Biomass and morphology of fine roots in temperate broad-leaved forests differing in tree species diversity: is there evidence of below-ground overyielding?

Biodiversity effects on ecosystem functioning in forests have only recently attracted increasing attention. The vast majority of studies in forests have focused on above-ground responses to differences in tree species diversity, while systematic analyses of the effects of biodiversity on root systems are virtually non-existent. By investigating the fine root systems in 12 temperate deciduous forest stands in Central Europe, we tested the hypotheses that (1) stand fine root biomass increases with tree diversity, and (2) ‘below-ground overyielding’ of species-rich stands in terms of fine root biomass is the consequence of spatial niche segregation of the roots of different species. The selected stands represent a gradient in tree species diversity on similar bedrock from almost pure beech forests to medium-diverse forests built by beech, ash, and lime, and highly-diverse stands dominated by beech, ash, lime, maple, and hornbeam. We investigated fine root biomass and necromass at 24 profiles per stand and analyzed species differences in fine root morphology by microscopic analysis. Fine root biomass ranged from 440 to 480 g m⁻² in the species-poor to species-rich stands, with 63–77% being concentrated in the upper 20 cm of the soil. In contradiction to our two hypotheses, the differences in tree species diversity affected neither stand fine root biomass nor vertical root distribution patterns. Fine root morphology showed marked distinctions between species, but these root morphological differences did not lead to significant differences in fine root surface area or root tip number on a stand area basis. Moreover, differences in species composition of the stands did not alter fine root morphology of the species. We conclude that ‘below-ground overyielding’ in terms of fine root biomass does not occur in the species-rich stands, which is most likely caused by the absence of significant spatial segregation of the root systems of these late-successional species.     

公共卫生大数据研究进展——生物信息的新领域

大数据时代的公共卫生面临新的机遇和挑战。为了推动公共卫生大数据的应用,准确把握其内涵,开发针对性的解决方案,达到改善人们健康状况的目的,基于此对公共卫生大数据的现状进行了分析和论证。研究表明:通过对多个不同来源公共卫生数据进行收集和整理,能够形成公共卫生大数据,通过深入挖掘和分析,能够获取重大疾病影响因素、流行病的传播规律等信息,帮助医疗卫生人员和相关机构进行预测和评估,以便采取有效的管理手段和措施,保护人民健康,减少医疗花费。发现通过同生物信息技术相结合,公共卫生数据的获取、管理、分析、安全和应用方面都会有很大的发展空间。认为计算机技术的进一步应用,针对性的大数据挖掘方法开发,以及新型公共卫生人才培养,是发展这一领域的关键因素。     

Aquatic hyphomycetes in a changing environment

In 1942, Ingold documented an ecologically defined group of fungi, aquatic hyphomycetes, on autumn-shed leaves decaying in streams. They were shown to be vital intermediaries between the nutritionally poor leaf substratum and leaf-eating invertebrates. Research has subsequently emphasized functional aspects such as leaf decomposition and nutritional conditioning by fungi. Structural aspects (community composition) have attracted less attention, partly because of the difficulties of identifying fungal mycelia in situ. Extraction, amplification (PCR, qPCR) and characterization of DNA and RNA, and, more recently, of proteins, allow much greater insights into the presence of fungal taxa, their metabolic status (dead, dormant or active), and their potential and actual participation in decomposition processes. This approach can yield huge amounts of data, and major challenges today are the development and application of suitable bioinformatics techniques. The complexity of data collection and evaluation favour interdisciplinary teams of researchers. Fungi are major players in most ecosystems and are increasingly affected by human impacts. Changing land use, eutrophication/pollution and climate change are among the major factors that affect diversity and ecological functions of aquatic hyphomycetes.     

Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae––Decapoda) in freshwater

The freshwater crayfishes are distributed across all but the Indian and Antarctic continents with centers of diversity in the southeastern Appalachian Mountains in the Northern Hemisphere and in south–east Australia in the Southern Hemisphere. There are currently over 640 described species of freshwater crayfishes with an average of 5–10 species still being described each year. Freshwater crayfishes can serve as keystone species in aquatic habitats, but a few species are also significantly invasive and can cause impressive damage to the fragile freshwater habitat. Crayfishes inhabit caves, burrows, streams, lakes and strong burrowers can even be found in terrestrial habitats where they have burrowed to the water table or where rainfall is sufficiently abundant to provide the needed moisture. The freshwater crayfishes, like the habitats in which they are encountered, are generally endangered to some degree and conservation efforts would do well to focus on them as key elements of the freshwater ecosystem. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

The paradox of the clumps mathematically explained

The lumpy distribution of species along a continuous one-dimensional niche axis recently found by Scheffer and van Nes (Scheffer and van Ness 2006) is explained mathematically. We show that it emerges simply from the eigenvalue and eigenvectors of the community matrix. Both the transient patterns—lumps and gaps between them—as well as the asymptotic equilibrium are explained. If the species are evenly distributed along the niche axis, the emergence of these patterns can be demonstrated analytically. The more general case, of randomly distributed species, shows only slight deviations and is illustrated by numerical simulation. This is a robust result whenever the finiteness of the niche is taken into account: it can be extended to different analytic dependence of the interaction coefficients with the distance on the niche axis (i.e., different kernel interactions), different boundary conditions, etc. We also found that there is a critical value both for the width of the species distribution σ and the number of species n below which the clusterization disappears.

Phylogenetic Analysis: How Old are the Parts of Your Body?

According to the National Academy of Sciences, biology students in the USA are not being adequately prepared for successful futures. Of paramount concern is a lack of sufficient training in quantitative and computational skills, which are needed to compete effectively for an array of educational and occupational opportunities. In this paper, we introduce a classroom exercise that invites students to solve a simple biological problem and illustrates the need for a computer-assisted strategy to arrive at a solution. The exercise invites students to consider the question “How old are the parts of your body?” Some features of the human body are more ancient than others. For example, our bodies have both hair and backbones, but backbones arose much earlier in evolutionary history. Our exercise relies upon MEGA 4.0, a free, visually appealing, and intuitive computer program that allows students to gather DNA or protein sequences from electronic databases, then use them to infer phylogenetic trees. Student-inferred phylogenies are used to explore the relative order in which diverse aspects of the human form evolved. In the process, students are trained to use powerful features of MEGA and encouraged through group discussion to consider additional applications of the technology they have learned. Our lesson plan includes a brief video, a web site with essential terminology and links for further exploration, a hands-on experience using MEGA, and a follow-up discussion.     

BitTorious: global controlled genomics data publication,research and archiving via BitTorrent extensions

Background

Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the interoperability of those deployments in a manner embracing the heterogeneous needs, terms and infrastructure of collaborating parties. This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent.

Results

The BitTorious portal was sucessfully used to manage many concurrent domestic Bittorrent clients across the United States: exchanging genomics data payloads in excess of 500GiB using the uTorrent client software on Linux, OSX and Windows platforms. Individual nodes were sporadically interrupted to verify the resilience of the system to outages of a single client node as well as recovery of nodes resuming operation on intermittent Internet connections.

Conclusions

The authorization-based extension of Bittorrent and accompanying BitTorious reference tracker and user management web portal provide a free, standards-based, general purpose and extensible data distribution system for large ‘omics collaborations.     

文本分析技术在蛋白质生物信息学中应用的案例综述

海量数据时代考察文本分析技术在生物信息学领域的应用具有重要的理论和现实价值。本文讨论了文本分析在蛋白质计算分析中的几个应用实例以及核心技术内容。文本分析技术应用于生物信息学领域可发挥引领和导向作用,在生物信息学中的应用又进一步促进了文本分析技术的发展。文本分析技术虽然广泛在生物信息学中应用,但是其发展仍然有需要尚待解决的几个问题,本文对此也进行了讨论。     

Morphological and physiological variation among seagrass (Zostera marina) genotypes

Intraspecific variation in habitat-forming species can have important ecological consequences at the population, community, and ecosystem level. However, the contribution of genetic variation among individuals to these effects is seldom documented. We quantified morphological and physiological variation among genotypes of a marine foundation species, the seagrass Zostera marina. We grew replicate shoots of eight genetically distinct Zostera individuals collected from Bodega Bay, California, in a common garden environment and then quantified shoot production and morphology, nutrient uptake, and key photosynthetic parameters. We found that genotypes differed in shoot production, biomass, and both root and shoot nutrient uptake rates, even when corrected for genotype-specific biomass differences. In addition, the rank order of uptake ability differed for ammonium and nitrate, indicating that genotypes may exhibit resource partitioning of different forms of nutrients. Our results suggest that both niche complementarity among genotypes and the sampling/selection effect could contribute to previously observed positive effects of seagrass clonal diversity on resource utilization and biomass production. Further, they highlight that genotypic variation in key traits of habitat-forming species could have measurable effects on community structure and function.     

核糖体rDNA序列分析在丛枝菌根真菌研究中的应用

丛枝菌根真菌(AMF)是一类古老、专性活体营养的共生菌物, 尚未获得纯培养, 在一定程度上限制了人们对AMF的深入研究。以DNA分析技术为基础的分子生物学技术增加了AMF检测的敏感性与特异性, rDNA序列的同源性和变化性可更真实地反映物种之间的亲缘关系及进化地位, 因而被广泛应用于AMF分类、鉴定、遗传、生态及物种多样性等研究中。本文简要综述了rDNA序列分析技术在AMF系统发育、分子检测及群落结构特征研究中的应用现状。     

ortholog ——— 概念、生物信息预测方法和数据库

orthologs指起源于不同物种的最近的共同祖先的一些基因。orthologous的基因,具有相近甚至相同的功能,由相似的途径调控,在不同的物种中扮演相似甚至相同的角色,因此在基因组序列的注释中,是最可靠的选择。orthologs的生物信息预测方法主要有两类：系统发生方法和序列比对方法。这两类方法都是基于序列的相似性,但又各有特点。系统发生方法通过重建系统发生树来预测orthologs,因此在概念上比较精确,但难于自动化,运算量也很大。序列比对方法在概念上比较粗糙,但简单实用,运算量相对较小,因此得到了较广泛的应用。     

Does plant phylogenetic diversity increase invertebrate herbivory in managed grasslands?

Plant diversity and land-use intensity have been shown to affect invertebrate herbivory. Several hypotheses predict positive (e.g. associational susceptibility) or negative (e.g. associational resistance) relationships of herbivory with plant species richness. Also, the strength and direction of reported relationships vary greatly between studies leading to the conclusion that relationships either depend on the specific system studied or that other unconsidered factors are more important. Here, we hypothesized that plant phylogenetic diversity is a stronger predictor of invertebrate herbivory than plant species richness because it integrates additional information about the phenotypical and functional composition of communities. We assessed the community-wide invertebrate herbivory, plant species richness and phylogenetic diversity across a range of land-use intensities including a total of 145 managed grasslands in three regions in Germany. Increasing land-use intensity decreased plant species richness and phylogenetic diversity. Plant species richness did not predict invertebrate herbivory. By contrast herbivory moderately increased with increasing plant phylogenetic diversity even after accounting for the effects of region and land use. The strength of direct effects of land-use intensity and indirect effects via altered phylogenetic diversity on herbivory, however, varied among regions. Our results suggest that increasing phylogenetic diversity of plant communities increases invertebrate herbivory probably by providing higher resource diversity. Differences between regions underline the need to account for regional peculiarities when attempting to generalize land-use effects on invertebrate herbivory.     

How well does online information-seeking behavior indicate public conservation orientation? Taxonomy and personal characteristics matter

Public conservation support for a species can powerfully influence the success of conservation policies and actions. To maximize the effectiveness of the limited resources available for conservation, it would be beneficial to develop a way to predict the degree of public conservation orientation. Here, we explore the utility of the frequency of accessing web content featuring particular species, a direct measure of information-seeking behavior, to predict public conservation orientation. Specifically, we tested whether pageviews of Wikipedia content featuring 100 threatened species in five taxonomic groups (mammals, birds, reptiles and amphibians, insects, and plants) is associated with public conservation orientation toward these species in Japan. Wikipedia pageviews predicted public conservation orientation for species conservation for the two most salient taxonomic groups (mammals and birds). This relationship, however, was not evident for the other three taxa. The relationship between Wikipedia pageviews and conservation orientation was influenced by respondent age and gender. We employed the national red list category of the species as a covariate, but it was not associated with public orientation for species conservation in any of the five taxonomic groups. Overall, information-seeking behavior could be used as a proxy for public conservation orientation for mammals and birds, but should be interpreted with caution.     

Reconciling niche and neutrality through the Emergent Group approach

Both niche and neutral theories have been suggested as potential frameworks for modelling biodiversity. Niche models assume that biological traits represent evolutionary adaptations and define individuals in terms of functional trade-offs. Neutral models assume that all individuals at a single trophic level are functionally equivalent on a per capita basis with respect to their birth, death, dispersal and speciation. The opinion of many researchers is that neutral and niche processes operate simultaneously to generate diversity without knowing how the unification of both models can be achieved. Recently, several theoretical papers have reported evidence on the evolutionary emergence of niche structures shaping the emergence of groups of similar species. In this way, an Emergent Group is defined as a set of species that have a similar functional niche owing to a convergent ecological strategy. Central to the Emergent Group concept are the assumptions of functional equivalence within and of functional divergence between Emergent Groups. Within an Emergent Group, species richness is subject to a zero-sum rule set by the balance between the rate of individual loss and of immigration. Between Emergent Groups, tradeoffs such as seed size/seedling competitivity, investment in reproductive system/investment in vegetative systems or competitive ability/predator invulnerability are cornerstones of the evolutionary divergence. Delineating Emergent Groups amounts to reaching a compromise between maximizing niche differentiation (i.e. maximizing differences in functional tradeoffs) between Emergent Groups and maximizing neutrality within Emergent Groups. Up to now, the Emergent Group concept has been mostly proposed by theoretical scientists but it should be tested by empirical ecologists. The way in which niche and neutral models could be combined provides a profitable opportunity for theoretical and empirical scientists to collaborate fruitfully.