Abundance and biomass of zooplankton from the Romanian littoral collected in April, June and September 1999

The SHELF 1999 dataset contains zooplankton data collected in April, June and September 1999 allong 5 transect in front of the Romanian littoral. Zooplankton sampling was undertaken using a Juday closing net in the 0-10, 10-25, and 25-50m layer (depending also on the water masses). The dataset includes samples analysed for mesozooplankton species composition and abundance. Sampling volume was estimated by multiplying the mouth area with the wire length. Taxon-specific mesozooplankton abundance was count under microscope. Total abundance is the sum of the counted individuals. Total biomass Fodder, Rotifera , Ctenophora and Noctiluca was estimated using a tabel with wet weight for each species an stage.

(Table 1) Species richness and diversity of tundra plants in herbivore exclosure and control plots near Barrow, Alaska

To determine the role lemmings play in structuring plant communities and their contribution to the 'greening of the Arctic', we measured plant cover and biomass in 50 + year old lemming exclosures and control plots in the coastal tundra near Barrow, Alaska. The response of plant functional types to herbivore exclusion varied among land cover types. In general, the abundance of lichens and bryophytes increased with the exclusion of lemmings, whereas graminoids decreased, although the magnitude of these responses varied among land cover types. These results suggest that sustained lemming activity promotes a higher biomass of vascular plant functional types than would be expected without their presence and highlights the importance of considering herbivory when interpreting patterns of greening in the Arctic. In light of the rapid environmental change ongoing in the Arctic and the potential regional to global implications of this change, further exploration regarding the long-term influence of arvicoline rodents on ecosystem function (e.g. carbon and energy balance) should be considered a research priority.

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.

Studies of the microbial diversity on analyzed samples from from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge

Marine sediments harbor an enormous quantity of microorganisms, including a multitude of novel species. The habitable zone of the marine sediment column begins at the sediment-water interface and probably extends to depths of several thousands of meters. Studies of the microbial diversity in this ecosystem have mostly relied on molecular biological techniques. We used a complementary method - analysis of intact polar membrane lipids - to characterize the in-situ microbial community in sediments covering a wide range of environmental conditions from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge. Bacterial and eukaryotic phospholipids were only detected in surface sediments from the Peru Margin. In contrast, deeply buried sediments, independent of their geographic location, were dominated by archaeal diether and tetraether lipids with various polar head groups and core lipids. We compared ring distributions of archaeal tetraether lipids derived from polar glycosidic precursors with those that are present as core lipids. The distributions of these related compound pools were distinct, suggestive of different archaeal sources, i.e., the polar compounds derive from sedimentary communities and the core lipids are fossil remnants from planktonic communities with possible admixtures of decayed sedimentary archaea. This in-situ production of distinct archaeal lipid populations potentially affects applications of the TEX86 paleotemperature proxy as demonstrated by offsets in reconstructed temperatures between both pools. We evaluated how varying cell and lipid stabilities will influence the sedimentary pool by using a box-model. The results are consistent with (i) a requirement of continuous inputs of freshly synthesized lipids in subsurface sediments for explaining the observed distribution of intact polar lipids, and (ii) decreasing lipid inputs with increasing burial depth.

Seawater carbonate chemistry and biological processes of bivalve shellfish Mercenaria mercenaria and Argopecten irradians during experiments, 2011

The combustion of fossil fuels has enriched levels of CO2 in the world's oceans and decreased ocean pH. Although the continuation of these processes may alter the growth, survival, and diversity of marine organisms that synthesize CaCO3shells, the effects of ocean acidification since the dawn of the industrial revolution are not clear. Here we present experiments that examined the effects of the ocean's past, present, and future (21st and 22nd centuries) CO2concentrations on the growth, survival, and condition of larvae of two species of commercially and ecologically valuable bivalve shellfish (Mercenaria mercenariaand Argopecten irradians). Larvae grown under near preindustrial CO2concentrations (250 ppm) displayed significantly faster growth and metamorphosis as well as higher survival and lipid accumulation rates compared with individuals reared under modern day CO2 levels. Bivalves grown under near preindustrial CO2 levels displayed thicker, more robust shells than individuals grown at present CO2 concentrations, whereas bivalves exposed to CO2 levels expected later this century had shells that were malformed and eroded. These results suggest that the ocean acidification that has occurred during the past two centuries may be inhibiting the development and survival of larval shellfish and contributing to global declines of some bivalve populations.

Svalbard 2010 mesocosm experiment: Protistan diversity

Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,.) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above.