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.

Ground beetle (Carabidae) abundance data from north-eastern Australian rainforest, between June 2008 - January 2010, using pitfall traps

Understanding how the environment influences patterns of diversity is vital for effective conservation management, especially in a changing global climate. While assemblage structure and species richness patterns are often correlated with current environmental factors, historical influences may also be considerable, especially for taxa with poor dispersal abilities. Mountain-top regions throughout tropical rainforests can act as important refugia for taxa characterised by low dispersal capacities such as flightless ground beetles (Carabidae), an ecologically significant predatory group. We surveyed flightless ground beetles along elevational gradients in five different subregions within the Australian Wet Tropics World Heritage Area to investigate (1) whether the diversity and composition of flightless ground beetles are elevationally stratified, and, if so, (2) what environmental factors (other than elevation per se) are associated with these patterns. Generalised linear models and model averaging techniques were used to relate patterns of diversity to environmental factors. Unlike most taxonomic groups, flightless ground beetles increased in species richness and abundance with elevation. Additionally, each subregion consisted of distinct assemblages containing a high level of regional endemic species. Species richness was most strongly positively associated with the historical climatic conditions and negatively associated with severity of recent disturbance (treefalls) and current climatic conditions. Assemblage composition was associated with latitude and current and historical climatic conditions. Our results suggest that distributional patterns of flightless ground beetles are not only likely to be associated with factors that change with elevation (current climatic conditions), but also factors that are independent of elevation (recent disturbance and historical climatic conditions). Variation in historical vegetation stability explained both species richness and assemblage composition patterns, probably reflecting the significance of upland refugia at a geographic time scale. These findings are important for conservation management as upland habitats are under threat from climate change.

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.

Fauna composition of benthos communities in bottom sediments from the edge and the central part of the shelf in the California upwelling zone

Two shelf communities from the central part off the California Peninsula are described. The community of Amphiodia urtica - Nephtys ferruginea develops in the central part of the shelf within the depth range 95-105 m. The community of Nephtys ferruginea - Amphiura acrystata develops on the shelf edge at depth 110 m. Biomasses of both communities are very low (about 10 g/m**2). Species richness of the shelf community is high; more than 60 species occur in samples (43-51 species per a community). Various echinoderms and some other groups are abundant on the Californian shelf; these groups are absent in shelf areas of Peruvian and Benguela upwellings. Species structures of the communities were analyzed; the communities were shown to consist of coexisting, but not interacting guilds; this indicates that the communities are undersaturated with individuals. At the same time values of ABC-indices indicate that the communities are stable. We suggest that in this case adaptation to unfavorable but stable environment is observed (selection of species-stressolarents). An explanation seems to lie in the penetrating type of the upwelling in the Californian upwelling zone. Low biomass values seem to result from mass development of necto-benthic carnivorous crustaceans-galateids Pleuroncodes planiceps.

Collection of data on plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, time series since 2002)

This data set contains a time series of plant height measurements (vegetative and reproductive) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In addition, data on species specific plant heights for the main experiment are available from 2002. In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. 1. Plant height was recorded, generally, twice a year just before biomass harvest (during peak standing biomass in late May and in late August). Methodologies of measuring height have varied somewhat over the years. In earlier year the streched plant height was measured, while in later years the standing height without streching the plant was measured. Vegetative height was measured either as the height of the highest leaf or as the length of the main axis of non-flowering plants. Regenerating height was measured either as the height of the highest flower on a plant or as the height of the main axis of flowering. Sampled plants were either randomly selected in the core area of plots or along transects in defined distances. For details refer to the description of individual years. Starting in 2006, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details in the general description of the Jena Experiment) were sampled. 2. Species specific plant height was recorded two times in 2002: in late July (vegetative height) and just before biomass harvest during peak standing biomass in late August (vegetative and regenerative height). For each plot and each sown species in the species pool, 3 plant individuals (if present) from the central area of the plots were randomly selected and used to measure vegetative height (non-flowering indviduals) and regenerative height (flowering individuals) as stretched height. Provided are the means over the three measuremnts per plant species per plot.

Collection of data on soil carbon (particulate and dissolved) in the Jena Experiment (Main Experiment, time series since 2002)

This data set contains three time series of measurements of soil carbon (particular and dissolved) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. 1. Particulate soil carbon: Stratified soil sampling was performed every two years since before sowing in April 2002 and was repeated in April 2004, 2006 and 2008 to a depth of 30 cm segmented to a depth resolution of 5 cm giving six depth subsamples per core. Total carbon concentration was analyzed on ball-milled subsamples by an elemental analyzer at 1150°C. Inorganic carbon concentration was measured by elemental analysis at 1150°C after removal of organic carbon for 16 h at 450°C in a muffle furnace. Organic carbon concentration was calculated as the difference between both measurements of total and inorganic carbon. 2. Particulate soil carbon (high intensity sampling): In one block of the Jena Experiment soil samples were taken to a depth of 1 m (segmented to a depth resolution of 5 cm giving 20 depth subsamples per core) with three replicates per block ever 5 years starting before sowing in April 2002. Samples were processed as for the more frequent sampling. 3. Dissolved organic carbon: Suction plates installed on the field site in 10, 20, 30 and 60 cm depth were used to sample soil pore water. Cumulative soil solution was sampled biweekly and analyzed for dissolved organic carbon concentration by a high TOC elemental analyzer. Annual mean values of DOC are provided.

Radiolarian faunal turnover across the Oligocene/Miocene boundary in the equatorial Pacific Ocean

The global warming trend of the latest Oligocene was interrupted by several cooling events associated with Antarctic glaciations. These cooling events affected surface water productivity and plankton assemblages. Well-preserved radiolarians were obtained from upper Oligocene to lower Miocene sediments at Ocean Drilling Program (ODP) Leg 199 Sites 1218 and 1219 in the equatorial Pacific, and 110 radiolarian species were identified. Four episodes of significant radiolarian faunal changes were identified: middle late Oligocene (27.5 to 27.3 Ma), latest Oligocene (24.4 Ma), earliest Miocene (23.3 Ma), and middle early Miocene (21.6 Ma). These four episodes approximately coincide with increases and decreases of biogenic silica accumulation rates and increases in delta18O values coded as "Oi" and "Mi" events. These data indicate that Antarctic glaciations were associated with change of siliceous sedimentation patterns and faunal changes in the equatorial Pacific. Radiolarian fauna was divided into three assemblages based on variations in radiolarian productivity, species richness and the composition of dominant species: a late Oligocene assemblage (27.6 to 24.4 Ma), a transitional assemblage (24.4 to 23.3 Ma) and an early Miocene assemblage (23.3 to 21.2 Ma). The late Oligocene assemblage is characterized by relatively high productivity, low species richness and four dominant species of Tholospyris anthophora, Stichocorys subligata, Lophocyrtis nomas and Lithelius spp. The transitional assemblage represents relatively low values of productivity and species richness, and consists of three dominant species of T. anthophora, S. subligata and L. nomas. The characteristics of the early Miocene assemblage are relatively low productivity, but high species richness. The two dominant species present in this assemblage are T. anthophora and Cyrtocapsella tetrapera. The most significant faunal turnover of radiolarians is marked at the boundary between the transitional/early Miocene assemblages.

Biostratigraphy of sediment core CRP-3 from the Ross Sea, Antarctica

Early Oligocene siliceous microfossils were recovered in the upper c. 193 m of the CRP-3 drillcore. Although abundance and preservation are highly variable through this section, approximately 130 siliceous microfossil taxa were identified, including diatoms, silicoflagellates, ebridians, chrysophycean cysts, and endoskeletal dinoflagellates. Well-preserved and abundant assemblages characterize samples in the upper c. 70 m and indicate deposition in a coastal setting with water depths between 50 and 200 m. Abundance fluctuations over narrow intervals in the upper c. 70 mbsf are interpreted to reflect environmental changes that were either conducive or deleterious to growth and preservation of siliceous microfossils. Only poorly-preserved (dissolved, replaced, and/or fragmented) siliceous microfossils are present from c. 70 to 193 mbsf. Diatom biostratigraphy indicates that the CRP-3 section down to c. 193 mbsf is early Oligocene in age. The lack of significant changes in composition of the siliceous microfossil assemblage suggests that no major hiatuses are present in this interval. The first occurrence (FO) of Cavitatus jouseanus at 48.44 mbsf marks the base of the Cavitatus jouseanus Zone. This datum is inferred to be near the base of Subchron C12n at c. 30.9 Ma. The FO of Rhizosolenia antarctica at 68.60 mbsf marks the base of the Rhizosolenia antarctica Zone. The FO of this taxon is correlated in deep-sea sections to Chron C13 (33.1 to 33.6 Ma). However, the lower range of R. antarctica is interpreted as incomplete in the CRP-3 drillcore, as it is truncated at an underlying interval of poor preservation: therefore, an age of c. 33.1 to 30.9 Ma is inferred for interval between c. 70 and 50 mbsf. The absence of Hemiaulus caracteristicus from diatom-bearing interval of CRP-3 further indicates an age younger than c. 33 Ma (Subchron C13n) for strata above c. 193 mbsf. Siliceous microfossil assemblages in CRP-3 are significantly different from the late Eocene assemblages reported CIROS-1 drillcore. The absence of H. caracteristicus, Stephanopyxis splendidus, and Pterotheca danica, and the ebridians Ebriopsis crenulata, Parebriopsis fallax, and Pseudoammodochium dictyoides in CRP-3 indicates that the upper 200 m of the CRP-3 drillcore is equivalent to part of the stratigraphic interval missing within the unconformity at c. 366 mbsf in CIROS-1.

Soil carbon in the Jena Experiment (all blocks Main Experiment up to 30cm depth, year 2006)

This data set contains soil carbon measurements (Organic carbon, inorganic carbon, and total carbon; all measured in dried soil samples) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed in April 2006 to a depth of 30 cm. Three samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Sampling locations were less than 30 cm apart from sampling locations in 2002. Soil samples were segmented into 5 cm depth segments in the field (resulting in six depth layers) and made into composite samples per depth. Subsequently, samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Because of much higher proportions of roots in the soil, samples in years after 2002 were further sieved to 1 mm according to common root removal methods. No additional mineral particles were removed by this procedure. Total carbon concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s**-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany). We measured inorganic carbon concentration by elemental analysis at 1150°C after removal of organic carbon for 16 h at 450°C in a muffle furnace. Organic carbon concentration was calculated as the difference between both measurements of total and inorganic carbon.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2002)

This data set contains measurements of plant height: vegetative height (non-flowering indviduals) and regenerative height (flowering individuals) in 2002 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2002, plant height was recorded twice a year: in late June and just before biomass harvest during peak standing biomass in late August. For 3 target plant individuals (if present) per sown species from the central area of the plots, vegetative height (non-flowering indviduals) and regenerative height (flowering individuals) were measured as stretched height. Provided are the indivdiual measurements and the mean over the measured plants per plot (in June) and the mean over the measured plants per plot (in August).

Maastrichtian planktic foraminifera of the South Atlantic Ocean

Stratigraphic, faunal and isotopic analyses of the Maastrichtian at DSDP sites 525A and 21 in the South Atlantic reveal a planktic foraminiferal fauna characterized by two major events, an early late Maastrichtian diversification and end-Maastrichtian mass extinction. Both events are accompanied by major changes in climate and productivity. The diversification event which occurred in two steps between 70.5 and 69.1 Ma increased species richness by a total of 43% and coincided with the onset of major cooling in surface and bottom waters and increased surface productivity. The onset of the terminal decline in Maastrichtian species richness began at 67.5 Ma and the first significant decline in surface productivity occurred at 66.2 Ma, coincident maximum cooling to 13°C in surface waters and the reduction of the surface-to-deep temperature gradient to less than 5°C. Major climatic and moderate productivity changes mark the mass extinction and the last 500 kyr of the Maastrichtian. Between 200 and 400 kyr before the K-T boundary surface and deep waters warmed rapidly by 3-4°C and cooled again during the last 100 kyr of the Maastrichtian. Surface productivity decreased only moderately across the K-T boundary. Species richness began to decline during the late Maastrichtian cooling and by K-T boundary time, the mass extinction had claimed 66% of the species. Viewed within the context of Maastrichtian climate and productivity changes, the K-T mass extinction could have resulted from extreme environmental stress even without the addition of an extraterrestrial impact.

Dissolved organic carbon in soil solution of the Jena Experiment (Main Experiment, year 2002)

This data set contains measurements of dissolved organic carbon in samples of soil water collected from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In April 2002 glass suction plates with a diameter of 12 cm, 1 cm thickness and a pore size of 1-1.6 mm (UMS GmbH, Munich, Germany) were installed in depths of 10, 20, 30 and 60 cm to collect soil solution. The sampling bottles were continuously evacuated to a negative pressure between 50 and 350 mbar, such that the suction pressure was about 50 mbar above the actual soil water tension. Thus, only the soil leachate was collected. Cumulative soil solution was sampled biweekly and analyzed for dissolved organic carbon concentration by a high TOC elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany). Samples were analyzed as soon as possible and stored at 4°C if necessary. Often in summer, no free soil solution was available for collection, especially in the upper soil layers. Annual mean values of measured biweekly concentrations of dissolved organic carbon are provided.