Influence of experimental soil disturbances on the diversity of plants in agricultural grasslands

Aims and Methods Disturbance is supposed to play an important role for biodiversity and ecosystem stability as described by the intermediate disturbance hypothesis (IDH), which predicts highest species richness at intermediate levels of disturbances. In this study, we tested the effects of artificial soil disturbances on diversity of annual and perennial vascular plants and bryophytes in a field experiment in 86 agricultural grasslands differing in land use in two regions of Germany. On each grassland, we implemented four treatments: three treatments differing in application time of soil disturbances and one control. One year after experimental disturbance, we recorded vegetation and measured biomass productivity and bare ground. We analysed the disturbance response taking effects of region and land-use-accompanied disturbance regimes into account.Important Findings Region and land-use type strongly determined plant species richness. Experimental disturbances had small positive effects on the species richness of annuals, but none on perennials or bryophytes. Bare ground was positively related to species richness of bryophytes. However, exceeding the creation of 12% bare ground further disturbance had a detrimental effect on bryophyte species richness, which corresponds to the IDH. As biomass productivity was unaffected by disturbance our results indicate that the disturbance effect on species richness of annuals was not due to decreased overall productivity, but rather due to short-term lowered inter- and intraspecific competition at the newly created microsites.Generally, our results highlight the importance of soil disturbances for species richness of annual plants and bryophytes in agricultural grasslands. However, most grasslands were disturbed naturally or by land-use practices and our additional experimental soil disturbances only had a small short-term effect. Overall, total plant diversity in grasslands seemed to be more limited by the availability of propagules rather than by suitable microsites for germination. Thus, nature conservation efforts to increase grassland diversity should focus on overcoming propagule limitation, for instance by additional sowing of seeds, while the creation of additional open patches by disturbance might only be appropriate where natural disturbances are scarce.

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

BACKGROUND A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. RESULTS Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters. CONCLUSIONS Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063).

Limitation of seedling growth by potassium and magnesium supply for two ectomycorrhizal tree species of a Central African rain forest and its implication for their recruitment

In the ectomycorrhizal caesalpiniaceous groves of southern Korup National Park, the dominant tree species, Microberlinia bisulcata, displays very poor in situ recruitment compared with its codominant, Tetraberlinia bifoliolata. The reported ex situ experiment tested whether availabilities of soil potassium and magnesium play a role. Seedlings of the two species received applications of K and Mg fertilizer in potted native soil in a local shade house, and their responses in terms of growth and nutrient concentrations were recorded over 2 years. Amended soil concentrations were also determined. Microberlinia responded strongly and positively in its growth to Mg, but less to K; Tetraberlinia responded weakly to both. Added Mg led to strongly increased Mg concentration for Microberlinia while added K changed that concentration only slightly; Tetraberlinia strongly increased its concentration of K with added K, but only somewhat its Mg concentration with added Mg. Additions of Mg and K had small but important antagonistic effects. Microberlinia is Mg-demanding and apparently Mg-limited in Korup soil; Tetraberlinia, whilst K-demanding, appeared not to be K-limited (for growth). Added K enhanced plant P concentrations of both species. Extra applied Mg may also be alleviating soil aluminum toxicity, and hence improving growth indirectly and especially to the benefit of Microberlinia. Mg appears to be essential for Microberlinia seedling growth and its low soil availability in grove soils at Korup may be an important contributing factor to its poor recruitment. Microberlinia is highly shade-intolerant and strongly light-responding, whilst Tetraberlinia is more shade-tolerant and moderately light-responding, which affords an interesting contrast with respect to their differing responses to Mg supply. The study revealed novel aspects of functional traits and likely niche-partitioning among ectomycorrhizal caesalps in African rain forests. Identifying the direct and interacting indirect effects of essential elements on tropical tree seedling growth presents a considerable challenge due the complex nexus of causes involved.

Decreasing Proportion of Recent Infections among Newly Diagnosed HIV-1 Cases in Switzerland, 2008 to 2013 Based on Line-Immunoassay-Based Algorithms.

BACKGROUND: HIV surveillance requires monitoring of new HIV diagnoses and differentiation of incident and older infections. In 2008, Switzerland implemented a system for monitoring incident HIV infections based on the results of a line immunoassay (Inno-Lia) mandatorily conducted for HIV confirmation and type differentiation (HIV-1, HIV-2) of all newly diagnosed patients. Based on this system, we assessed the proportion of incident HIV infection among newly diagnosed cases in Switzerland during 2008-2013. METHODS AND RESULTS: Inno-Lia antibody reaction patterns recorded in anonymous HIV notifications to the federal health authority were classified by 10 published algorithms into incident (up to 12 months) or older infections. Utilizing these data, annual incident infection estimates were obtained in two ways, (i) based on the diagnostic performance of the algorithms and utilizing the relationship 'incident = true incident + false incident', (ii) based on the window-periods of the algorithms and utilizing the relationship 'Prevalence = Incidence x Duration'. From 2008-2013, 3'851 HIV notifications were received. Adult HIV-1 infections amounted to 3'809 cases, and 3'636 of them (95.5%) contained Inno-Lia data. Incident infection totals calculated were similar for the performance- and window-based methods, amounting on average to 1'755 (95% confidence interval, 1588-1923) and 1'790 cases (95% CI, 1679-1900), respectively. More than half of these were among men who had sex with men. Both methods showed a continuous decline of annual incident infections 2008-2013, totaling -59.5% and -50.2%, respectively. The decline of incident infections continued even in 2012, when a 15% increase in HIV notifications had been observed. This increase was entirely due to older infections. Overall declines 2008-2013 were of similar extent among the major transmission groups. CONCLUSIONS: Inno-Lia based incident HIV-1 infection surveillance proved useful and reliable. It represents a free, additional public health benefit of the use of this relatively costly test for HIV confirmation and type differentiation.

Antibiotic Susceptibility and Sequence Type Distribution of Ureaplasma Species Isolated from Genital Samples in Switzerland.

Antibiotic resistance in Ureaplasma urealyticum/Ureaplasma parvum and Mycoplasma hominis is an issue of increasing importance. However, data regarding the susceptibility and, more importantly, the clonality of these organisms are limited. We analyzed 140 genital samples obtained in Bern, Switzerland, in 2014. Identification and antimicrobial susceptibility tests were performed by using the Mycoplasma IST 2 kit and sequencing of 16S rRNA genes. MICs for ciprofloxacin and azithromycin were obtained in broth microdilution assays. Clonality was analyzed with PCR-based subtyping and multilocus sequence typing (MLST), whereas quinolone resistance and macrolide resistance were studied by sequencing gyrA, gyrB, parC, and parE genes, as well as 23S rRNA genes and genes encoding L4/L22 ribosomal proteins. A total of 103 samples were confirmed as positive for U. urealyticum/U. parvum, whereas 21 were positive for both U. urealyticum/U. parvum and M. hominis. According to the IST 2 kit, the rates of nonsusceptibility were highest for ciprofloxacin (19.4%) and ofloxacin (9.7%), whereas low rates were observed for clarithromycin (4.9%), erythromycin (1.9%), and azithromycin (1%). However, inconsistent results between microdilution and IST 2 kit assays were recorded. Various sequence types (STs) observed previously in China (ST1, ST2, ST4, ST9, ST22, and ST47), as well as eight novel lineages, were detected. Only some quinolone-resistant isolates had amino acid substitutions in ParC (Ser83Leu in U. parvum of serovar 6) and ParE (Val417Thr in U. parvum of serovar 1 and the novel Thr417Val substitution in U. urealyticum). Isolates with mutations in 23S rRNA or substitutions in L4/L22 were not detected. This is the first study analyzing the susceptibility of U. urealyticum/U. parvum isolates in Switzerland and the clonality outside China. Resistance rates were low compared to those in other countries. We hypothesize that some hyperepidemic STs spread worldwide via sexual intercourse. Large combined microbiological and clinical studies should address this important issue.

Evaluation of the Newly-developed, Least-cost Experimental Diet for Bluegill at Commercial Densities in Ponds

A substantial need exists to reduce costs and develop more nutritionally adequate diets for established as well as emerging aquaculture species in the North Central Region (NCR). The study evaluated a diet for juvenile northern bluegill (Lepomis macrochirus) that is significantly less costly than currently available diets for sunfish, while yielding a growth rate that is at least equal to an industry standard sunfish diet. Such a diet formulation is now available to the NCR as the result of a recently funded North Central Regional Aquaculture Center (NCRAC) project.

Chemobiostratigraphy of the Cretaceous/Paleocene boundary at ODP Hole 120-750A

An integrated biostratigraphic and stable isotope investigation was conducted on a high-latitude sequence across the Cretaceous/Paleogene (K/P) boundary recovered in Hole 750A in the southern Indian Ocean. The sequence consists of nannofossil chalk and is discontinuous across the boundary; missing is an estimated 0.3-m.y. late Maestrichtian and early Danian interval. Nonetheless, because calcareous nannofossil Zones NP1 and NP2 are well-developed, micropaleontological studies of the sequence have yielded a detailed record of Danian high-latitude microplankton evolution. In addition, stable carbon isotope analyses of planktonic and benthic foraminifer and bulk samples provide a record of late Maestrichtian and early Danian surface- and deep-water carbon isotope variations. Together, the carbon isotope and carbonate accumulation records serve as an index of regional marine net productivity across the boundary. Earliest Danian nannoplankton assemblages consisted mainly of persistent genera that were generally rare or absent in the Upper Cretaceous at Hole 750A. However, by 0.5-0.6 m.y. after the boundary, newly evolving Danian taxa became dominant. The turnover in nannofossil assemblages was accompanied by significant changes in rates of net productivity as gauged by carbon isotope distributions and carbonate accumulation rates. During the period dominated by persistent taxa, net productivity was extremely low, as reflected by the absence of vertical delta13C gradients and reduced carbonate accumulation rates. Later in the Danian, as new species evolved and flourished, vertical delta13C gradients reappeared and carbonate accumulation rates increased, signaling partial recovery of net productivity in this region. The absolute timing and magnitude of late Maestrichtian and early Danian biotic and geochemical changes in the southern Indian Ocean were similar to those recorded in other pelagic K/P boundary sequences from low- and mid-latitude Atlantic and Pacific sites, indicating that these events were ubiquitous.

Mean cover and frequencies of vascular plant species during three decades around Abisko Scientific Research Station

Plant species distributions are expected to shift and diversity is expected to decline as a result of global climate change, particularly in the Arctic where climate warming is amplified. We have recorded the changes in richness and abundance of vascular plants at Abisko, sub-Arctic Sweden, by re-sampling five studies consisting of seven datasets; one in the mountain birch forest and six at open sites. The oldest study was initiated in 1977-1979 and the latest in 1992. Total species number increased at all sites except for the birch forest site where richness decreased. We found no general pattern in how composition of vascular plants has changed over time. Three species, Calamagrostis lapponica, Carex vaginata and Salix reticulata, showed an overall increase in cover/frequency, while two Equisetum taxa decreased. Instead, we showed that the magnitude and direction of changes in species richness and composition differ among sites.

Effect of Prosopis flexuosa on understory species and its importance to pastoral management in woodlands of the Central Monte Desert

In the Monte Biogeographic Province, located in the arid region of Argentina, the presence of Prosopis flexuosa DC. produces spatial heterogeneity through edaphic modifications and microclimate changes. This results in vegetation patches differing in species composition and abundance. However, this interaction can be modified by the occurrence of gradients of biotic stress or disturbance intensity. In particular, grazing has been observed to enhance or reduce vegetation heterogeneity. Such complex of interactions could determine forage availability for cattle in one of the driest areas of the Monte Desert. We assessed the effect of Prosopis on understory species and analyzed whether the outcomes of this interaction differed with distance to watering points, as a proxy of grazing intensity, in the Northeast of Mendoza Province, Argentina. We used a two-way factorial design including the following factors: 1) microsite (under the cover of P. flexuosa trees and in intercanopy microsites) and 2) distance to watering points ("near the watering point", 500-700 m away, and "far from the watering point", 3-4 km away). Cover of each species, total cover, bare soil, and litter were recorded, and plant diversity, richness, and evenness were estimated with the modified Point Quadrat method. Results showed that P. flexuosa cover, distance from watering points, and the interaction between them determined species composition, abundance and spatial distribution of understory species, and were, consequently, a determining factor for forage availability. The presence of P. flexuosa enhances carrying capacity by supporting higher abundance of grasses under its canopy. Near watering points, high grazing intensity appears to disrupt the patches formed under P. flexuosa canopies, reducing the differences between microsites.

List of plant species found on Victoria Island

While engaged in geoecological field work on Victoria Island, 277 new plants could be recorded for the vicinities of Holman, Cambridge Bay, Wellington Bay, Mt. Pelly, Richardson Islands, Hadley Bay, and Minto lnlet; 8 of them were new for Victoria Island, 6 for the western Canadian arctic archipelago.

Total phytoplankton abundance and biomass in the surface and fluorescence maximum layers and contributions of dominant species to their values in the Werstern Arctic in July-August 2003

Phytoplankton community was studied in the Bering Strait and over the shelf, continental slope, and deep-water zones of the Chukchi and Beaufort Seas in the middle of the vegetative season (July-August 2003). Its structure was analyzed in relation to ice conditions and seasonal patterns of water warming, stratification, and nutrient concentrations. Overall variations in phytoplankton abundance from 200 to 6000000 cells/l and biomass from 0.1 to 444.1 µg C/l.were estimated. The bulk of phytoplankton cells concentrated in the seasonal picnocline at depths 10-25 m. The highest values of cell abundance and biomass were recorded in regions influenced by inflow of Bering Sea waters or characterized by intense hydrodynamics, such as the Bering Strait, Barrow Canyon, and the outer shelf and slope of the Chukchi Sea. In the middle of the vegetative season, phytoplankton in the study region of the Western Arctic proved to comprise three successional (seasonal) assemblages: early spring, late spring, and summer assemblages. Their spatial distribution was dependent mainly on local features of hydrological and nutrient regimes rather than on general latitudinal trends of seasonal succession characteristic of arctic ecosystems.

Species-specific plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2002)

This data set contains measurements of species-specific plant height: vegetative height (non-flowering indviduals) and regenerative height (flowering individuals) measured for all sown species separetly in 2002. Data was recorded in 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 two times: 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.

Temperatures, salinity, and stable oxygen isotope values of bottom water and of the mollusc shell Arctica islandica from Nantucket Shoals

The carbonate shell of the bivalve Arctica islandica has been recognized, for more than a decade, as a potentially important marine geochemical biorecorder owing to this species' great longevity (200+ years) and wide geographic distribution throughout the northern North Atlantic Ocean, a region vital to global climate and ocean circulation. However, until now this potential has not been realized owing to the difficulty of precisely sampling the shell of this slow growing species. Using newly available automated microsampling techniques combined with micromass stable isotope mass spectrometry, a stable oxygen isotope record (1956-1957 and 1961-1970) has been obtained from a live-captured, 38-year-old A. islandica specimen collected near the former position of the Nantucket Shoals Lightship (41°N. 69°W). The shell's delta18O signal is compared with an expected signal derived from ambient bottom temperature and salinity data recorded at the lightship for the same period. The results show that A islandica's delta18O record (1) is in phase with its growth banding, confirming the annual periodicity of this species' growth bands, (2) is in oxygen isotopic equilibrium with the ambient seawater, (3) shows a consistent shell growth shutdown temperature of ~6°C. which translates into an ~8-month (May-December) shell growth period at this location, and (4) records the ambient bottom temperature with a precision of ~ +/-1.2°C. These results add important information on the life history of this commercially important shellfish species and demonstrate that A. islandica shells can be used to reconstruct inter- and intra-annual records of the continental shelf bottom temperature.

Stratigraphic occurrence of selected marine palynomorph species recorder in the Paleogene of ODP Hole 105-647A (Table 3)

Dinoflagellate cysts were recovered throughout the Paleogene succession of Hole 647A, which contains an almost complete deep-water record of early Eocene through early late Oligocene sedimentation in the Labrador Sea. Dinoflagellate cyst biostratigraphy is in general accord with that provided by other microfossil groups and is consistent with a lower Eocene age, as determined by nannofossils, for basal sediments in Hole 647A. These sediments overlie oceanic crust of Chron 24 age. Dinocyst assemblages indicate outer neritic to oceanic conditions throughout, although the persistent occurrence of Wetzeliellaceae specimens in the lower Eocene suggests a greater influence from shelf environments during this time. Lower Eocene dinocyst assemblages are similar to coeval assemblages from the Rockall Plateau, but those from the middle to upper Eocene have mixed affinities and may be related to the intensification of the proto-Gulf Stream from middle Eocene time. Oligocene dinocyst assemblages suggest the influence of both arctic and North Atlantic wate rmasses at this site. The presence of protoperidineacean species in the upper Eocene and Oligocene may indicate increased availability of nutrients, perhaps related to increased upwelling or the effects of water-mass mixing. Productive samples are dominated by dinocysts and acritarchs, while sporomorphs are represented mainly by bisaccate pollen. Preservational differences within samples may reflect mixing of penecontemporaneous dinocyst populations during the Eocene, and all samples examined may have a considerable allochthonous component. Variability in relative abundance of many species during the Eocene may be related to fluctuating water-mass properties. A total 175 dinocyst and acritarch taxa were recorded from 53 productive samples from the Paleogene. Only one Paleogene sample was barren of palynomorphs. Of three Miocene samples processed, all were barren.

Species list of the flora on Banks Island

While engaged in palaeo-botanical and plantgeographical field work on Banks Island, N. W. T. during the summer of 1973, 225 new plants could be recorded for the vicinities of Sachs Harbour, Shoran Lake and Johnson Point; 21 of them were new for Banks Island, 7 for the western Canadian archipelago.