Uses and Misuses of the Journal Impact Factor

The second in a series of articles published in OSU This Week by members of the Faculty Senate Library Committee regarding threats to an open and sustainable system of scholarly communication and potential solutions. Article describes what journal impact factors are and how they are determined and makes recommendations for their proper use.Keywords: Scholarly publishing, Scholarly communication, Journal impact factorsKeywords: Scholarly publishing, Scholarly communication, Journal impact factor

Introduction to special section : Coastal Advances in Shelf Transport

The Coastal Ocean Advances in Shelf Transport (COAST) program conducted an interdisciplinary study of coastal upwelling off central Oregon during summer 2001. Two intensive field efforts during May–June and August 2001 were coordinated with ocean circulation, ecosystem, and atmospheric modeling of the region. A primary goal was to contrast the coastal ocean response to wind forcing in a region of relatively simple alongshore bottom topography versus that associated with a substantial submarine bank. In this overview we provide background motivation for the COAST project and summarize the major research findings

Uptake of ammonium and urea in the northeast Pacific: comparison between netplankton and nanoplankton

The stable isotope 15N was used to measure nitrogen uptake in the coastal upwelling region off Oregon and Washington, USA, where nitrate concentrations in the surface water ranged from 0.7 to 49.1 μM. Nanoplankton biomass (1 to 10 pm) was relatively more abundant at low-nitrate stations, while netplankton biomass (10 to 200 μm) was dominant at high-nitrate stations. Ammonium was more important than urea as a regenerated nitrogen source for both size classes of plankton, and ambient ammonium concentrations appeared to inhibit urea assimilation. Nanoplankton and netplankton were equally important in use of regenerated nitrogen in low-nitrate waters, while netplankton dominated nitrogen use in high-nitrate waters. In high-nitrate waters, the percent uptake in each size fraction was proportional to the percent particulate nitrogen (PN) and chlorophyll a (chl a) in that fraction. At low-nitrate stations, uptake in each fraction was proportional to PN but not to chl a. Nitrogen-specific (mass N taken up/mass particulate N) uptake rates ranged from 0.2 to 2.6 d-l, and were generally higher for the netplankton than for the nanoplankton fraction. However, these rates are not directly proportional to phytoplankton use as a result of varying amounts of non-phytoplankton N. Phytoplankton N was estimated by assuming a constant chl a/PN ratio for each size class, and used to calculate phytoplankton-specific uptake rates. Phytoplankton growth rates were estimated by extrapolating the short-term uptake rates to daily rates. Since calculated growth rates exceeded the expected maxima for phytoplankton In the low-nitrate coastal water, we postulate heterotrophic utilization of nitrogen

Seasonal and across-shelf trends of the phytoplankton community of the Oregon coastal environment

This project, part of the Northeast Pacific GLOBEC Long Term Observation Project (NEPGLOBEC- LTOP), constitutes the first multi-year study of phytoplankton variability in the Oregon coastal environment. The work divides into two studies: analysis of interseasonal change and analysis of detailed changes within the summer upwelling period. In the first study, I found that the majority of variability in phytoplankton biomass in this system is due to changes in the abundance of chain forming diatoms, particularly diatoms of the genera Chaetoceros and Skeletonema. The abundance of nanoflagellates (<10 μm) remains constant across the shelf. They dominate the phytoplankton community in the offshore stations and larger cells, usually diatoms, are added inshore. Cyanobacteria, though numerically abundant, never comprise more than approximately 10% of phytoplankton biomass. Variation within the summer phytoplankton bloom over the shelf was analyzed based on results from the four NEP-GLOBEC-LTOP summer cruises between August 1998 and July 2001. Nutrient concentrations during the summer upwelling blooms show a linear decrease with increasing temperature from 8 to 12° C. Over this range of temperatures, total Chl a and phytoplankton biomass increase, though not significantly, and the % Chl a >10 μm remains high (>50 %). Above 12° C, when inorganic nutrients are depleted or greatly reduced, total Chl a and % Chl a >10 μm decrease. The diatom genera Chaetoceros and Skeletonema are also responsible for the majority of the variability in phytoplankton stock during the summer phytoplankton bloom. Dinoflagellates, although present, are consistently less abundant than diatoms

Ammonium uptake and regeneration rates in a coastal upwelling regime

Ammonium uptake and regeneration rates were measured in time course experiments with 15N as a tracer. Both ammonium uptake and regeneration rates measured over 12 to 18 h remained essentially constant. However, as the length of the incubations increased the amount of usable data decreased dramatically due to substrate depletion and recycling of 15N. Mass balance calculations indicated that 22 to 51 % of the ammonium removed from the dissolved pool was not recovered in the particulate fraction. This appeared to be a more serious problem at 0 and 8 m (47%) than at 25 m (22%). As a result, ammonium uptake rates were probably underestimated. At 0, 12, and 20 m uptake rates either balanced or exceeded regeneration rates, while at 8 and 25 m net regeneration occurred. The fastest rates were measured during upwelling-induced phytoplankton blooms, intermediate rates characterized post-bloom conditions and the lowest rates coincided with an active upwelling event. Ammonium uptake rates were highest during the upwelling season (11 to 17 mmol N m-2 d-1) and lowest during the non-upwelling season (3 mmol N m-2 d-1), whereas regeneration rates did not differ significantly between seasons (11 to 20 mmol N m-2 d-1 ).Keywords: Ammonium uptake, Coastal upwelling, Ammonium regeneratio

Production and partitioning of organic matter during simulated phytoplankton blooms

Few studies have examined the partitioning of organic matter in upwelling systems, despite the fact that these systems play a key role in carbon and nitrogen budgets in the ocean. We examined the production and partitioning of phytoplankton-derived organic matter in deck incubations off Oregon during the upwelling season. During exponential growth of the phytoplankton, ≥78% of total accumulated organic matter was in particulate (POM) form. This suggests that dissolved organic matter (DOM) is a small fraction of primary production during the exponential growth of coastal phytoplankton blooms. After nitrate depletion, carbon-rich (C:N ≥ 16) DOM accumulated in incubations dominated by the diatom Chaetoceros sp., accounting for 38% (±8.5%) of accumulated total organic carbon (TOC) and 24% (±8%) of accumulated total organic nitrogen (TON). However, in a bloom dominated by the diatom Leptocylindrus minimus, a relatively smaller amount of DOM accumulated, accounting for only 15% of accumulated TOC and 7% of accumulated TON. On the basis of measured concentrations of nitrate and accumulated TOC, ~70%–157% more carbon was fixed than would be predicted by Redfield stoichiometry (referred to as "excess carbon fixation"), with 20%–69% of the excess carbon fixation occurring after nitrate depletion. The accumulation of carbon-rich DOM and excess carbon fixation suggests that nitrate assimilation (i.e., new production) might not equate to net production of POM in coastal upwelling systems

Release of dissolved organic matter by coastal diatoms

Dissolved organic matter (DOM) production was examined in axenic batch cultures of five coastal diatom species. For Chaetoceros decipiens, dissolved organic carbon (DOC) accumulated beginning in late exponential growth as a result of increased cell density. For Cylindrotheca closterium, DOC actually decreased in late exponential growth and reached zero by the end of the experiment. This coincided with continued particulate organic carbon (POC) production and a threefold increase in the per‐cell concentration of transparent exopolymer particles after nutrients were depleted. DOC release rates varied between species but were significantly higher for all five species in exponential or transition growth than during stationary growth. On average, 5% of the total fixed C was released as DOC for four of the diatoms, whereas C. decipiens released ~21% of its fixed C as DOC. The percentage of fixed C released as DOC varied little with nutrient availability or diatom growth stage. The DOM produced by some diatom species adheres to filters and is measured in the particulate organic matter (POM) fraction when cells are separated from the medium by filtration. This may be an important problem when diatom species with known benthic life histories are prevalent. In contrast, for species like Chaetoceros that have no benthic life history, DOM release rates estimated by bulk measurements or ¹⁴C appear to be accurate. Overall, these results indicate that the species composition of phytoplankton blooms has the potential to influence the relative importance of POM and DOM production and can complicate interpretation of those measurements.Keywords: Coastal diatoms, Dissolved organic matte

Two coastal upwelling domains in the northern California Current system

A pair of hydrographic sections, one north and one south of Cape Blanco at 42.9N, was sampled in five summers (1998–2000 and 2002–2003). The NH line at 44.6N lies about 130 km south of the Columbia River, and spans a relatively wide shelf off Newport, Oregon. The CR line at 41.9N off Crescent City, California, lies 300 km farther south and spans a narrower shelf. Summer winds are predominantly southward in both locations but the southward winds are stronger on the CR line. Sampling included CTD/rosette casts (to measure temperature, salinity, dissolved oxygen, nutrients, chlorophyll), zooplankton net tows and continuous operation of an Acoustic Doppler Current Profiler. We summarize and compare July-August observations from the two locations. We find significant summer-season differences in the coastal upwelling domains north and south of Cape Blanco. Compared to the domain off Newport, the domain off Crescent City has a more saline, cooler, denser and thicker surface mixed layer, a wider coastal zone inshore of the upwelling front and jet, higher nutrient concentrations in the photic zone and higher phytoplankton biomass. The southward coastal jet lies near the coast (about 20–30 km offshore, over the shelf) on the NH line, but far from shore (about 120 km) on the CR line; a weak secondary jet lies near the shelf-break (35 km from shore) off Crescent City. Phytoplankton tend to be light-limited on the CR line and nutrient-limited on the NH line. Copepod biomass is high (15 mg C m−3) inshore of the mid-shelf on both NH and CR lines, and is also high in the core of the coastal jet off Crescent City. The CR line shows evidence of deep chlorophyll pockets that have been subducted from the surface layer. We attribute these significant differences to stronger mean southward wind stress over the southern domain, to strong small-scale wind stress curl in the lee of Cape Blanco, and to the reduced influence of the Columbia River discharge in this region