An example of Holocene vegetation stability from Camerons Lagoon,a near treeline site on the Central Plateau,Tasmania

Abstract A discontinuous record of vegetation over the past 7500 years was obtained through pollen analysis of pond sediments from an extensive treeless plain on the relatively dry Central Plateau of Tasmania. The results demonstrate continuity of treeless conditions, which probably persisted from the Pleistocene throughout the Holocene, up to the present day. Some changes to the structure of the grassland were observed, especially over the past 200 years. Analysis of carbonized particles showed that fires had been infrequent over the period examined. It seems that this area, close to the altitudinal tree limit, has remained a natural grassland, and the hypothesis of Jackson (1973), that unreliable summer conditions may be a major factor in maintaining open conditions, is supported. Parts of the Central Plateau may thus preserve plant communities with some of the floristic elements and structure of widespread Bassian grasslands of the Late Pleistocene.     

The Holocene vegetation history of northern West Jutland, Denmark

Holocene sediments of three closed Danish lake basins (Solsø, Skånsø, Kragsø) were used for the inference of post-glacial vegetational dynamics in former heathland areas in northern West Jutland, Denmark. The sites were selected to represent the major geomorphological units of West Jutland. The Holocene history of each lake basin was investigated by mapping of sediment distribution, analysis of loss-on-ignition, coarse inorganic matter, humus content, mineral magnetics, δ¹³C, pollen and selected other microfossils. These techniques were supplemented by plant macrofossil analysis at one site. Holocene terrestrial vegetational development was inferred at each site from analyses of pollen and microscopical charred particles. Chronologies were provided by numerous ¹⁴C dates. Stratigraphies of wet ground and terrestrial pollen and spore types were zooned by stratigraphically constrained cluster analysis. Based on the resultant site pollen asemblage zones (site PAZ), regional PAZ were proposed. Using modern analogues, Holocene floristic richness was estimated from pollen richness in the microfossil assemblages. The results support the hypothesis that disturbance is one of the most important mechanisms behind the maintenance of floristic richness. In particular, the response of estimated floristic richness to the intensity of vegetational fires followed the predictions of the Intermediate Disturbance Hypothesis. A period of elevated palynological richness and inferred vegetational disturbance was identified at all sites between 6000 and 5200 BC (calendar years). Using correspondence analysis (CA), the major gradient in the terrestrial pollen sequences was identified as a light-shade gradient, and CA first axis sample scores were used as a supplement to standard AP/NAP pollen ratios as an indicator of the shade-tolerance/light-demand of Holocene terrestrial plant communities. In spite of different vegetational developments since 4000 BC, the timing of major changes towards more light-demanding vegetation types were broadly synchronous at the three sites. Using chord distance as a dissimilarity index, rates of palynological change suggest that the interval between 8000 and 7500 BC (calendar years) was the period of most rapid vegetational change during the Holocene, both in terrestrial as well as lacustrine ecosystems. While climatic forcing of the rapid events around 8000 BC is hypothesised, the synchronous timing of relatively rapid inferred change in lake and terrestrial vegetation around AD 600 may reflect changes in climate as well as in land-use. Reducdancy analysis was used to develop a model between fire intensity (inferred from microscopical charred particles) and vegetational response, as reflected by pollen assemblages. Formulated at one site and tested at the two other sites, the model explains regional Calluna-heathland expansions as a result of vegetational burning. Similarly, declines in heathland cover are explained by lack of maintenance by fire. Regional vegetational development in northern West Jutland is reconstructed and special consideration is given to heathland history. The Holocene heathland development is interpreted as resulting from its importance for grazing. It is hypothesized that on poor soils, Calluna-dominated heathland was a better grazing resource than grass-dominated pasture, due to the winter-grazing offered by Calluna and the low palatibility of dominant grasses on poor soils. This hypothesis is relevant for the explanation of the variation in timing of heathland expansions on the different soil types represented by the study sites.     

The Holocene vegetation history of northern West Jutland, Denmark

Holocene sediments of three closed Danish lake basins (Solsø, Skånsø, Kragsø) were used for the inference of post-glacial vegetational dynamics in former heathland areas in northern West Jutland, Denmark. The sites were selected to represent the major geomorphological units of West Jutland. The Holocene history of each lake basin was investigated by mapping of sediment distribution, analysis of loss-on-ignition, coarse inorganic matter, humus content, mineral magnetics, δ¹³C, pollen and selected other microfossils. These techniques were supplemented by plant macrofossil analysis at one site. Holocene terrestrial vegetational development was inferred at each site from analyses of pollen and microscopical charred particles. Chronologies were provided by numerous ¹⁴C dates. Stratigraphies of wet ground and terrestrial pollen and spore types were zooned by stratigraphically constrained cluster analysis. Based on the resultant site pollen asemblage zones (site PAZ), regional PAZ were proposed. Using modern analogues, Holocene floristic richness was estimated from pollen richness in the microfossil assemblages. The results support the hypothesis that disturbance is one of the most important mechanisms behind the maintenance of floristic richness. In particular, the response of estimated floristic richness to the intensity of vegetational fires followed the predictions of the Intermediate Disturbance Hypothesis. A period of elevated palynological richness and inferred vegetational disturbance was identified at all sites between 6000 and 5200 BC (calendar years). Using correspondence analysis (CA), the major gradient in the terrestrial pollen sequences was identified as a light-shade gradient, and CA first axis sample scores were used as a supplement to standard AP/NAP pollen ratios as an indicator of the shade-tolerance/light-demand of Holocene terrestrial plant communities. In spite of different vegetational developments since 4000 BC, the timing of major changes towards more light-demanding vegetation types were broadly synchronous at the three sites. Using chord distance as a dissimilarity index, rales of palynological change suggest that the interval between 8000 and 7500 BC (calendar years) was the period of most rapid vegetational change during the Holocene, both in terrestrial as well as lacustrine ecosystems. While climatic forcing of the rapid events around 8000 BC is hypothesised, the synchronous timing of relatively rapid inferred change in lake and terrestrial vegetation around AD 600 may reflect changes in climate as well as in land-use. Reducdancy analysis was used to develop a model between fire intensity (inferred from microscopical charred particles) and vegetational response, as reflected by pollen assemblages. Formulated at one site and tested at the two other sites, the model explains regional Colluna-heathland expansions as a result of vegetational burning. Similarly, declines in heathland cover are explained by lack of maintenance by fire. Regional vegetational development in northern West Jutland is reconstructed and special consideration is given to heathland history. The Holocene heathland development is interpreted as resulting from its importance for grazing. It is hypothesized that on poor soils, Calluna-dominated heathland was a better grazing resource than grass-dominated pasture, due to the winter-grazing offered by Calluna and the low palatibility of dominant grasses on poor soils. This hypothesis is relevant for the explanation of the variation in timing of heathland expansions on the different soil types represented by the study sites.     

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system

Background  

Mass spectrometry has become a powerful tool for the analysis of large numbers of proteins in complex samples, enabling much of proteomics. Due to various analytical challenges, so far no proteome has been sequenced completely. O'Shea, Weissman and co-workers have recently determined the copy number of yeast proteins, making this proteome an excellent model system to study factors affecting coverage.     

低覆盖度行带式固沙林对土壤及植被的修复效应

在我国干旱、半干旱地区由于水分条件的制约,经过漫长的自然演替过程,逐步发育形成了广泛分布的低覆盖度植被,这些低覆盖度植被类型中存在大量的天然乔木疏林或稀疏灌丛,地表处于半流动状态,而配置成行带式后,能够完全固定流沙,并且不同配置模式下行带式固沙林土壤与植被自然恢复程度不同.因此,通过对不同带宽的低覆盖度行带式固沙林对土壤及植被修复的影响研究,揭示了不同带宽行带式固沙林带间土壤因子与植被因子的变化过程,从而阐明行带式固沙林对带间植被自然恢复和土壤发育的促进作用.结果表明,行带式杨树固沙林能够明显的促进带间土壤与植被修复;带间距离的宽窄影响植被恢复及土壤发育效果;宽带间距固沙林带间植被多样性指数高,地上生物量大,根系生物量,总长度及表面积均高,土壤水分养分条件好,微生物数量大植物残体分解快,有利于植被的生长;模糊综合评估结果表明,不同带间距行带式固沙林土壤植被恢复程度不同,宽带间距20m的恢复效果＞带间距15m＞带间距10m.行带式固沙林通过带间宽度的变化可以调节植被与土壤之间的相互作用,窄带间距固沙林土壤与植被的相互作用则由于造林密度大而受到抑制.宽带间距可以明显加快土壤及植被修复的速度,进而缩短土壤及植被修复的时间.     

Reassessment of Holocene vegetation change on the upper Tibetan Plateau using the pollen-based REVEALS model

Previous studies based on fossil pollen data have reported significant changes in vegetation on the alpine Tibetan Plateau during the Holocene. However, since the relative proportions of fossil pollen taxa are largely influenced by individual pollen productivities and the dispersal characteristics, such inferences on vegetation have the potential to be considerably biased. We therefore examined the modern pollen–vegetation relationships for four common pollen species on the Tibetan Plateau, using Extended R-value (ERV) models. Assuming an average radius of 100 m for the sampled lakes, we estimated the relevant source area of pollen (RSAP) to be 2200 m (which represents the distance from the lake). Using Poaceae as the reference taxa (Pollen Productivity Estimate, PPE = 1), ERV Submodel 2 derived relative high PPEs for the steppe and desert taxa: 2.079 ± 0.432 for Artemisia and 5.379 ± 1.077 for Chenopodiaceae. Low PPEs were estimated for the Cyperaceae (1.036 ± 0.012), whose plants are characteristic of the alpine Kobresia meadows. Applying these PPEs to four fossil pollen sequences since the Late Glacial, the plant abundances on the central and north-eastern Tibetan Plateau were quantified using the “Regional Estimates of Vegetation Abundance from Large Sites” (REVEALS) model. The proportions of Artemisia and Chenopodiaceae were greatly reduced compared to their original pollen percentages in the reconstructed vegetation, owing to their high productivities and their dispersal characteristics, while Cyperaceae showed a relative increase in the vegetation reconstruction. The reconstructed vegetation assemblages of the four pollen sequence sites always yielded smaller compositional species turnovers than suggested by the pollen spectra, as revealed by Detrended Canonical Correspondence Analyses (DCCA) of the Holocene sections. The strength of the previously reported vegetation changes may therefore have been overestimated, which indicates the importance of taking into account pollen–vegetation relationships when discussing the potential drivers (such as climate, land use, atmospheric CO₂ concentrations) and implications (such as for land surface–climate feedbacks, carbon storage, and biodiversity) of vegetation change.     

Revegetation of a Taxodium-Nyssa forested wetland following complete vegetation destruction

Revegetation is described for a portion of a Taxodium distichum-Nyssa aquatica (bald cypress-water tupelo) forested wetland in South Carolina. Thermal effluent from nuclear production reactors from 1954 to 1968 eliminated most of the original vegetation from the study area. Vegetation in disturbed and adjacent undisturbed areas was sampled in 1981 and 1985 using permanent plots. Herbs invaded rapidly throughout the disturbed portion of the wetland after thermal discharge ceased. Shrubs (Salix spp. and Cephalanthus occidentalis) followed soon thereafter, and have gradually occupied more of the area. Taxodium and Nyssa regeneration is rare because of the inability of seedlings of these species to compete with the dense cover of herbs and shrubs. Species composition is correlated with water depth, substrate type, and severity of disturbance. Because of substrate diversity, several successional mechanisms may account for the revegetation patterns.Abbreviation DCA Detrended Correspondence Analysis     

Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta

Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe–host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host–microbe interactions and provide a basis for in-depth physiological experiments.     

Initial establishment of vegetation in a man-made coastal area in Denmark

A man-made coastal area (8 km long, 300 m wide), constructed from seed-free, marine sand was investigated from 1978 to 1983 as regards relief, soil properties, and establishment of vegetation.
The following developments were apparent:

• 1. 

  The outer shore zone changed from a Cakile -dominated vegetation to a sparse and less diverse vegetation.
• 2. 

  The inner shore zone maintained spontaneous Ammophila as dominant and developed into a mobile dune with changing species.
• 3. 

  The outer dune slope with planted Ammophila developed into a mobile dune dominated by vigorous Ammophila.
• 4. 

  The dune zone with planted Ammophila: The outer part developed towards a somewhat fixed dune with increasing diversity. The inner part developed into a diverse and more fixed dune community with mainly Festuca rubra.
• 5. 

  The inner dune slope developed into a vegetation comprising few species.
• 1. 

  The grassland zone, initially sown with Festuca rubra and Lolium perenne , changed into a grass-herb-vegetation dominated by Festuca rubra , with a slowly increasing number of immigrating species, changing from annuals to perennials, in particular species of Fabaceae and Hippophaë.

     

Nitrogen fertilizer enhances vegetation establishment of a high-altitude machine-graded ski slope

Machine grading is frequently required to prepare the terrain when building high-altitude ski slopes in the Alps. However, this kind of disturbance alters the natural environment, destroying the vegetation and hampering its reestablishment. Thus, specific restoration plans are necessary to encourage the recovery of vegetation, which is already affected by different natural constraints in this harsh environment. One of the main critical factors affecting plant growth in high-altitude areas is the lack of available nitrogen (N) in the soil. In this context, the addition of a slow-release N fertilizer was carried out in an experimental revegetated ski slope between 2,800 and 2,900 m above sea level in the western Italian Alps. Both vegetation and soil were monitored during a 5-year period in order to test the effectiveness of N addition on the restoration process. Even if effects on soil carbon and N contents were negligible, vegetation was remarkably affected by the fertilization, since the total vegetation cover and the species richness significantly increased. Against the expectations, there was a remarkable increase in spontaneous forbs, rather than in most of the sown graminoids, which slightly varied during the experimental period. Actually, graminoids responded in different ways, mostly increasing (likewise forbs), but the slight decrease of the dominant Festuca nigrescens (Chewing's Fescue) masked their spread. This study confirms the noteworthy role of N in high-altitude alpine soils and consequently its importance to improve the restoration process of degraded ecosystems.     

A tale of two green walls: a functional trait approach to assess vegetation establishment on restored steep slopes

Green walls (GWs) have been increasingly recognized as an important restoration technique for steep slopes resulting from quarrying activities or major infrastructure construction projects. In practice, GW irrigation is considered essential, although studies evaluating vegetation establishment under different irrigation regimes are lacking. Besides taxonomic metrics, functional diversity measures were used to compare the diversity and composition of plant communities of two hydroseeded GWs, with different irrigation regimes (irrigated vs. low‐irrigated). The studied GWs were installed in Peneda‐Gerês National Park (NW Portugal) to minimize the visual impact of shotcrete walls, along a road infrastructure, and promote their ecological restoration. Species' cover was recorded 3 years after installation. Species were classified according to their growth form, life form, and life strategy. Despite hydroseeding approximately 57 species, GW vegetation was dominated by spontaneous species, particularly acrocarpous mosses, regardless of irrigation regime. Species and functional richness were higher under irrigated conditions, while no differences were observed for species diversity and functional dispersion. Functional trait composition did not differ between GWs, indicating that both systems potentially provide the same ecosystem functions and services. Our results also suggest that spontaneous species colonizing GWs are highly adapted to local environmental conditions, given their dominance in both irrigated and low‐irrigated communities. Overall, irrigation did not affect the structure and functioning of GW communities, only their redundancy, since more species exhibiting similar traits were established in the irrigated GW. Therefore, our findings suggest that low‐irrigated GWs, hydroseeded with native species, represent a more cost‐effective solution to reduce the ecological impacts of steep slopes.     

The southern limit of the Mediterranean vegetation in the Sahara during the Holocene

Holocene records from the southern Sahara in Niger allow a reconstruction of the vegetation history and inform us about the former extension of the Mediterranean. Both pollen and charcoal analyses evidenced the direct contact of Sudanian and Saharan savannas during the middle Holocene at about 19°N, whereas at 20°N the transition from the Saharan savanna to the desert was found. In southwestern Libya (26°N) a combination of a Saharan desert vegetation and a semi‐desert Artemisia shrub on the plateaus demonstrated the contact with Mediterranean influenced formations. Regular ash and charcoal layers in middle‐Holocene sediments of the northern Niger prove an early interference of man with the vegetation development. One has to imagine that, in combination with the cattle‐keeping and the later metal production, man could have changed the former northern Sudanian vegetation into the present Sahelian savanna system from the middle Holocene on.     

Charcoal analysis, a method to study vegetation and climate of the Holocene: The case of Lago di Pergusa (Sicily, Italy)

The direct comparison between microcharcoal and pollen data from the Holocene sediment core of Lago di Pergusa (central Sicily, Italy) led us to investigate the linkages between fire, vegetation, and climate in the Mediterranean Basin. The role of human populations in shaping the environment of the last millennia was closely examined as well. Pollen and charcoal were extracted using a standard pollen methodology and both identified from the same pollen slides. At Lago di Pergusa the importance of fire in maintaining and favouring a Mediterranean vegetation, a basic concept in ecology, seems to be inconsistent, as important fires took place in the open environments with xeric vegetation at the beginning of the Holocene well before the expansion of evergreen vegetation. On the contrary some big fires seem to have happened in the period (around 8000 years BP) in which the greatest wetness, the thickest forest canopy, and the most important expansion of submontane vegetation of the record are found. A probable explanation of this phenomenon can be found in the precipitation regime, in the increased available biomass and in the resulting increase in combustible material, indicating also that the highest humidity achieved in central Sicily during the Holocene was not strong enough to prevent fires. During this period drops in arboreal pollen concentration match in minima in the charcoal curves. Fires were practically absent during the Neolithic and Eneolithic periods and not responsible for the general trend towards aridification identified in the pollen record, at times in which prehistoric populations are generally believed to have caused forest clearance by burning. Important and frequent burnings are documented for the Bronze and Iron Ages and probably not all of them were fires of living trees, but burning of wood for producing metals, cooking or heating. The occurrence of a fire around 3700 years BP temporarily caused a minor decrease of arboreal pollen concentration. In the open landscapes of the two last millennia an almost continuous sign of regional burnings is recognized, confirming the historical evidence of an intense land use in central Sicily at least since Roman times.     

Towards the establishment of a porcine model to study human amebiasis

Background

Entamoeba histolytica is an important parasite of the human intestine. Its life cycle is monoxenous with two stages: (i) the trophozoite, growing in the intestine and (ii) the cyst corresponding to the dissemination stage. The trophozoite in the intestine can live as a commensal leading to asymptomatic infection or as a tissue invasive form producing mucosal ulcers and liver abscesses. There is no animal model mimicking the whole disease cycle. Most of the biological information on E. histolytica has been obtained from trophozoite adapted to axenic culture. The reproduction of intestinal amebiasis in an animal model is difficult while for liver amebiasis there are well-described rodent models. During this study, we worked on the assessment of pigs as a new potential model to study amebiasis.

Methodology/Principal Findings

We first co-cultured trophozoites of E. histolytica with porcine colonic fragments and observed a disruption of the mucosal architecture. Then, we showed that outbred pigs can be used to reproduce some lesions associated with human amebiasis. A detailed analysis was performed using a washed closed-jejunal loops model. In loops inoculated with virulent amebas a severe acute ulcerative jejunitis was observed with large hemorrhagic lesions 14 days post-inoculation associated with the presence of the trophozoites in the depth of the mucosa in two out four animals. Furthermore, typical large sized hepatic abscesses were observed in the liver of one animal 7 days post-injection in the portal vein and the liver parenchyma.

Conclusions

The pig model could help with simultaneously studying intestinal and extraintestinal lesion development.     

The Xenopus retinal ganglion cell as a model neuron to study the establishment of neuronal connectivity

Neurons receive inputs through their multiple branched dendrites and pass this information on to the next neuron via long axons, which branch within the target. The shape the neuron acquires is thus the key to its proper functioning in the neural circuit in which it participates. Both axons and dendrites grow in a directed fashion to their target partner neurons by responding to a large number of molecular cues in the milieu through which they extend. They then go through the process of synaptogenesis, first choosing a neuron on which to synapse, and then the appropriate subcellular location. How a neuron acquires its unique shape, establishes and modifies appropriate synaptic connectivity, and the molecular signals involved, are key questions in developmental neurobiology. Such questions of nervous system wiring are being pursued actively with a variety of different animal models and neuron types, each with its own unique advantages. Among these, the developing retinal ganglion cell (RGC) of the South African clawed frog, Xenopus laevis, has proven particularly fruitful for revealing the secrets of how axons and dendrites acquire their final morphology and connectivity. In this review, we describe how this system can be used to understand the multiple molecular events that instruct the incorporation of RGCs into the neural circuit that controls vision.     

The complete classification for dynamics in a homosexually-transmitted disease model

A sexually-transmitted disease model for two strains of pathogen in a one-sex, heterogeneously-mixing population was proposed by Li et al. in (J Math Biol 10:1037–1052, 1986). The sufficient and necessary conditions for coexistence and the sufficient conditions for stability of the boundary equilibria were provided. This paper will present a thorough classification of dynamics for this model in terms of the first and second so called reproductive numbers of infection in strains I and J. This classification not only solves a conjecture proposed in (Li et al., J Math Biol 10:1037–1052, 1986) but also gives the sufficient and necessary conditions for the competitive exclusion. Supported by the NSF of China grants 10531030 and 10671143.     

Contributions of large wood to the initial establishment and diversity of riparian vegetation in a bar-braided temperate river

The purpose of this study was to examine the effects of large wood (LW) on the physical environment and the initial establishment of vascular plant species in the Rekifune River, a large bar-braided monsoonal river in Japan. The physical environment and the diversity and composition of plant species were compared in relation to the orientation of LW pieces. We found that shading effects were more prevalent in the immediate vicinity of LW pieces than in quadrats distant from LW. The effect was especially strong at the center of LW jams (the “jam center”). Fine sand and silt were concentrated in the quadrats downstream from the LW pieces. In contrast, cobbles dominated the upstream quadrats. The highest diversity was found in the jam center, while intermediate values were observed in the quadrats surrounding LW. Indicator species analysis detected 21 indicator species only in the jam center. The LW jams favored the deposition of plant fragments and sediment and created shaded areas within and around the structures. Buried seeds may be transported with LW during a flood, and seeds dispersed by wind and stream flows may be trapped by the complex structure of LW jams. The specific environmental conditions and the trapping of seeds and plant fragments result in the early establishment of mid-successional tree species at LW jams. In conclusion, the LW pieces deposited on gravel bars altered the light and substrate conditions and thereby provided specific safe sites for various riparian plant species.