysts are identified. Oligotrophic tropical shelf assemblages on the Sunda Shelf are dominated by gonyaulacoids such as Spiniferites species, Operculodinium centmcarpum and Operculodinium israelianum. Concentrations of dinoflagellate cysts in the shelf sediments are generally low and correlate well with the content of fine‐grained (clay and silt fraction) sediments. Detailed comparisons of sediment grain‐size distributions to concentrations of dominant dinoflagellate taxa (Spiniferites species, 0. centmcarpum and 0. israelianum) in the shelf sediments indicate that these taxa behave in water like sediment particles with size range φ 5.75–6.25 (13–18 μm). In contrast, slope assemblages in fine‐grained sediments are dominated by protoperidinioids. This may reflect higher nutrient availability as a result of weak winter upwelling. The concentrations of dinoflagellate cysts in the shelf sediments are mainly controlled by transport and winnowing processes and are probably not representative of surface water conditions.     

Bacterial activity in sea ice and open water of the Weddell Sea,Antarctica: A microautoradiographic study

Metabolic activity of bacteria was investigated in open water, newly forming sea ice, and successive stages of pack ice in the Weddell Sea. Microautoradiography, using [³H]leucine as substrate, was compared with incorporation rates of [³H]leucine into proteins. Relation of [³H]leucine incorporation to the biomass of active bacteria provides information about changes of specific metabolic activity of cells. During a phytoplankton bloom in an ice-free, stratified water column, total numbers of bacteria in the euphotic zone averaged 2.3 × 10⁵ ml^–1, but only about 13% showed activity via leucine uptake. Growth rate of the active bacteria was estimated as 0.3–0.4 days^–1. Total cell concentration of bacteria in 400 m depth was 6.6 × 10⁴ ml^–1. Nearly 50% of these cells were active, although biomass production and specific growth rate were only about one-tenth that of the surface populations. When sea ice was forming in high concentrations of phytoplankton, bacterial biomass in the newly formed ice was 49.1 ng C ml^–1, exceeding that in open water by about one order of magnitude. Attachment of large bacteria to algal cells seems to cause their enrichment in the new ice, since specific bacterial activity was reduced during ice formation, and enrichment of bacteria was not observed when ice formed at low algal concentration. During growth of pack ice, biomass of bacteria increased within the brine channel system. Specific activity was still reduced at these later stages of ice development, and percentages of active cells were as low as 3–5%. In old, thick pack ice, bacterial activity was high and about 30% of cells were active. However, biomass-specific activity of bacteria remained significantly lower than that in open water. It is concluded that bacterial assemblages different to those of open water developed within the ice and were dominated by bacteria with lower average metabolic activity than those of ice-free water.     

Productivity, growth rates and cell size distributions of phytoplankton in the SW Tasman Sea: implications for carbon metabolism in the photic zone

Data are presented on primary productivity, cell size distributionsand the standing stocks of living and detrital paniculate organiccarbon (POC) in the waters of the SW Tasman Sea. Primary productivitywas measured by both standard 4- and 12-h incubations as wellas time-series incubations. Data are presented for ¹⁴C uptakeand loss in 12L/12D methods. The importance of time zero anddark controls is demonstrated. The uptake of ¹⁴C in the lightwas linear and the loss of label in the following dark periodranged from zero to 39%. The loss of label in the dark was correlatedwith the particle size distribution, being greatest in oligotrophicwaters dominated by small cells (25–30%) and least inspring bloom areas (0–20%) dominated by large diatoms.Kinetic data were strongly supportive of a major grazing impactby microphagous organisms. The data were an experimental confirmationof recent theoretical models of ¹⁴C uptake and grazing. Sizedistributions of phytoplankton and detritus were measured byHIAC and by microscopic counting. The phytoplankton consistedof a ubiquitous group of picoplankton, and variable contributionsfrom small flagellates and diatoms. The distribution of totalcell volume was dominated by large cells in spring bloom areas.Chlorophyll concentrations were strongly correlated with themean cell size of the phytoplankton. Comparison of the resultsof ¹⁴C uptake experiments with the results of experiments todetermine changes in POC, by counting particles, gave good correlation.In detail, the comparison of the methods revealed systematicerrors with the greatest discrepancy between the methods atlow apparent growth rates. The detritus showed constant sizedistributions in surface waters. The mean size of detritus particlesreduced rapidly with depth and declined in a way suggestingbiological reprocessing and removal by grazing. These resultsare discussed in the context of the patterns of carbon metabolismin the photic zone, the role of living and detrital POC andthe balance of ‘new’ versus ‘regenerated’production in surface waters.     

Science, Salmon, and Sea Lice: Constructing Practice and Place in an Environmental Controversy

Over the last three decades salmon aquaculture has become both a significant coastal industry and a focus of controversy regarding its environmental impacts. Both circumstances have also provoked a great deal of environmental research. This article examines one episode in the history of this research. The Broughton Archipelago is a region of islands and channels on the Pacific coast of Canada, densely populated with salmon farms. Beginning in 2001 this region attracted researchers from several institutions, who examined the ecology of the farms, and particularly the possibility that they release large numbers of parasites (known as sea lice), which then infect wild salmon. This local research community drew on aspects of the regional environment, including its ecological conditions, and opportunities for surveys, field experiments, and ecological modeling, to construct methods that were both situated in this place, yet intended to be persuasive to audiences outside the region. Knowledge of this environment was also influenced by knowledge from elsewhere, including the results of European research on sea lice, and various disciplinary perspectives. Research results were invoked to support opposing views of the impacts of salmon farms, as well as contrasting perspectives on the region's identity. Sea lice themselves, within the context of the ecosystem that gave them meaning, were objectified as the ecological link between salmon farms and the environment, and the basis for research and debate over these farms. This historical episode therefore demonstrates the inseparability of scientific practice, knowledge and place, particularly in the context of controversy.