Wave breaking turbulence at the offshore front of the Columbia River Plume

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geophysical Research Letters 41 (2014): 8987–8993, doi:10.1002/2014GL062274.Observations at the Columbia River plume show that wave breaking is an important source of turbulence at the offshore front, which may contribute to plume mixing. The lateral gradient of current associated with the plume front is sufficient to block (and break) shorter waves. The intense whitecapping that then occurs at the front is a significant source of turbulence, which diffuses downward from the surface according to a scaling determined by the wave height and the gradient of wave energy flux. This process is distinct from the shear-driven mixing that occurs at the interface of river water and ocean water. Observations with and without short waves are examined, especially in two cases in which the background conditions (i.e., tidal flows and river discharge) are otherwise identical.This work was supported by the Office of Naval Research, as part of the Data Assimilation and Remote Sensing for Littoral Applications (DARLA) project and in coordination with the Rivers and Inlets (RIVET) program

Filtration rates of the non-native Chinese mystery snail (Bellamya chinensis) and potential impacts on microbial communities

Invasive species in the phylum Mollusca, including gastropods and bivalves, have caused substantial impacts in freshwater ecosystems. The Chinese mystery snail, Bellamya chinensis, is a large viviparid snail native to Southeastern Asia and widely introduced throughout United States and parts of Canada and Europe. B. chinensis is a facultative filter-feeding detritivore that can both graze epiphytic diatoms using its radula and filter-feed its breathing water. Despite mounting concern associated with the expanding range and increasing abundance of B. chinensis in many parts of its invaded range, the potential ecological impacts of this non-native species remain largely unknown. Here, we used a series of laboratory experiments to assess filtration rates of B. chinensis and quantify its effects on microbial communities. According to both microcosm (24-hour, 4-L suspension) and mesocosm (5-day, 90-L suspension) experimental trials, B. chinensis exhibited an average filtration rate of 106-113 mL snail-1h-1(1.45 mL mg DW-1h-1) and an individual maximum of 471 mL snail-1h-1(6.15 mL mg DW-1h-1). These values are comparable to reported filtration rates for high-profile invasive, freshwater bivalves. Relationships between snail size and filtration rate relationship suggests that B. chinensis display an ontogenetic shift in feeding behavior from primarily radular grazing to increased filter-feeding at threshold size of approximately 44 mm shell height. Our experiments also revealed that high snail densities can result in small, significant shifts in bacterial community composition. These results suggest that B. chinensis may influence microbial communities either directly by using bacteria as a food source or indirectly by producing sufficiently large quantities of fecal and pseudo-fecal material to affect bacterial activity and growth. The overall ecological effects and importance of B. chinensis filtration behavior remain unclear, but our experimental results suggest that these impacts may be large and should be further investigated to better understand its potential role in coupling benthic and pelagic food webs in lake ecosystems.Las especies invasoras del phyllum Mollusca, incluyendo los gasterópodos y bivalvos, han causado impactos importantes en los ecosistemas dulceacuícolas. Bellamya chinensis, es un vivíparo de gran tamaño, nativo del sureste de Asia y ampliamente introducido a lo largo de los Estados Unidos y parte de Canadá y Europa. B. chinensis es una especie detritivora- filtradora facultativa, que puede tanto ramonear diatomeas epifitas usando su rádula como filtrar el agua que respiran. A pesar de la creciente preocupación asociada al incremento en la abundancia y rango de distribución de B. chinensis en las regiones ya colonizadas, el potencial impacto ecológico de esta especie introducida permanece ampliamente desconocido. En este estudio, usamos series de experimentos de laboratorio para evaluar las tasas de filtración de B. chinensis y cuantificar su efecto en las comunidades microbianas. De acuerdo con los experimentos realizados tanto en los microcosmos (24-hour, 4-L suspensión) como en los mesocosmos (5-day, 90-L suspensión), B. chinensis mostró una tasa promedio de filtración de 106-113 mL caracol-1h-1(1.45 mL mg peso seco-1h-1) y un máximo por individuo de 471 mL caracol-1h-1(6.15 mL mg peso seco-1h-1). Estos valores son comparables a otros reportados para especies de bivalvos dulceacuícolas altamente invasivas. La relación entre el tamaño de los caracoles y las tasas de filtración sugieren que B. chinensis muestra un cambio ontogénico en la manera de alimentarse, de ramoneo a una mayor alimentación por filtración, a partir de un umbral de tamaño de la concha de aproximadamente 44 mm de altura. Nuestros experimentos también revelan que altas densidades de caracoles generan pequeños cambios pero significativos en las comunidades microbianas. Estos resultados sugieren que B. chinensis afectaría las comunidades microbianas de forma directa usando las bacterias como fuente de alimentación o indirectamente al producir una cantidad de materia fecal o seudo-fecal, suficiente para afectar la actividad y crecimiento bacteriano. El impacto ecológico global y el comportamiento como filtrador de B. chinensis aún no son claros, pero nuestros resultados experimentales sugieren que estos impactos pueden ser importantes y se deben investigar mejor para entender más su papel potencial en el acoplamiento de las redes tróficas bentónicas y pelágicas en los sistemas lacustres

A comparison of taxon co-occurrence patterns for macro- and microorganisms

We examine co-occurrence patterns of microorganisms to evaluate community assembly “rules.” We use methods previously applied to macroorganisms, both to evaluate their applicability to microorganisms and to allow comparison of co-occurrence patterns observed in microorganisms to those found in macroorganisms. We use a null model analysis of 124 incidence matrices from microbial communities, including bacteria, archaea, fungi, and algae, and we compare these results to previously published findings from a meta-analysis of almost 100 macroorganism data sets. We show that assemblages of microorganisms demonstrate nonrandom patterns of co-occurrence that are broadly similar to those found in assemblages of macroorganisms. These results suggest that some taxon co-occurrence patterns may be general characteristics of communities of organisms from all domains of life. We also find that co-occurrence in microbial communities does not vary among taxonomic groups or habitat types. However, we find that the degree of co-occurrence does vary among studies that use different methods to survey microbial communities. Finally, we discuss the potential effects of the undersampling of microbial communities on our results, as well as processes that may contribute to nonrandom patterns of co-occurrence in both macrobial and microbial communities such as competition, habitat filtering, historical effects, and neutral processes

Mississippi River and Sea Surface Height Effects on Oil Slick Migration

Millions of barrels of oil escaped into the Gulf of Mexico (GoM) after the 20 April, 2010 explosion of Deepwater Horizon (DH). Ocean circulation models were used to forecast oil slick migration in the GoM, however such models do not explicitly treat the effects of secondary eddy-slopes or Mississippi River (MR) hydrodynamics. Here we report oil front migration that appears to be driven by sea surface level (SSL) slopes, and identify a previously unreported effect of the MR plume: under conditions of relatively high river discharge and weak winds, a freshwater mound can form around the MR Delta. We performed temporal oil slick position and altimeter analysis, employing both interpolated altimetry data and along-track measurements for coastal applications. The observed freshwater mound appears to have pushed the DH oil slick seaward from the Delta coastline. We provide a physical mechanism for this novel effect of the MR, using a two-layer pressure-driven flow model. Results show how SSL variations can drive a cross-slope migration of surface oil slicks that may reach velocities of order km/day, and confirm a lag time of order 5–10 days between mound formation and slick migration, as observed form the satellite analysis. Incorporating these effects into more complex ocean models will improve forecasts of slick migration for future spills. More generally, large SSL variations at the MR mouth may also affect the dispersal of freshwater, nutrients and sediment associated with the MR plume

River Influences on Shelf Ecosystems: Introduction and Synthesis

River Influences on Shelf Ecosystems (RISE) is the first comprehensive interdisciplinary study of the rates and dynamics governing the mixing of river and coastal waters in an eastern boundary current system, as well as the effects of the resultant plume on phytoplankton standing stocks, growth and grazing rates, and community structure. The RISE Special Volume presents results deduced from four field studies and two different numerical model applications, including an ecosystem model, on the buoyant plume originating from the Columbia River. This introductory paper provides background information on variability during RISE field efforts as well as a synthesis of results, with particular attention to the questions and hypotheses that motivated this research. RISE studies have shown that the maximum mixing of Columbia River and ocean water occurs primarily near plume liftoff inside the estuary and in the near field of the plume. Most plume nitrate originates from upwelled shelf water, and plume phytoplankton species are typically the same as those found in the adjacent coastal ocean. River-supplied nitrate can help maintain the ecosystem during periods of delayed upwelling. The plume inhibits iron limitation, but nitrate limitation is observed in aging plumes. The plume also has significant effects on rates of primary productivity and growth (higher in new plume water) and microzooplankton grazing (lower in the plume near field and north of the river mouth); macrozooplankton concentration (enhanced at plume fronts); offshelf chlorophyll export; as well as the development of a chlorophyll ?shadow zone? off northern Oregon

EnvMine: A text-mining system for the automatic extraction of contextual information

<p>Abstract</p> <p>Background</p> <p>For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.</p> <p>Results</p> <p>EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.</p> <p>Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.</p> <p>Conclusion</p> <p>EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.</p

Bacterial activity in cystic fibrosis lung infections

BACKGROUND: Chronic lung infections are the primary cause of morbidity and mortality in Cystic Fibrosis (CF) patients. Recent molecular biological based studies have identified a surprisingly wide range of hitherto unreported bacterial species in the lungs of CF patients. The aim of this study was to determine whether the species present were active and, as such, worthy of further investigation as potential pathogens. METHODS: Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiles were generated from PCR products amplified from 16S rDNA and Reverse Transcription Terminal Restriction Fragment Length Polymorphism (RT-T-RFLP) profiles, a marker of metabolic activity, were generated from PCR products amplified from 16S rRNA, both extracted from the same CF sputum sample. To test the level of activity of these bacteria, T-RFLP profiles were compared to RT-T-RFLP profiles. RESULTS: Samples from 17 individuals were studied. Parallel analyses identified a total of 706 individual T-RF and RT-T-RF bands in this sample set. 323 bands were detected by T-RFLP and 383 bands were detected by RT-T-RFLP (statistically significant; P ≤ 0.001). For the group as a whole, 145 bands were detected in a T-RFLP profile alone, suggesting metabolically inactive bacteria. 205 bands were detected in an RT-T-RFLP profile alone and 178 bands were detected in both, suggesting a significant degree of metabolic activity. Although Pseudomonas aeruginosa was present and active in many patients, a low occurrence of other species traditionally considered to be key CF pathogens was detected. T-RFLP profiles obtained for induced sputum samples provided by healthy individuals without CF formed a separate cluster indicating a low level of similarity to those from CF patients. CONCLUSION: These results indicate that a high proportion of the bacterial species detected in the sputum from all of the CF patients in the study are active. The widespread activity of bacterial species in these samples emphasizes the potential importance of these previously unrecognized species within the CF lung

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Effects of social approval bias on self-reported fruit and vegetable consumption: a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Self-reports of dietary intake in the context of nutrition intervention research can be biased by the tendency of respondents to answer consistent with expected norms (social approval bias). The objective of this study was to assess the potential influence of social approval bias on self-reports of fruit and vegetable intake obtained using both food frequency questionnaire (FFQ) and 24-hour recall methods.</p> <p>Methods</p> <p>A randomized blinded trial compared reported fruit and vegetable intake among subjects exposed to a potentially biasing prompt to that from control subjects. Subjects included 163 women residing in Colorado between 35 and 65 years of age who were randomly selected and recruited by telephone to complete what they were told would be a future telephone survey about health. Randomly half of the subjects then received a letter prior to the interview describing this as a study of fruit and vegetable intake. The letter included a brief statement of the benefits of fruits and vegetables, a 5-A-Day sticker, and a 5-a-Day refrigerator magnet. The remainder received the same letter, but describing the study purpose only as a more general nutrition survey, with neither the fruit and vegetable message nor the 5-A-Day materials. Subjects were then interviewed on the telephone within 10 days following the letters using an eight-item FFQ and a limited 24-hour recall to estimate fruit and vegetable intake. All interviewers were blinded to the treatment condition.</p> <p>Results</p> <p>By the FFQ method, subjects who viewed the potentially biasing prompts reported consuming more fruits and vegetables than did control subjects (5.2 vs. 3.7 servings per day, p < 0.001). By the 24-hour recall method, 61% of the intervention group but only 32% of the control reported eating fruits and vegetables on 3 or more occasions the prior day (p = 0.002). These associations were independent of age, race/ethnicity, education level, self-perceived health status, and time since last medical check-up.</p> <p>Conclusion</p> <p>Self-reports of fruit and vegetable intake using either a food frequency questionnaire or a limited 24-hour recall are both susceptible to substantial social approval bias. Valid assessments of intervention effects in nutritional intervention trials may require objective measures of dietary change.</p

What Ecological Factors Shape Species-Area Curves in Neutral Models?

Understanding factors that shape biodiversity and species coexistence across scales is of utmost importance in ecology, both theoretically and for conservation policies. Species-area relationships (SARs), measuring how the number of observed species increases upon enlarging the sampled area, constitute a convenient tool for quantifying the spatial structure of biodiversity. While general features of species-area curves are quite universal across ecosystems, some quantitative aspects can change significantly. Several attempts have been made to link these variations to ecological forces. Within the framework of spatially explicit neutral models, here we scrutinize the effect of varying the local population size (i.e. the number of individuals per site) and the level of habitat saturation (allowing for empty sites). We conclude that species-area curves become shallower when the local population size increases, while habitat saturation, unless strongly violated, plays a marginal role. Our findings provide a plausible explanation of why SARs for microorganisms are flatter than those for larger organisms