Spatial changes in soil stable isotopic composition in response to carrion decomposition

Decomposition provides a critical mechanism for returning nutrients to the surrounding environment. In terrestrial systems, animal carcass, or carrion, decomposition results in a cascade of biogeochemical changes. Soil microbial communities are stimulated, resulting in transformations of carbon (C) and nitrogen (N) sourced from the decaying carrion soft tissues, changes to soil pH, electrical conductivity, and oxygen availability as microbial communities release CO2 and mineralize organic N. While many of the rapid changes to soil biogeochemistry observed during carrion decomposition return to background or starting conditions shortly after soft tissues are degraded, some biogeochemical parameters, particularly bulk soil stable δ15N isotopic composition, have the potential to exhibit prolonged perturbations, extending for several years. The goal of this study was to evaluate the lateral and vertical changes to soil stable isotopic composition 1 year after carrion decomposition in a forest ecosystem. Lateral transects extending 140 cm from three decomposition “hotspots” were sampled at 20 cm intervals, and subsurface cores were collected beneath each hotspot to a depth of 50 cm. Bulk soil stable isotopic composition (δ15N and δ13C) indicated that 1 year after complete soft tissue removal and decay, soils were significantly 15N enriched by 7.5±1.0 ‰ compared to control soils up to 60 cm from the hotspot center, and enrichment extended to a depth of 10 cm. Hotspot soils also contained 10 % more N compared to control soils, indicating that decomposition perturbs N pools. Our results demonstrate that carrion decomposition has the potential to result in long-term changes to soil biogeochemistry, up to at least 1 year after soft tissue degradation, and to contribute to bulk soil stable isotopic composition

Classifying hyperspectral airborne imagery for vegetation survey along coastlines

This paper studies the potential of airborne hyperspectral imagery for classifying vegetation along the Belgian coastlines. Here, the aim is to build vegetation maps using automatic classification. Besides a general linear multiclass classifier (Linear Discriminant Analysis), several strategies for combining binary classifiers are proposed: one based on a hierarchical decision tree, one based on the Hamming distance between the codewords obtained by binary classifiers and one based on the coupling of posterior probabilities. In addition, a new procedure is proposed for spatial classification smoothing. This procedure takes into account spatial information by letting the decision for classification of a pixel depend on the classification probabilities of neighboring pixels. This is shown to render smoother classification images

Hyperspectral data for coral reef monitoring. A case study: Fordate, Tanimbar, Indonesia

Coral reefs are endangered world-wide by devastating fishing methods (overfishing, dynamite and cyanide fishery), pollution, tourism, environmental changes and bleaching. The aim of this project is to monitor coral reefs and associated ecosystems (mangroves, sea-grass beds) by integrating different remote sensing data with spectral libraries and field measurements. The study area is Fordate, a small island to the northeast of Tanimbar, Indonesia. The monitoring system under development will enable not only the mapping of the coral reefs but also the localisation of those parts of the reefs that are most affected by degradation. A first test with hyperspectral data from the CHRIS/PROBA sensor shows promising results for the discrimination of different bottom-types on the Pulau Nukaha patch reef east of Fordate. Further field sampling and spectral measurements are needed to validate this preliminary classification

Enhancing Genome Investigations in the Mosquito Culex quinquefasciatus via BAC Library Construction and Characterization

Background Culex quinquefasciatus (Say) is a major species in the Culex pipiens complex and an important vector for several human pathogens including West Nile virus and parasitic filarial nematodes causing lymphatic filariasis. It is common throughout tropical and subtropical regions and is among the most geographically widespread mosquito species. Although the complete genome sequence is now available, additional genomic tools are needed to improve the sequence assembly. Findings We constructed a bacterial artificial chromosome (BAC) library using the pIndigoBAC536 vector and HindIII partially digested DNA isolated from Cx. quinquefasciatus pupae, Johannesburg strain (NDJ). Insert size was estimated by NotI digestion and pulsed-field gel electrophoresis of 82 randomly selected clones. To estimate genome coverage, each 384-well plate was pooled for screening with 29 simple sequence repeat (SSR) and five gene markers. The NDJ library consists of 55,296 clones arrayed in 144 384-well microplates. Fragment insert size ranged from 50 to 190 kb in length (mean = 106 kb). Based on a mean insert size of 106 kb and a genome size of 579 Mbp, the BAC library provides ~10.1-fold coverage of the Cx. quinquefasciatus genome. PCR screening of BAC DNA plate pools for SSR loci from the genetic linkage map and for four genes associated with reproductive diapause in Culex pipiens resulted in a mean of 9.0 positive plate pools per locus. Conclusion The NDJ library represents an excellent resource for genome assembly enhancement and characterization in Culex pipiens complex mosquitoes

Genome-Based Microsatellite Development in the Culex pipiens Complex and Comparative Microsatellite Frequency with Aedes aegypti and Anopheles gambiae

Mosquitoes in the Culex pipiens complex are among the most medically important vectors for human disease worldwide and include major vectors for lymphatic filariasis and West Nile virus transmission. However, detailed genetic studies in the complex are limited by the number of genetic markers available. Here, we describe methods for the rapid and efficient identification and development of single locus, highly polymorphic microsatellite markers for Cx. pipiens complex mosquitoes via in silico screening of the Cx. quinquefasciatus genome sequence.Six lab colonies representing four Cx. pipiens and two Cx. quinquefasciatus populations were utilized for preliminary assessment of 38 putative loci identified within 16 Cx. quinquefasciatus supercontig assemblies (CpipJ1) containing previously mapped genetic marker sequences. We identified and validated 12 new microsatellite markers distributed across all three linkage groups that amplify consistently among strains representing the complex. We also developed four groups of 3-5 microsatellite loci each for multiplex-ready PCR. Field collections from three cities in Indiana were used to assess the multiplex groups for their application to natural populations. All were highly polymorphic (Mean  = 13.0 alleles) per locus and reflected high polymorphism information content (PIC) (Mean  = 0.701). Pairwise F(ST) indicated population structuring between Terre Haute and Fort Wayne and between Terre Haute and Indianapolis, but not between Fort Wayne and Indianapolis. In addition, we performed whole genome comparisons of microsatellite motifs and abundance between Cx. quinquefasciatus and the primary vectors for dengue virus and malaria parasites, Aedes aegypti and Anopheles gambiae, respectively.We demonstrate a systematic approach for isolation and validation of microsatellites for the Cx. pipiens complex by direct screen of the Cx. quinquefasciatus genome supercontig assemblies. The genome density of microsatellites is greater in Cx. quinquefasciatus (0.26%) than in Ae. aegypti (0.14%), but considerably lower than in An. gambiae (0.77%)

Microbial control of diatom bloom dynamics in the open ocean

Diatom blooms play a central role in supporting foodwebs and sequestering biogenic carbon to depth. Oceanic conditions set bloom initiation, whereas both environmental and ecological factors determine bloom magnitude and longevity. Our study reveals another fundamental determinant of bloom dynamics. A diatom spring bloom in offshore New Zealand waters was likely terminated by iron limitation, even though diatoms consumed <1/3 of the mixed-layer dissolved iron inventory. Thus, bloom duration and magnitude were primarily set by competition for dissolved iron between microbes and small phytoplankton versus diatoms. Significantly, such a microbial mode of control probably relies both upon out-competing diatoms for iron (i.e., K-strategy), and having high iron requirements (i.e., r-strategy). Such resource competition for iron has implications for carbon biogeochemistry, as, blooming diatoms fixed three-fold more carbon per unit iron than resident non-blooming microbes. Microbial sequestration of iron has major ramifications for determining the biogeochemical imprint of oceanic diatom blooms. Citation: Boyd, P. W., et al. (2012), Microbial control of diatom bloom dynamics in the open ocean, Geophys. Res. Lett., 39, L18601

Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly

In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology

Effect of Phosphorus Amendments on Present Day Plankton Communities in Pelagic Lake Erie

To address questions regarding the potential impact of elevated total phosphorus (TP) inputs (due to relaxed regulations of TP loading), a series of TP enrichment experiments were conducted at pelagic stations in the 3 hydrologically distinct basins of Lake Erie. Results of nutrient assimilation measurements and assays for nutrient bioavailability suggest that the chemical speciation, and not concentration, of nitrogenous compounds may influence phytoplankton community structure; this in turn may lead to the selective proliferation of cyanobacteria in the eastern basin of the lake. Assays with cyanobacterial bioluminescent reporter systems for P and N availability as well as N-tot:P-tot assimilation ratios from on-deck incubation experiments support this work. Considered in the context of a microbial food web relative to a grazing food web, the results imply that alterations in current TP loading controls may lead to alterations in the phytoplankton community structure in the different basins of the Lake Erie system