Consequences of fish kills for long-term trophic structure in shallow lakes: implications for theory and restoration

Fish kills are a common occurrence in shallow, eutrophic lakes, but their ecological consequences, especially in the long-term, are poorly understood. We studied the decadal-scale response of two UK shallow lakes to fish kills using a palaeolimnological approach. Eutrophic and turbid Barningham Lake experienced two fish kills in the early 1950s and late 1970s with fish recovering after both events, whereas less eutrophic, macrophyte-dominated Wolterton Lake experienced one kill event in the early 1970s from which fish failed to recover. Our palaeo-data show fish-driven trophic cascade effects across all trophic levels (covering benthic and pelagic species) in both lakes regardless of pre-kill macrophyte coverage and trophic status. In turbid Barningham Lake, similar to long-term studies of biomanipulations in other eutrophic lakes, effects at the macrophyte-level are shown to be temporary after the first kill (c.20 years) and non-existent after the second kill. In plant-dominated Wolterton Lake permanent fish disappearance failed to halt a long-term pattern of macrophyte community change (e.g. loss of charophytes and over-wintering macrophyte species) symptomatic of eutrophication. Important implications for theory and restoration ecology arise from our study. Firstly, our data support ideas of slow eutrophication-driven change in shallow lakes where perturbations are not necessary prerequisites for macrophyte loss. Secondly, the study emphasises a key need for lake managers to reduce external nutrient-loading if sustainable and long-term lake restoration is to be achieved. Our research highlights the enormous potential of multi-indicator palaeolimnology and alludes to an important need to consider potential fish kill signatures when interpreting results

Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen-enriched conditions

© 2016 Association for the Sciences of Limnology and Oceanography. Anthropogenic activities are altering total nutrient loads to many estuaries and freshwaters, resulting in high loads not only of total nitrogen (N), but in some cases, of chemically reduced forms, notably NH4+. Long thought to be the preferred form of N for phytoplankton uptake, NH4+ may actually suppress overall growth when concentrations are sufficiently high. NH4+ has been well known to be inhibitory or repressive for NO3- uptake and assimilation, but the concentrations of NH4+ that promote vs. repress NO3- uptake, assimilation, and growth in different phytoplankton groups and under different growth conditions are not well understood. Here, we review N metabolism first in a "generic" eukaryotic cell, and the contrasting metabolic pathways and regulation of NH4+ and NO3- when these substrates are provided individually under equivalent growth conditions. Then the metabolic interactions of these substrates are described when both are provided together, emphasizing the cellular challenge of balancing nutrient acquisition with photosynthetic energy balance in dynamic environments. Conditions under which dissipatory pathways such as dissimilatory NO3-/ NO2- reduction to NH4+ and photorespiration that may lead to growth suppression are highlighted. While more is known about diatoms, taxon-specific differences in NH4+ and NO3- metabolism that may contribute to changes in phytoplankton community composition when the composition of the N pool changes are presented. These relationships have important implications for harmful algal blooms, development of nutrient criteria for management, and modeling of nutrient uptake by phytoplankton, particularly in conditions where eutrophication is increasing and the redox state of N loads is changing

Identifying the needs of brain tumor patients and their caregivers

The purpose of this study is to identify the needs of brain tumor patients and their caregivers to provide improved health services to these populations. Two different questionnaires were designed for patients and caregivers. Both questionnaires contained questions pertaining to three realms: disease symptoms/treatment, health care provider, daily living/finances. The caregivers’ questionnaires contained an additional domain on emotional needs. Each question was evaluated for the degree of importance and satisfaction. Exploratory analyses determined whether baseline characteristics affect responder importance or satisfaction. Also, areas of high agreement/disagreement in satisfaction between the participating patient-caregiver pairs were identified. Questions for which >50% of the patients and caregivers thought were “very important” but >30% were dissatisfied include: understanding the cause of brain tumors, dealing with patients’ lower energy, identifying healthful foods and activities for patients, telephone access to health care providers, information on medical insurance coverage, and support from their employer. In the emotional realm, caregivers identified 9 out of 10 items as important but need further improvement. Areas of high disagreement in satisfaction between participating patient-caregiver pairs include: getting help with household chores (P value = 0.006) and finding time for personal needs (P value < 0.001). This study provides insights into areas to improve services for brain tumor patients and their caregivers. The caregivers’ highest amount of burden is placed on their emotional needs, emphasizing the importance of providing appropriate medical and psychosocial support for caregivers to cope with emotional difficulties they face during the patients’ treatment process

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

An architecture for the autonomic curation of crowdsourced knowledge

Human knowledge curators are intrinsically better than their digital counterparts at providing relevant answers to queries. That is mainly due to the fact that an experienced biological brain will account for relevant community expertise as well as exploit the underlying connections between knowledge pieces when offering suggestions pertinent to a specific question, whereas most automated database managers will not. We address this problem by proposing an architecture for the autonomic curation of crowdsourced knowledge, that is underpinned by semantic technologies. The architecture is instantiated in the career data domain, thus yielding Aviator, a collaborative platform capable of producing complete, intuitive and relevant answers to career related queries, in a time effective manner. In addition to providing numeric and use case based evidence to support these research claims, this extended work also contains a detailed architectural analysis of Aviator to outline its suitability for automatically curating knowledge to a high standard of quality

Reconstructing terrestrial nutrient cycling using stable nitrogen isotopes in wood

Although recent anthropogenic effects on the global nitrogen (N) cycle have been significant, the consequences of increased anthropogenic N on terrestrial ecosystems are unclear. Studies of the impact of increased reactive N on forest ecosystems—impacts on hydrologic and gaseous loss pathways, retention capacity, and even net primary productivity— have been particularly limited by a lack of long-term baseline biogeochemical data. Stable nitrogen isotope analysis (ratio of ¹⁵N to ¹⁴N, termed δ¹⁵N) of wood chronologies offers the potential to address changes in ecosystem N cycling on millennial timescales and across broad geographic regions. Currently, nearly 50 studies have been published utilizing wood δ¹⁵N records; however, there are significant differences in study design and data interpretation. Here, we identify four categories of wood δ¹⁵N studies, summarize the common themes and primary findings of each category, identify gaps in the spatial and temporal scope of current wood δ¹⁵N chronologies, and synthesize methodological frameworks for future research by presenting eight suggestions for common methodological approaches and enhanced integration across studies. Wood δ¹⁵N records have the potential to provide valuable information for interpreting modern biogeochemical cycling. This review serves to advance the utility of this technique for long-term biogeochemical reconstructions

The regional and global significance of nitrogen removal in lakes and reservoirs

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 93 (2009): 143-157, doi:10.1007/s10533-008-9272-x.Human activities have greatly increased the transport of biologically available N through watersheds to potentially sensitive coastal ecosystems. Lentic water bodies (lakes and reservoirs) have the potential to act as important sinks for this reactive N as it is transported across the landscape because they offer ideal conditions for N burial in sediments or permanent loss via denitrification. However, the patterns and controls on lentic N removal have not been explored in great detail at large regional to global scales. In this paper we describe, evaluate, and apply a new, spatially explicit, annual-scale, global model of lentic N removal called NiRReLa (Nitrogen Retention in Reservoirs and Lakes). The NiRReLa model incorporates small lakes and reservoirs than have been included in previous global analyses, and also allows for separate treatment and analysis of reservoirs and natural lakes. Model runs for the mid-1990s indicate that lentic systems are indeed important sinks for N and are conservatively estimated to remove 19.7 Tg N yr-1 from watersheds globally. Small lakes (< 50 km2) were critical in the analysis, retaining almost half (9.3 Tg N yr-1) of the global total. In model runs, capacity of lakes and reservoirs to remove watershed N varied substantially (0-100%) both as a function of climate and the density of lentic systems. Although reservoirs occupy just 6% of the global lentic surface area, we estimate they retain approximately 33% of the total N removed by lentic systems, due to a combination of higher drainage ratios (catchment surface area : lake or reservoir surface area), higher apparent settling velocities for N, and greater N loading rates in reservoirs than in lakes. Finally, a sensitivity analysis of NiRReLa suggests that, on-average, N removal within lentic systems will respond more strongly to changes in land use and N loading than to changes in climate at the global scale.The NSF26 Research Coordination Network on denitrification for support for collaboration (award number DEB0443439 to S.P. Seitzinger and E.A. Davidson). This project was also supported by grants to J.A. Harrison from California Sea Grant (award number RSF8) and from the U.S. Geological Survey 104b program and R. Maranger (FQRNT Strategic Professor)

Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies

A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1

The expansion field: The value of H_0

Any calibration of the present value of the Hubble constant requires recession velocities and distances of galaxies. While the conversion of observed velocities into true recession velocities has only a small effect on the result, the derivation of unbiased distances which rest on a solid zero point and cover a useful range of about 4-30 Mpc is crucial. A list of 279 such galaxy distances within v<2000 km/s is given which are derived from the tip of the red-giant branch (TRGB), from Cepheids, and from supernovae of type Ia (SNe Ia). Their random errors are not more than 0.15 mag as shown by intercomparison. They trace a linear expansion field within narrow margins from v=250 to at least 2000 km/s. Additional 62 distant SNe Ia confirm the linearity to at least 20,000 km/s. The dispersion about the Hubble line is dominated by random peculiar velocities, amounting locally to <100 km/s but increasing outwards. Due to the linearity of the expansion field the Hubble constant H_0 can be found at any distance >4.5 Mpc. RR Lyr star-calibrated TRGB distances of 78 galaxies above this limit give H_0=63.0+/-1.6 at an effective distance of 6 Mpc. They compensate the effect of peculiar motions by their large number. Support for this result comes from 28 independently calibrated Cepheids that give H_0=63.4+/-1.7 at 15 Mpc. This agrees also with the large-scale value of H_0=61.2+/-0.5 from the distant, Cepheid-calibrated SNe Ia. A mean value of H_0=62.3+/-1.3 is adopted. Because the value depends on two independent zero points of the distance scale its systematic error is estimated to be 6%. Typical errors of H_0 come from the use of a universal, yet unjustified P-L relation of Cepheids, the neglect of selection bias in magnitude-limited samples, or they are inherent to the adopted models.Comment: 44 pages, 4 figures, 6 tables, accepted for publication in the Astronony and Astrophysics Review 15

Global patterns and drivers of ecosystem functioning in rivers and riparian zones

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.peerReviewe