Dissolved Organic Phosphorus Production during Simulated Phytoplankton Blooms in a Coastal Upwelling System

Dissolved organic phosphorus (DOP) is increasingly recognized as an important phosphorus source to marine primary producers. Despite its importance, the production rate and fate of DOP is poorly understood. In this study, patterns of DOP production were evaluated by tracking the evolution of DOP during simulated phytoplankton blooms initiated with nutrient amended surface waters, relative to controls, from the Oregon (USA) coastal upwelling system. Nitrogen (N) and phosphorus (P) additions were used to decouple DOP production and hydrolysis by inducing or repressing, respectively, community alkaline phosphatase activity. In order to examine the progression of nutrient uptake and DOP production under upwelling versus relaxation conditions, two experiments were initiated with waters collected during upwelling events, and two with waters collected during relaxation events. Maximum [under (+P) conditions] and minimum [under (+N) conditions] DOP production rates were calculated and applied to in situ DOP levels to evaluate which end-member rate most closely approximates the in situ DOP production rate at the four study sites in this coastal system. Increases in DOP concentration occurred by day-5 in control treatments in all experiments. N treatments displayed increased chlorophyll a, increased alkaline phosphatase activity, and yielded lower net DOP production rates relative to controls, suggesting that DOP levels were depressed as a consequence of increased hydrolysis of bioavailable DOP substrates. Phosphorus additions resulted in a significant net production of DOP at all stations, but no increase in chlorophyll a relative to control treatments. The contrasting patterns in DOP production between treatments suggests that changes in the ambient dissolved inorganic nitrogen:dissolved inorganic phosphorus (DIN:DIP) ratio could exert profound control over DOP production rates in this system. Patterns of DOP production across the different experiments also suggest that bathymetry-driven differences in water residence times can influence DOP cycling. Taken together, these factors may impact the potential export of DOP to offshore ecosystems

Importance of Suspended Particulates in Riverine Delivery of Bioavailable Nitrogen to Coastal Zones

Total nitrogen (TN) loadings in riverine sediments and their coastal depocenters were compared for Il river systems worldwide to assess the potential impact of riverine particulates on coastal nitrogen budgets. Strong relationships between sediment specific surface area and TN allow these impacts to be estimated without the intense sampling normally required to achieve such budgets. About half of the systems showed higher nitrogen loadings in the riverine sediments than those from the coastal depocenter. In spite of uncertainties, these comparisons indicate that large, turbid rivers, such as the Amazon, Huanghe, and the Mississippi, deliver sediments that in turn release significant or major fractions of the total riverine nitrogen delivery. Riverine particulates must therefore be considered an essential factor in watershed nutrient loading to coastal ecosystems and may affect delivered nutrient ratios as well as total nutrient loading. The relative importance of particulate versus dissolved delivery has decreased over recent decades in the Mississippi as a result of damming and fertilizer use in the watershed

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

Predator-Induced Demographic Shifts in Coral Reef Fish Assemblages

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ∼10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management

Polyphosphates as a source of enhanced P fluxes in marine sediments overlain by anoxic waters: Evidence from (31)P NMR

Sedimentary phosphorus (P) composition was investigated in Effingham Inlet, a fjord located on the west coast of Vancouver Island in Barkley Sound. Solid-state (31)P nuclear magnetic resonance (NMR) spectroscopy was applied to demineralized sediment samples from sites overlain by oxic and anoxic bottom waters. The two sites were similar in terms of key diagenetic parameters, including the mass accumulation rate, integrated sulfate reduction rate, and bulk sediment organic carbon content. In contrast, P benthic fluxes were much higher at the anoxic site. (31)P NMR results show that P esters and phosphonates are the major organic P species present at the surface and at depth in sediments at both sites. Polyphosphates were only found in the surface sediment of the site overlain by oxic waters. The varying stability of polyphosphates in microorganisms under different redox conditions may, in part, explain their distribution as well as differences in P flux between the two sites

Word add-in for ontology recognition: semantic enrichment of scientific literature

<p>Abstract</p> <p>Background</p> <p>In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles.</p> <p>Results</p> <p>The Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at <url>http://www.codeplex.com/UCSDBioLit</url>.</p> <p>Conclusions</p> <p>The Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata.</p