Epiphytic orchid diversity and community composition in managed and natural moist evergreen Afromontane forest in SW Ethiopia

In SW Ethiopia, the moist evergreen Afromontane forest has become extremely fragmented and most of the remnants are intensively managed for coffee cultivation (Coffea arabica), with considerable impacts on biodiversity and ecosystem functioning. Because epiphytic orchids are potential indicators for forest quality and a proxy for overall forest biodiversity, we assessed the effect of forest management and forest fragmentation on epiphytic orchid diversity. We selected managed forest sites from both large and small forest remnants and compared their epiphytic orchid diversity with the diversity of natural unfragmented forest. We surveyed 339 canopy trees using rope climbing techniques. Orchid richness decreased and community composition changed, from the natural unfragmented forest, over the large managed forest fragments to the small managed forest fragments. This indicates that both forest management and fragmentation contribute to the loss of epiphytic orchids. Both the removal of large canopy trees typical for coffee management, and the occurrence of edge effects accompanying forest fragmentation are likely responsible for species loss and community composition changes. Even though some endangered orchid species persist even in the smallest fragments, large managed forest fragments are better options for the conservation of epiphytic orchids than small managed forests. Our results ultimately show that even though shade coffee cultivation is considered as a close-to-nature practice and is promoted as biodiversity conservation friendly, it cannot compete with the epiphytic orchid conservation benefit generated by unmanaged moist evergreen Afromontane forests.

Characterization of late Campanian and Maastrichtian planktonic foraminiferal depth habitats and vital activities based on stable isotopes

Depth habitats of 56 late Cretaceous planktonic foraminiferal species from cool and warm climate modes were determined based on stable isotope analyses of deep-sea samples from the equatorial Pacific DSDP Sites 577A and 463, and South Atlantic DSDP Site 525A. The following conclusions can be reached: Planoglobulina multicamerata (De Klasz) and Heterohelix rajagopalani (Govindan) occupied the deepest plankton habitats, followed by Abathomphalus mayaroensis (Bolli), Globotruncanella havanensis (Voorwijk), Gublerina cuvillieri Kikoine, and Laeviheterohelix glabrans (Cushman) also at subthermocline depth. Most keeled globotruncanids, and possibly Globigerinelliodes and Racemiguembelina species, lived at or within the thermocline layer. Heterohelix globulosa (Ehrenberg) and Rugoglobigerina, Pseudotextularia and Planoglobulina occupied the subsurface depth of the mixed layer, and Pseudoguembelina species inhabited the surface mixed layer. However, depth ranking of some species varied depending on warm or cool climate modes, and late Campanian or Maastrichtian age. For example, most keeled globotruncanids occupied similar shallow subsurface habitats as Rugoglobigerina during the warm late Campanian, but occupied the deeper thermocline layer during cool climatic intervals. Two distinct types of "vital effect" mechanisms reflecting photosymbiosis and respiration effects can be recognized by the exceptional delta13C signals of some species. (1) Photosymbiosis is implied by the repetitive pattern of relatively enriched delta13C values of Racemiguembelina (strongest), Planoglobulina, Rosita and Rugoglobigerina species, Pseudoguembelina excolata (weakest). (2) Enriched respiration 12C products are recognized in A. mayaroensis, Gublerina acuta De Klasz, and Heterohelix planata (Cushman). Isotopic trends between samples suggest that photosymbiotic activities varied between localities or during different climate modes, and may have ceased under certain environmental conditions. The appearance of most photosymbiotic species in the late Maastrichtian suggests oligotrophic conditions associated with increased water-mass stratification.

Barnacle recurit density, biomass, and reproductive output measured in rocky intertidal habitats in Glasgow Head, on the Atlantic coast of Nova Scotia, Canada

Through a field experiment, we show that a predator has negative nonconsumptive effects (NCEs) on different life-history stages of the same prey species. Shortly before the recruitment season of the barnacle Semibalanus balanoides (May-June), we established experimental cages in rocky intertidal habitats in Nova Scotia, Canada. The cages were used to manipulate the presence and absence of dogwhelks, Nucella lapillus, the main predators of barnacles. At the centre of each cage, we installed a tile where barnacle pelagic larvae could settle and the resulting recruits grow. Mesh prevented caged dogwhelks from accessing the tiles, but allowed waterborne dogwhelk cues to reach the tiles. Results in May indicated that barnacle larvae settled preferentially on tiles from cages without dogwhelks. In November, at the end of the dogwhelk activity period and once the barnacle recruits had grown to adult size, barnacle body mass was lower in the presence of dogwhelks. This limitation may have resulted from a lower barnacle feeding activity with nearby dogwhelks, as found by a previous study. The observed larval and adult responses in barnacles are consistent with attempts to decrease predation risk. November data also indicated that dogwhelk cues limited barnacle reproductive output, a possible consequence of the limited growth of barnacles. Overall, this study suggests that a predator species might influence trait evolution in a prey species through NCEs on different life-history stages.

Environmental conditions and habitats of GOS sites and bottle data of HOT-ALOHA station

The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis, and the results were inspected in the context of oceanographic environmental variables and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove), were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity were observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades.

Metadata und statistic analysis of archael and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)

DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162.

Acid-base physiology response to ocean acidification of two ecologically and economically important holothuroids from contrasting habitats, Holothuria scabra and Holothuria parva

Sea cucumbers are dominant invertebrates in several ecosystems such as coral reefs, seagrass meadows and mangroves. As bioturbators, they have an important ecological role in making available calcium carbonate and nutrients to the rest of the community. However, due to their commercial value, they face overexploitation in the natural environment. On top of that, occurring ocean acidification could impact these organisms, considered sensitive as echinoderms are osmoconformers, high-magnesium calcite producers and have a low metabolism. As a first investigation of the impact of ocean acidification on sea cucumbers, we tested the impact of short-term (6 to 12 days) exposure to ocean acidification (seawater pH 7.7 and 7.4) on two sea cucumbers collected in SW Madagascar, Holothuria scabra, a high commercial value species living in the seagrass meadows, and H. parva, inhabiting the mangroves. The former lives in a habitat with moderate fluctuations of seawater chemistry (driven by day-night differences) while the second lives in a highly variable intertidal environment. In both species, pH of the coelomic fluid was significantly negatively affected by reduced seawater pH, with a pronounced extracellular acidosis in individuals maintained at pH 7.7 and 7.4. This acidosis was due to an increased dissolved inorganic carbon content and pCO2 of the coelomic fluid, indicating a limited diffusion of the CO2 towards the external medium. However, respiration and ammonium excretion rates were not affected. No evidence of accumulation of bicarbonate was observed to buffer the coelomic fluid pH. If this acidosis stays uncompensated for when facing long-term exposure, other processes could be affected in both species, eventually leading to impacts on their ecological role.

Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH

Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50-100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals (Acropora palmata and Porites astreoides) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats.

Object-based image analysis for mapping Natura 2000 habitats.

Clasificación de una imagen de alta resolución "Quickbird" con la técnica de análisis de imágenes en base a objetos.

Objects-based Image Analysis for Mapping Natura 2000 Habitats to Improve Forest Management.

Clasificación de una imagen de alta resolución "Quickbird" con la técnica de análisis de imágenes en base a objetos

Architectures for Video-on-Demand content distribution in managed networks

La demanda de contenidos de vídeo ha aumentado rápidamente en los últimos años como resultado del gran despliegue de la TV sobre IP (IPTV) y la variedad de servicios ofrecidos por los operadores de red. Uno de los servicios que se ha vuelto especialmente atractivo para los clientes es el vídeo bajo demanda (VoD) en tiempo real, ya que ofrece una transmisión (streaming) inmediata de gran variedad de contenidos de vídeo. El precio que los operadores tienen que pagar por este servicio es el aumento del tráfico en las redes, que están cada vez más congestionadas debido a la mayor demanda de contenidos de VoD y al aumento de la calidad de los propios contenidos de vídeo. Así, uno de los principales objetivos de esta tesis es encontrar soluciones que reduzcan el tráfico en el núcleo de la red, manteniendo la calidad del servicio en el nivel adecuado y reduciendo el coste del tráfico. La tesis propone un sistema jerárquico de servidores de streaming en el que se ejecuta un algoritmo para la ubicación óptima de los contenidos de acuerdo con el comportamiento de los usuarios y el estado de la red. Debido a que cualquier algoritmo óptimo de distribución de contenidos alcanza un límite en el que no se puede llegar a nuevas mejoras, la inclusión de los propios clientes del servicio (los peers) en el proceso de streaming puede reducir aún más el tráfico de red. Este proceso se logra aprovechando el control que el operador tiene en las redes de gestión privada sobre los equipos receptores (Set-Top Box) ubicados en las instalaciones de los clientes. El operador se reserva cierta capacidad de almacenamiento y streaming de los peers para almacenar los contenidos de vídeo y para transmitirlos a otros clientes con el fin de aliviar a los servidores de streaming. Debido a la incapacidad de los peers para sustituir completamente a los servidores de streaming, la tesis propone un sistema de streaming asistido por peers. Algunas de las cuestiones importantes que se abordan en la tesis son saber cómo los parámetros del sistema y las distintas distribuciones de los contenidos de vídeo en los peers afectan al rendimiento general del sistema. Para dar respuesta a estas preguntas, la tesis propone un modelo estocástico preciso y flexible que tiene en cuenta parámetros como las capacidades de enlace de subida y de almacenamiento de los peers, el número de peers, el tamaño de la biblioteca de contenidos de vídeo, el tamaño de los contenidos y el esquema de distribución de contenidos para estimar los beneficios del streaming asistido por los peers. El trabajo también propone una versión extendida del modelo matemático mediante la inclusión de la probabilidad de fallo de los peers y su tiempo de recuperación en el conjunto de parámetros del modelo. Estos modelos se utilizan como una herramienta para la realización de exhaustivos análisis del sistema de streaming de VoD asistido por los peers para la amplia gama de parámetros definidos en los modelos. Abstract The demand of video contents has rapidly increased in the past years as a result of the wide deployment of IPTV and the variety of services offered by the network operators. One of the services that has especially become attractive to the customers is real-time Video on Demand (VoD) because it offers an immediate streaming of a large variety of video contents. The price that the operators have to pay for this convenience is the increased traffic in the networks, which are becoming more congested due to the higher demand for VoD contents and the increased quality of the videos. Therefore, one of the main objectives of this thesis is finding solutions that would reduce the traffic in the core of the network, keeping the quality of service on satisfactory level and reducing the traffic cost. The thesis proposes a system of hierarchical structure of streaming servers that runs an algorithm for optimal placement of the contents according to the users’ behavior and the state of the network. Since any algorithm for optimal content distribution reaches a limit upon which no further improvements can be made, including service customers themselves (the peers) in the streaming process can further reduce the network traffic. This process is achieved by taking advantage of the control that the operator has in the privately managed networks over the Set-Top Boxes placed at the clients’ premises. The operator reserves certain storage and streaming capacity on the peers to store the video contents and to stream them to the other clients in order to alleviate the streaming servers. Because of the inability of the peers to completely substitute the streaming servers, the thesis proposes a system for peer-assisted streaming. Some of the important questions addressed in the thesis are how the system parameters and the various distributions of the video contents on the peers would impact the overall system performance. In order to give answers to these questions, the thesis proposes a precise and flexible stochastic model that takes into consideration parameters like uplink and storage capacity of the peers, number of peers, size of the video content library, size of contents and content distribution scheme to estimate the benefits of the peer-assisted streaming. The work also proposes an extended version of the mathematical model by including the failure probability of the peers and their recovery time in the set of parameters. These models are used as tools for conducting thorough analyses of the peer-assisted system for VoD streaming for the wide range of defined parameters.