Protein expression signatures: an application of proteomics

The methods of proteomics, the study of the protein complement of the genome, are applicable to environmental testing. Sets of proteins specific to different stressors can be isolated using computer imaging software. Individual proteins can be identified by mass spectrometry. The Protein Expression Signatures (PES) obtained have potential in diagnosing adverse factors in the environment. The challenge is to demonstrate their feasibility in complex environments. We have shown that PES for three endocrine disrupting compounds in trout (Onchorhynchus mykiss), can be detected in mixed sewage effluent. Other studies support these results. As protein databases expand, identification becomes routine, and capture molecules specific to each protein are developed, the possibility of simple field tests for multiple stressors becomes real.     

Long-term fish and macro-crustacean community variation in a Mediterranean lagoon

The fish and macro-crustacean community of the Vaccarès lagoon (Rhône River delta, South France) was sampled monthly from 1993 to 2002. The lagoon salinity shifted from 15 in 1993 to 5 in 1994–1997 and went back to 15 in 1999–2002. Connections with the sea also varied during the study period with larger openings in 1996–1997. During the study period, the community changed to revert in 2002 to a state similar to 1993. These changes consisted of a sequence of increased and decreased patterns of freshwater species and some marine species. Typical lagoon species tended to resist to salinity changes. Freshwater species colonised the lagoon when the salinity was low. Marine species may have varied both in relation to connections with the sea and to indirect effects of freshwater outflow. This study shows that community changes following environmental variations can be delayed in time, and emphasises the need for long-term studies.     

Tracing terrigenous dissolved organic matter and its photochemical decay in the ocean by using liquid chromatography/mass spectrometry

Reversed-phase liquid chromatography/mass spectrometry (LC/MS) is introduced as a new molecular fingerprinting technique for tracing terrigenous dissolved organic matter (DOM) and its photochemical decay in the ocean. DOM along a transect from the mangrove-fringed coast in Northern Brazil to the shelf edge was compared with mangrove-derived porewater DOM exposed to natural sunlight for 2–10 days in a photodegradation experiment. DOM was isolated from all samples via solid-phase extraction (C18) for LC/MS analysis. DOM in the estuary and ocean showed a bimodal mass distribution with two distinct maxima in the lower m/z range from 400 to 1000 Da (intensity-weighted average of 895 Da). Terrigenous porewater DOM from the mangroves was characterized by a broad molecular mass distribution over the detected range from 150 to 2000 Da (intensity-weighted average of 1130 Da). Polar compounds, i.e., those that eluted early in the reversed-phase chromatography, absorbed more UV light and had on average smaller molecular masses than the more apolar compounds.     

Climate change and control of the southeastern Bering Sea pelagic ecosystem

We propose a new hypothesis, the Oscillating Control Hypothesis (OCH), which predicts that pelagic ecosystem function in the southeastern Bering Sea will alternate between primarily bottom-up control in cold regimes and primarily top-down control in warm regimes. The timing of spring primary production is determined predominately by the timing of ice retreat. Late ice retreat (late March or later) leads to an early, ice-associated bloom in cold water (e.g., 1995, 1997, 1999), whereas no ice, or early ice retreat before mid-March, leads to an open-water bloom in May or June in warm water (e.g., 1996, 1998, 2000). Zooplankton populations are not closely coupled to the spring bloom, but are sensitive to water temperature. In years when the spring bloom occurs in cold water, low temperatures limit the production of zooplankton, the survival of larval/juvenile fish, and their recruitment into the populations of species of large piscivorous fish, such as walleye pollock (Theragra chalcogramma), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias). When continued over decadal scales, this will lead to bottom-up limitation and a decreased biomass of piscivorous fish. Alternatively, in periods when the bloom occurs in warm water, zooplankton populations should grow rapidly, providing plentiful prey for larval and juvenile fish. Abundant zooplankton will support strong recruitment of fish and will lead to abundant predatory fish that control forage fish, including, in the case of pollock, their own juveniles. Piscivorous marine birds and pinnipeds may achieve higher production of young and survival in cold regimes, when there is less competition from large piscivorous fish for cold-water forage fish such as capelin (Mallotus villosus). Piscivorous seabirds and pinnipeds also may be expected to have high productivity in periods of transition from cold regimes to warm regimes, when young of large predatory species of fish are numerous enough to provide forage. The OCH predicts that the ability of large predatory fish populations to sustain fishing pressure will vary between warm and cold regimes.The OCH points to the importance of the timing of ice retreat and water temperatures during the spring bloom for the productivity of zooplankton, and the degree and direction of coupling between zooplankton and forage fish. Forage fish (e.g., juvenile pollock, capelin, Pacific herring [Clupea pallasii]) are key prey for adult pollock and other apex predators. In the southeastern Bering Sea, important changes in the biota since the mid-1970s include a marked increase in the biomass of large piscivorous fish and a concurrent decline in the biomass of forage fish, including age-1 walleye pollock, particularly over the southern portion of the shelf. Populations of northern fur seals (Callorhinus ursinus) and seabirds such as kittiwakes (Rissa spp.) at the Pribilof Islands have declined, most probably in response to a diminished prey base. The available evidence suggests that these changes are unlikely the result of a decrease in total annual new primary production, though the possibility of reduced post-bloom production during summer remains. An ecosystem approach to management of the Bering Sea and its fisheries is of great importance if all of the ecosystem components valued by society are to thrive. Cognizance of how climate regimes may alter relationships within this ecosystem will facilitate reaching that goal.     

The effect of oceanographic variability and interspecific competition on juvenile pollock (Theragra chalcogramma) and capelin (Mallotus villosus) distributions on the Gulf of Alaska shelf

Results from this study suggest that small-scale variability in the Alaska Coastal Current (ACC) and competition between juvenile pollock and capelin are potential mechanisms affecting the distribution and abundance of fishes in the Gulf of Alaska (GOA). Fish distributions in Barnabus Trough, off the east coast of Kodiak Island, were assessed using acoustic data collected with a calibrated echosounder during August–September 2002 and 2004. Trawl hauls were conducted to determine the species composition of the fish making up the acoustic backscatter. Oceanographic data were collected from moorings, conductivity–temperature–depth (CTD) probes, trawl-mounted microbathythermographs (MBT) and expendable bathythermographs (XBT). National Centers for Environmental Prediction (NCEP) reanalysis data were used to assess area winds, and information on regional transport was derived from current meters deployed on moorings north and south of Kodiak Island. The distribution of water-mass properties and fish during 2002 showed variability at the temporal scale of weeks. Juvenile pollock (age-1 and age-2) were initially most abundant in warm, low-salinity water on the inner shelf, whereas capelin were distributed primarily on the outer shelf in cool, high-salinity waters. During a 2-week period juvenile pollock distribution expanded with the offshore expansion of warm, low-salinity water, and capelin abundance in outer-shelf waters decreased. We hypothesize that wind-driven pulsing of the ACC resulted in increased transport of warm, low-salinity water through the study area. In 2004, warm, low-salinity water characterized the inner shelf and cool, high-salinity water was found on the outer shelf. However, the distribution of water-mass properties did not show the weekly scale variability observed in 2002. Area winds were consistently toward the southwest during 2004, such that we would not expect to see the wind-driven pulsing of ACC water that occurred in 2002. Age-1 and age-2 pollock were not observed in Barnabus Trough in 2004. Instead, the midwater acoustic backscatter was composed of capelin mixed with age-0 pollock, and these capelin were not restricted to the outer-shelf waters, but were found primarily in warm, low-salinity inner-shelf waters that had been previously occupied exclusively by age-1 and age-2 pollock. We suggest that this is consistent with inner-shelf waters being preferred foraging habitat for juvenile pollock and capelin. Further study of the mechanisms linking climate change with variability in the ACC is needed, as are studies of the potential for competition between juvenile pollock and capelin.     

Sea-level rise impact models and environmental conservation: A review of models and their applications

Conservation managers and policy makers need tools to identify coastal habitats and human communities that are vulnerable to sea-level rise. Coastal impact models can help determine the vulnerability of areas and populations to changes in sea level. Model outputs may be used to guide decisions about the location and design of future protected areas and development, and to prioritize adaptation of existing protected area investments. This paper reviews state-of-the-art coastal impact models that determine sea-level rise vulnerability and provides guidance to help managers and policy makers determine the appropriateness of various models at local, regional, and global scales. There are a variety of models, each with strengths and weaknesses, that are suited for different management objectives. We find important trade-offs exist regarding the cost and capacity needed to run and interpret the models, the range of impacts they cover, and regarding the spatial scale that each operates which may overstate impacts at one end and underestimate impacts at the other. Understanding these differences is critical for managers and policy makers to make informed decisions about which model to use and how to interpret and apply the results.     

The influence of urbanization of sinkhole development in central Pennsylvania

The karsted limestone valleys of central Pennsylvania contain two populations of sinkholes. Solution sinkholes occur in the Champlainian limestone units along the margins of the valleys. Solution sinkholes are permanent parts of the landscape and, although a nuisance to construction, do not present other problems. The second population is the suffosional or soil-piping sinkholes These occur on all carbonate rock units including the Beekmantown and Gatesburg dolomites that comprise the two principal carbonate aquifers in the valley. Suffosional sinkholes are the principal land-use hazard. Suffosional sinkholes are transient phonomena. They occur naturally but are exacerbated by runoff modifications that accompany urbanization Suffosional sinkholes are typically 1.5–2.5 m in diameter depending on soil thickness and soil type. The vertical transport of soil to form the void space and soil arch that are the precursors to sinkhole collapse is through solutionally widened fractures and cross-joints and less often through large vertical openings in the bedrock. The limited solution development on the dolomite bedrock combined with soil thickness, seldom greater than 2 m, limits the size of the sinkholes. All aspects of suffosional sinkhole development are shallow processes: transport, piping, void and arch formation, and subsequent collapse take place usually less than 10 m below the land surface Factors exacerbating sinkhole development include pavement, street, and roof runoff which accelerates soil transport Such seemingly minor activities as replacing high grass and brush with mowed grass is observed to accelerate sinkhole development. Dewatering of the aquifer is not a major factor in this region     

Urban Perennials: How Diversification has Created a Sustainable Community Garden Movement in The United States

Our research seeks to understand how the contemporary community garden movement in the United States differs from its predecessors and whether its new foundation increases the political and financial sustainability of today's gardens. To this end, this article reviews historical and contemporary literature, and surveys participants in three distinctive community gardens, to answer several related research questions. First, what is the current state of the US community garden movement, and how have its historical roots shaped its response to current policy concerns? Second, which populations comprise today's community gardeners, and what motivates them to participate? After considering the findings from our three study gardens, and from a review of secondary and “gray” literature, we conclude by positing that a greater diversity of gardeners and gardening motivations, accompanied by changing leading views on urban land uses, will lead to such urban gardens remaining a more lasting feature of city neighborhood landscapes.     

The origin of Samoa: new evidence from Sr, Nd, and Pb isotopes

We report Sr, Nd and Pb isotope ratios and parent and daughter element concentrations in 34 volcanic rocks from Samoa. The highly undersaturated post-erosional volcanics, which have erupted in Recent to Historic time along a 250-km-long fissure, have isotopic compositions that define fields distinct from those of the tholeiitic to alkalic lavas of the older Samoan shield volcanoes. Most shield lavas have²⁰⁶Pb/²⁰⁴Pb of 18.9–19.4,⁸⁷Sr/⁸⁶Sr of 0.7045–0.7055 and⁸⁷Sr/⁸⁶Sr (to 0.7075). In general, isotopic compositions of the shield lavas are similar to those of the Marquesas and Society Islands. Post-erosional samples have lower²⁰⁶Pb/²⁰⁴Pb and¹⁴³Nd/¹⁴⁴Nd and higher⁸⁷Sr/⁸⁶Sr than most shield lavas. The most striking feature of the post-erosional data is a negative correlation between²⁰⁷Pb/²⁰⁴Pb and²⁰⁶Pb/²⁰⁴Pb. This suggests that post-erosional lavas are derived from mixtures of the shield source and a high-²⁰⁷Pb/²⁰⁴Pb,⁸⁷Sr/⁸⁶Sr, low-²⁰⁶Pb/²⁰⁴Pb and¹⁴³Nd/¹⁴⁴Nd post-erosional source which may contain recycled ancient sediment. This enriched mantle domain may also underlie the Ontong-Java and Manihiki Plateaus to the north and west. Although both the Samoan shield and post-erosional lavas show chemical characteristics often associated with mantle plumes, only the shield volcanism can plausibly be related to a plume. The post-erosional eruptions appear to be the result of flexure and rifting due to plate bending at the northern termination of the Tonga Trench.