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.

(Table 3) Collembola species density and diversity in control and OTC plots near Abisco Research Station

Ecosystems at high northern latitudes are subject to strong climate change. Soil processes, such as carbon and nutrient cycles, which determine the functioning of these ecosystems, are controlled by soil fauna. Thus assessing the responses of soil fauna communities to environmental change will improve the predictability of the climate change impacts on ecosystem functioning. For this purpose, trait assessment is a promising method compared to the traditional taxonomic approach, but it has not been applied earlier. In this study the response of a sub-arctic soil Collembola community to long-term (16 years) climate manipulation by open top chambers was assessed. The drought-susceptible Collembola community responded strongly to the climate manipulation, which substantially reduced soil moisture and slightly increased soil temperature. The total density of Collembola decreased by 51% and the average number of species was reduced from 14 to 12. Although community assessment showed species-specific responses, taxonomically based community indices, species diversity and evenness, were not affected. However, morphological and ecological trait assessments were more sensitive in revealing community responses. Drought-tolerant, larger-sized, epiedaphic species survived better under the climate manipulation than their counterparts, the meso-hydrophilic, smaller-sized and euedaphic species. Moreover it also explained the significant responses shown by four taxa. This study shows that trait analysis can both reveal responses in a soil fauna community to climate change and improve the understanding of the mechanisms behind them.

Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle Findings: Plankton WP2 replicate net hauls (200 µm) were taken at the Western Channel Observatory long-term monitoring station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,042 sequences were obtained for all samples. The sequences clustered in to 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 138 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 75 taxonomic groups. Conclusions: The percentage of OTUs assigned to major eukaryotic taxonomic groups broadly aligns between the metagenetic and morphological analysis and are dominated by Copepoda. However, the metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for estimating diversity and species richness of zooplankton communities.

(Table 1) Stage of the lemming cycle and nesting parameters of the greater snow geese between 1996-2005, Bylot Island

Resource pulses are common in various ecosystems and often have large impacts on ecosystem functioning. Many animals hoard food during resource pulses, yet how this behaviour affects pulse diffusion through trophic levels is poorly known because of a lack of individual-based studies. Our objective was to examine how the hoarding behaviour of arctic foxes (Alopex lagopus) preying on a seasonal pulsed resource (goose eggs) was affected by annual and seasonal changes in resource availability. We monitored foraging behaviour of foxes in a greater snow goose (Chen caerulescens atlanticus) colony during 8 nesting seasons that covered 2 lemming cycles. The number of goose eggs taken and cached per hour by foxes declined 6-fold from laying to hatching, while the proportion of eggs cached remained constant. In contrast, the proportion of eggs cached by foxes fluctuated in response to the annual lemming cycle independently of the seasonal pulse of goose eggs. Foxes cached the majority of eggs taken (> 90%) when lemming abundance was high or moderate but only 40% during the low phase of the cycle. This likely occurred because foxes consumed a greater proportion of goose eggs to fulfill their energy requirement at low lemming abundance. Our study clearly illustrates a behavioural mechanism that extends the energetic benefits of a resource pulse. The hoarding behaviour of the main predator enhances the allochthonous nutrients input brought by migrating birds from the south into the arctic terrestrial ecosystem. This could increase average predator density and promote indirect interactions among prey.

Intraspecific facilitation by allelochemical mediated grazing protection within a toxigenic dinoflagellate population, link to supplementary material

Dinoflagellates are a major cause of harmful algal blooms, with consequences for coastal marine ecosystem functioning and services. Alexandrium tamarense is one of the most abundant and widespread toxigenic species in the temperate northern and southern hemisphere, and produces paralytic shellfish poisoning toxins as well as lytic allelochemical substances. These bioactive compounds may support the success of A. tamarense and its ability to form blooms. Here we investigate the impact of grazing on monoclonal and mixed set-ups of highly (Alex2) and moderately (Alex4) allelochemically active A. tamarense strains and on a non-allelochemically active conspecific (Alex5) by the heterotrophic dinoflagellate Polykrikos kofoidii. While Alex4 and particularly Alex5 were strongly grazed by P. kofoidii when offered alone, both strains grew well in the mixed assemblages (Alex4+Alex5 and Alex2+Alex5). Hence, the allelochemical active strains facilitated growth of the non-active strain by protecting the population as a whole against grazing. Based on our results, we argue that facilitation among clonal lineages within a species may partly explain the high genotypic and phenotypic diversity of Alexandrium populations. Populations of Alexandrium may comprise multiple cooperative traits that act in concert with intraspecific facilitation, and hence promote the success of this notorious harmful algal bloom species.

Temperature modulates coccolithophorid sensitivity of growth, photosynthesis and calcification to increasing seawater pCO2

Increasing atmospheric CO2 concentrations are expected to impact pelagic ecosystem functioning in the near future by driving ocean warming and acidification. While numerous studies have investigated impacts of rising temperature and seawater acidification on planktonic organisms separately, little is presently known on their combined effects. To test for possible synergistic effects we exposed two coccolithophore species, Emiliania huxleyi and Gephyrocapsa oceanica, to a CO2 gradient ranging from ~0.5-250 µmol/kg (i.e. ~20-6000 µatm pCO2) at three different temperatures (i.e. 10, 15, 20°C for E. huxleyi and 15, 20, 25°C for G. oceanica). Both species showed CO2-dependent optimum-curve responses for growth, photosynthesis and calcification rates at all temperatures. Increased temperature generally enhanced growth and production rates and modified sensitivities of metabolic processes to increasing CO2. CO2 optimum concentrations for growth, calcification, and organic carbon fixation rates were only marginally influenced from low to intermediate temperatures. However, there was a clear optimum shift towards higher CO2 concentrations from intermediate to high temperatures in both species. Our results demonstrate that the CO2 concentration where optimum growth, calcification and carbon fixation rates occur is modulated by temperature. Thus, the response of a coccolithophore strain to ocean acidification at a given temperature can be negative, neutral or positive depending on that strain's temperature optimum. This emphasizes that the cellular responses of coccolithophores to ocean acidification can only be judged accurately when interpreted in the proper eco-physiological context of a given strain or species. Addressing the synergistic effects of changing carbonate chemistry and temperature is an essential step when assessing the success of coccolithophores in the future ocean.

Temporal biomass dynamics of an Arctic plankton bloom

Ocean acidification and carbonation, driven by anthropogenic emissions of carbon dioxide (CO2), have been shown to affect a variety of marine organisms and are likely to change ecosystem functioning. High latitudes, especially the Arctic, will be the first to encounter profound changes in carbonate chemistry speciation at a large scale, namely the under-saturation of surface waters with respect to aragonite, a calcium carbonate polymorph produced by several organisms in this region. During a CO2 perturbation study in 2010, in the framework of the EU-funded project EPOCA, the temporal dynamics of a plankton bloom was followed in nine mesocosms, manipulated for CO2 levels ranging initially from about 185 to 1420 ?atm. Dissolved inorganic nutrients were added halfway through the experiment. Autotrophic biomass, as identified by chlorophyll a standing stocks (Chl a), peaked three times in all mesocosms. However, while absolute Chl a concentrations were similar in all mesocosms during the first phase of the experiment, higher autotrophic biomass was measured at high in comparison to low CO2 during the second phase, right after dissolved inorganic nutrient addition. This trend then reversed in the third phase. There were several statistically significant CO2 effects on a variety of parameters measured in certain phases, such as nutrient utilization, standing stocks of particulate organic matter, and phytoplankton species composition. Interestingly, CO2 effects developed slowly but steadily, becoming more and more statistically significant with time. The observed CO2 related shifts in nutrient flow into different phytoplankton groups (mainly diatoms, dinoflagellates, prasinophytes and haptophytes) could have consequences for future organic matter flow to higher trophic levels and export production, with consequences for ecosystem productivity and atmospheric CO2.

(Table 1) Number of invertebrate species per bottom trawl haul in the Kapp Norvegia to Halley Bay area on cruise EASIZ I (ANT-XIII/3) and in the Kapp Norvegia - Austasen area on cruise EASIZ III (ANT-XVII/3)

Ecological work carried out on the Antarctic and Magellan shelves since the first IBMANT conference held at the UMAG, Punta Arenas in 1997 is summarized to identify areas where progress has been made and others, where impor- tant gaps have remained in understanding past and present interaction between the Antarctic and the southern tip of South America. This information is complementary to a review on shallow-water work along the Scotia Arc (Barnes, 2005) and recent work done in the deep sea (Brandt and Hilbig, 2004). While principally referring to shipboard work in deeper water, above all during the recent international EASIZ and LAMPOS campaigns, relevant work from shore stations is also included. Six years after the first IBMANT symposium, significant progress has been made along the latitudinal gradient from the Magellan region to the high Antarctic in the fields of biodiversity, biogeography and community structure, life strategies and adaptations, the role of disturbance and its significance for biodiversity, and trophic coupling of the benthic realm with the water column and sea ice. A better understanding has developed of the role of evolutionary and ecological factors in shaping past and present-day environmental conditions, species composition and distribution, and ecosystem functioning. Furthermore, the science community engaged in unravelling Antarctic-Magellan interactions has advanced in methodological aspects such as new analytical approaches for comparing biodiversity derived from visual methods, growth and age determination, trophic modelling using stable isotope ratios, and molecular approaches for taxonomic and phylogenetic purposes. At the same time, much effort has been invested to complement the species inventory of the two adjacent regions. However, much work remains to be done to fill the numerous gaps. Some perspectives are outlined in this review, and sug- gestions are made where particular emphasis should be placed in future work, much of which will be developed in the frame of SCAR's EBA (Evolution and Biodiversity in the Antarctic) programme.

Seawater carbonate chemistry and calcification during incubation experiments with Mytilus edulis and Grassostrea gigas, 2006

Ocean acidification resulting from human emissions of carbon dioxide has already lowered and will further lower surface ocean pH. The consequent decrease in calcium carbonate saturation potentially threatens calcareous marine organisms. Here, we demonstrate that the calcification rates of the edible mussel (Mytilus edulis) and Pacific oyster (Crassostrea gigas) decline linearly with increasing pCO2. Mussel and oyster calcification may decrease by 25 and 10%, respectively, by the end of the century, following the IPCC IS92a scenario (?740 ppmv in 2100). Moreover, mussels dissolve at pCO2 values exceeding a threshold value of ?1800 ppmv. As these two species are important ecosystem engineers in coastal ecosystems and represent a large part of worldwide aquaculture production, the predicted decrease of calcification in response to ocean acidification will probably have an impact on coastal biodiversity and ecosystem functioning as well as potentially lead to significant economic loss.

Coastal plankton communities under elevated CO2: community barcoding results, link to data files in FASTA format

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidifications on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~760 µatm) and those exposed to present day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients.

Contribution of woody habitat islands to the conservation of birds and their potential ecosystem services in an extensive Colombian rangeland

The conservation of birds and their habitats is essential to maintain well-functioning ecosystems including human-dominated habitats. In simplified or homogenized landscapes, patches of natural and semi-natural habitat are essential for the survival of plant and animal populations. We compared species composition and diversity of trees and birds between gallery forests, tree islands and hedges in a Colombian savanna landscape to assess how fragmented woody plant communities affect forest bird communities and how differences in habitat characteristics influenced bird species traits and their potential ecosystem function. Bird and tree diversity was higher in forests than in tree islands and hedges. Soil depth influenced woody species distribution, and canopy cover and tree height determined bird species distribution, resulting in plant and bird communities that mainly differed between forest and non-forest habitat. Bird and tree species and traits widely co-varied. Bird species in tree islands and hedges were on average smaller, less specialized to habitat and more tolerant to disturbance than in forest, but dietary differences did not emerge. Despite being less complex and diverse than forests, hedges and tree islands significantly contribute to the conservation of forest biodiversity in the savanna matrix. Forest fragments remain essential for the conservation of forest specialists, but hedges and tree islands facilitate spillover of more tolerant forest birds and their ecological functions such as seed dispersal from forest to the savanna matrix.

(Table 1) Tree age, post fire stand age, and soil organic matter thickness in the western Quebec black spruce boreal ecosystem

The observed long-term decrease in the regional fire activity of Eastern Canada results in excessive accumulation of organic layer on the forest floor of coniferous forests, which may affect climate-growth relationships in canopy trees. To test this hypothesis, we related tree-ring chronologies of black spruce (Picea mariana (Mill.) B.S.P.) to soil organic layer (SOL) depth at the stand scale in the lowland forests of Quebec's Clay Belt. Late-winter and early-spring temperatures and temperature at the end of the previous year's growing season were the major monthly level environmental controls of spruce growth. The effect of SOL on climate-growth relationships was moderate and reversed the association between tree growth and summer aridity from a negative to a positive relationship: trees growing on thin organic layers were thus negatively affected by drought, whereas it was the opposite for sites with deep (>20-30 cm) organic layers. This indicates the development of wetter conditions on sites with thicker SOL. Deep SOL were also associated with an increased frequency of negative growth anomalies (pointer years) in tree-ring chronologies. Our results emphasize the presence of nonlinear growth responses to SOL accumulation, suggesting 20-30 cm as a provisional threshold with respect to the effects of SOL on the climate-growth relationship. Given the current climatic conditions characterized by generally low-fire activity and a trend toward accumulation of SOL, the importance of SOL effects in the black spruce ecosystem is expected to increase in the future.

Impact of elevated levels of CO2 on animal mediated ecosystem function: The modification of sediment nutrient fluxes by burrowing urchins

A mesocosm experiment was conducted to quantify the relationships between the presence and body size of two burrowing heart urchins (Brissopsis lyrifera and Echinocardium cordatum) and rates of sediment nutrient flux. Furthermore, the impact of seawater acidification on these relationships was determined during this 40-day exposure experiment. Using carbon dioxide (CO2) gas, seawater was acidified to pHNBS 7.6, 7.2 or 6.8. Control treatments were maintained in natural seawater (pH = 8.0). Under normocapnic conditions, burrowing urchins were seen to reduce the sediment uptake of nitrite or nitrate whilst enhancing the release of silicate and phosphate. In acidified (hypercapnic) treatments, the biological control of biogeochemical cycles by urchins was significantly affected, probably through the combined impacts of high CO2 on nitrifying bacteria, benthic algae and urchin behaviour. This study highlights the importance of considering biological interactions when predicting the consequences of seawater acidification on ecosystem function.

R-script modified VS-Lite model

Drought is a key factor affecting forest ecosystem processes at different spatio-temporal scales. For accurately modeling tree functioning ? and thus for producing reliable simulations of forest dynamics ? the consideration of the variability in the timing and extent of drought effects on tree growth is essential, particularly in strongly seasonal climates such as in the Mediterranean area. Yet, most dynamic vegetation models (DVMs) do not include this intra-annual variability of drought effects on tree growth. We present a novel approach for linking tree-ring data to drought simulations in DVMs. A modified forward model of tree-ring width (VS-Lite) was used to estimate seasonal- and site-specific growth responses to drought of Scots pine (Pinus sylvestris L.), which were subsequently implemented in the DVM ForClim. Ring-width data from sixteen sites along a moisture gradient from Central Spain to the Swiss Alps, including the dry inner Alpine valleys, were used to calibrate the forward ring-width model, and inventory data from managed Scots pine stands were used to evaluate ForClim performance. The modified VS-Lite accurately estimated the year-to-year variability in ring-width indices and produced realistic intra-annual growth responses to soil drought, showing a stronger relationship between growth and drought in spring than in the other seasons and thus capturing the strategy of Scots pine to cope with drought. The ForClim version including seasonal variability in growth responses to drought showed improved predictions of stand basal area and stem number, indicating the need to consider intra-annual differences in climate-growth relationships in DVMs when simulating forest dynamics. Forward modeling of ring-width growth may be a powerful tool to calibrate growth functions in DVMs that aim to simulate forest properties in across multiple environments at large spatial scales.