In silico Analysis of Sequential,Structural and Functional Diversity of Wheat Cystatins and Its Implication in Plant Defense

Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases.Cereal crops like wheat are continuously threatened by a multitude of pathogens,therefore cystatins offer to play a pivotal role in deciding the plant response.In order to study the need of having diverse specificities and activities of various cystatins,we conducted comparative analysis of six wheat cystatins(WCs) with twelve rice,seven barley,one sorghum and ten corn cystatin sequences employing different bioinformatics tools.The obtained results identified highly conserved signature sequences in all the cystatins considered.Several other motifs were also identified,based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering.Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins.Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs.Thus there is a significant conservation at the sequential and structural levels;however,concomitant variations maintain the functional diversity in this protein family,which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.     

利用PLFA、CLPPs和ARDRA标记分析甲胺磷对土壤微生物群落的影响

利用磷脂脂肪酸(PLFA)、群落水平生理活性(CLPPs)和扩增核糖体DNA限制性分析(ARDRA)标记,综合评估低浓度和高浓度甲胺磷连续施用2和4 yr后对土壤微生物群落结构、功能和遗传多样性的影响。结果表明,甲胺磷胁迫使土壤微生物生物量减少而细菌(革兰氏阴性菌)数量增加,同时使微生物群落功能多样性下降而遗传多样性提高;处理2 yr后高浓度甲胺磷胁迫对微生物群落的影响较低浓度胁迫更为明显,处理4 yr后两个浓度胁迫则具有相似的显著影响,表明不同浓度甲胺磷的长期胁迫均能对微生物群落造成严重破坏。     

多元排序法解析城市空气微生物时空分布

采用自然沉降法测定2012年3月—2013年2月天津滨海地区城市不同功能区的空气微生物浓度。结果显示,该地区空气微生物中细菌占76.5%,真菌占19.4%,放线菌占4.1%;对空气微生物浓度变化进行多元排序分析,结果表明,依据城市功能区的不同,空气微生物在空间上具有明显聚类(5类),46.0%的微生物变异可以被前2轴解释,其中建筑工业区微生物浓度最高,居住区微生物浓度最低;在时间上表现为季节性聚类(3类),78.7%的微生物变异可以被前2轴解释,夏天微生物浓度最高,而冬天最低,空气微生物与温度具有显著的正相关性(P0.01);空气微生物在时间尺度上的变化要高于空间尺度上的变化,季节气温的影响要大于采样区功能作用的影响;空气中PM10与SO2显著正相关(P=0.011),表明天津滨海地区的烟雾属于二氧化硫型。     

Severe limitations of the FEve metric of functional evenness and some alternative metrics

The metric of functional evenness FEve is an example of how approaches to conceptualizing and measuring functional variability may go astray. This index has several critical conceptual and practical drawbacks:

1. Different values of the FEve index for the same community can be obtained if the species have unequal species abundances; this result is highly likely if most of the traits are categorical.
2. Very minor differences in even one pairwise distance can result in very different values of FEve.
3. FEve uses only a fraction of the information contained in the matrix of species distances. Counterintuitively, this can cause very similar FEve scores for communities with substantially different patterns of species dispersal in trait space.
4. FEve is a valid metric only if all species have exactly the same abundances. However, the meaning of FEve in such an instance is unclear as the purpose of the metric is to measure the variability of abundances in trait space.

We recommend not using the FEve metric in studies of functional variability. Given the wide usage of FEve index over the last decade, the validity of the conclusions based on those estimates is in question. Instead, we suggest three alternative metrics that combine variability in species distances in trait space with abundance in various ways. More broadly, we recommend that researchers think about which community properties (e.g., trait distances of a focus species to the nearest neighbor or all other species, variability of pairwise interactions between species) they want to measure and pick from among the appropriate metrics.     

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.     

泛基因组研究在遗传多样性和功能基因组学中的应用

相对于单个参考基因组仅聚焦于个体遗传信息的挖掘,泛基因组研究则能够反映整个物种或类群全部的遗传信息。随着基因组测序和分析技术的不断发展,泛基因组学逐渐成为新的研究热点,并已在植物、动物和微生物多个物种中获得了广泛应用,为全面解析物种或类群水平的遗传变异和多样性、功能基因组和系统进化重建等研究提供了强有力的工具,取得了很多显著的研究成果。尽管如此,由于泛基因组学研究尚处于发展阶段,测序费用和分析成本仍然较高,难以广泛普及; 且存在分析标准不一、数据挖掘不够全面深入、理论难以应用于生产实际等尚待解决的问题,仍有较大的发展空间。该文系统总结了泛基因组在生物遗传多样性挖掘和功能基因组学中的研究进展,主要包括其在泛基因组图谱的构建、基因组变异和有利基因的发掘、功能基因的多态性、群体遗传多样性和系统进化等多个领域中的应用和研究,探讨了其在不同领域的应用潜力。同时,讨论了目前泛基因组研究中存在的局限性和可能的解决方法,并对其将来的发展前景进行了展望。     

城市建成区自生草本植物群落的物种多样性与功能多样性——以深圳市为例

城市自生草本植物的物种多样性和功能多样性直接影响城市生态系统的功能和稳定性,但目前相关研究依然很缺乏。以深圳市为例,基于建成区600个1hm²样地的现场调查数据,分析自生草本植物的群落结构、物种多样性、群落功能特征及功能多样性。结果显示:①调查共记录自生草本植物61科178属273种,其中多年生草本占54.6%,乡土植物占65.6%。②占明显优势的功能特征有中小型叶(91.85%)、草质叶(42.59%)、纸质叶(32.96%)、叶片无毛或近无毛(56.67%)、中等密度绒毛(40.37%)、叶面较粗糙(52.59%)、花期4-6个月(50.78%)、果期4-6个月(49.22%)、干果(86.03%)。③群落类型间功能丰富度FDp、功能离散度Rao二次熵差异极显著(P ＜ 0.01)、功能均匀度FEve差异显著(P ＜ 0.05)。④公园绿地的物种多样性指数明显高于其他三类绿地;不同绿地类型间的功能丰富度和功能离散度在滞尘、降噪、降温增湿及生物多样性保护方面都有极显著差异(P ＜ 0.01),功能均匀度只在滞尘及生物多样性保护方面差异极显著(P ＜ 0.01)。⑤各功能多样性指数均与Margalef指数、Simpson指数及Shannon-Wiener指数呈极显著正相关关系(P ＜ 0.01)。研究结论和方法为维护城市生态系统稳定性、建设生态宜居城市、促进城市可持续发展提供理论依据。     

湿地生物连通性影响因素及测度方法研究进展

湿地是地球上最多样化和最具生产力的生态系统之一,但近年来由于人类活动的频繁干扰,自然环境以前所未有的速度变化,两者的协同作用导致湿地呈现破碎化趋势。湿地的退化、转化使得湿地生物连通性减弱。良好的湿地生物连通性有利于湿地生态系统服务功能的维持、生物多样性的保护以及生物对气候变化适应水平的提高。因此理解、评估和保护生物连通性对于湿地生态系统而言至关重要。综述了湿地生物连通性的定义、总结了生物连通发生与变化的四个相互作用因子,从结构连通性、功能连通性两个测定角度,论述动物、植物和微生物三类研究对象生物连通性的测度方法,最后从湿地生物连通的时空尺度,连通与物质循环的耦合关系,湿地生物连通性评估分析模型改进角度提出了未来的研究方向,从而确保湿地生物连通网络的完整有效。可为湿地生物多样性、湿地保护和管理提供新的思路。     

环境因子对山西太岳山典型森林类型物种多样性及其功能多样性的影响

该研究采用典型样地法,调查群落内物种分布并测量植物功能性状(叶面积和植株高度),对山西太岳山不同坡位华北落叶松-白桦混交林以及辽东栎次生林物种多样性及其功能多样性进行比较分析,探究环境因子对不同群落层次(乔木、灌木、草本)物种多样性及其功能多样性的影响机制,以及环境因子与群落构建之间的联系,为森林生态系统多样性研究以及经营管理提供理论依据。结果显示:(1)华北落叶松-白桦混交林的物种分布更加均匀,物种多样性和功能多样性(乔木层)均显著高于辽东栎次生林。(2)华北落叶松-白桦混交林乔木层功能均匀度与功能分散指数显著高于辽东栎次生林,但灌木草本层低于辽东栎次生林。(3)不同群落层次的物种多样性与功能多样性均呈正相关关系,影响物种分布和性状分布的环境因子存在差异,物种多样性受多种环境因子的综合影响,而单个环境因子对功能多样性影响较大,环境解释力与林分类型和群落层次相关。(4)乔木层物种多样性主要受土壤pH、冠层结构(MLA、林分开度)以及光照影响,灌木层物种多样性与土壤pH和MLA密切相关,林下总辐射、土壤养分(SOC、STN)、土壤相对含水率是影响草本层物种分布的主要环境因子;冠层结构(MLA、林分开度)是影响乔木层功能多样性最主要的环境因子,土壤pH和坡位分别是华北落叶松-白桦混交林和辽东栎次生林灌木层功能多样性的主要影响因子,影响草本层功能多样性的主要环境因子是土壤相对含水率与LAI。研究表明,在垂直分层的森林生态系统中,不同群落层次竞争的主要环境资源存在差异,乔木层通过改变冠层结构和林内环境限制林下物种分布和性状分布。     

Structures of domains I and IV from YbbR are representative of a widely distributed protein family

YbbR domains are widespread throughout Eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. Although the precise role of these domains remains undefined, the location of the multiple YbbR domain‐encoding ybbR gene in the Bacillus subtilis glmM operon and its previous identification as a substrate for a surfactin‐type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. To further characterize the YbbR domains, structures of two of the four domains (I and IV) from the YbbR‐like protein of Desulfitobacterium hafniense Y51 were solved by solution nuclear magnetic resonance and X‐ray crystallography. The structures show the domains to have nearly identical topologies despite a low amino acid identity (23%). The topology is dominated by β‐strands, roughly following a “figure 8” pattern with some strands coiling around the domain perimeter and others crossing the center. A similar topology is found in the C‐terminal domain of two stress‐responsive bacterial ribosomal proteins, TL5 and L25. Based on these models, a structurally guided amino acid alignment identifies features of the YbbR domains that are not evident from naïve amino acid sequence alignments. A structurally conserved cis‐proline (cis‐Pro) residue was identified in both domains, though the local structure in the immediate vicinities surrounding this residue differed between the two models. The conservation and location of this cis‐Pro, plus anchoring Val residues, suggest this motif may be significant to protein function.     

Identifying the Relative Importance of Leaf versus Shredder Species Loss on Litter Decomposition in Streams

Understanding how species loss influences ecosystem function is a contemporary issue in ecology. However, most research has focused on species loss at one trophic‐level. We explored the relationship between functional diversity (FD) and species richness separately for trees and aquatic leaf‐shredding detritivores. For trees, we collected information on species‐specific leaf tissue chemistry and species co‐occurrences in the mid‐Atlantic region (USA). For shredders, we used a published trait database with information on communities from 38 streams in the same region. We used a clustering algorithm to estimate FD for each community and for randomly assembled communities. If FD was high, we concluded that species loss was important to change in function; if low, species were functionally redundant and insensitive to species loss. We found tree FD to be significantly different than expected, but shredders exhibited FD levels similar to patterns based on random assembly. Furthermore, there were more leaf species exclusively associated with very high or very low levels of functional diversity compared to shredders. This approach revealed greater implications for leaf than shredder species loss for litter breakdown. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Elevation,Topography, and Edge Effects Drive Functional Composition of Woody Plant Species in Tropical Montane Forests

Tropical montane forests comprise heterogeneous environments along natural gradients of topography and elevation. Human‐induced edge effects further increase the environmental heterogeneity in these forests. The simultaneous effects of natural and human‐induced gradients on the functional diversity of plant leaf traits are poorly understood. In a tropical montane forest in Bolivia, we studied environmental gradients associated with elevation (from 1900 m to 2500 m asl), topography (ridge and gorge), and edge effects (forest edge vs. forest interior), and their relationship with leaf traits and resource‐use strategies. First, we investigated associations of environmental conditions (soil properties and microclimate) with six leaf traits, measured on 119 woody plant species. Second, we evaluated changes in functional composition with community‐weighted means and functional structure with multidimensional functional diversity indices (FRic, FEve and FDiv). We found significant associations between leaf traits and soil properties in accordance with the trade‐off between acquisition and conservation of resources. Functional composition of leaf traits shifted from the dominance of acquisitive species in habitats at low altitudes, gorges, and forest interior to the dominance of conservative species in habitats at high altitudes, ridges, and forest edges. Functional structure was only weakly associated with the environmental gradients. Natural and human‐induced environmental gradients, especially soil properties, are important for driving leaf traits and resource‐use strategies of woody plants. Nevertheless, weak associations between functional structure and environmental gradients suggest a high redundancy of functional leaf traits in this tropical montane forest.     

Functional and phylogenetic diversity determine woody productivity in a temperate forest

Understanding the relationships between biodiversity and ecosystem productivity has become a central issue in ecology and conservation biology studies, particularly when these relationships are connected with global climate change and species extinction. However, which facets of biodiversity (i.e. taxonomic, functional, and phylogenetic diversity) account most for variations in productivity are still not understood very well. This is especially true with regard to temperate forest ecosystems. In this study, we used a dataset from a stem‐mapped permanent forest plot in northeastern China exploring the relationships between biodiversity and productivity at different spatial scales (20 × 20 m; 40 × 40 m; and 60 × 60 m). The influence of specific environmental conditions (topographic conditions) and stand maturity (expressed by initial stand volume and biomass) were taken into account using the multivariate approach known as structural equation models. The variable “Biodiversity” includes taxonomic (Shannon), functional (FDis), and phylogenetic diversity (PD). Biodiversity–productivity relationships varied with the spatial scales. At the scale of 20 × 20 m, PD and FDis significantly affected forest biomass productivity, while Shannon had only indirect effects. At the 40 × 40 m and 60 × 60 m scales, biodiversity and productivity were weakly correlated. The initial stand volume and biomass were the most important drivers of forest productivity. The local environmental conditions significantly influenced the stand volume, biomass, biodiversity, and productivity. The results highlight the scale dependency of the relationships between forest biodiversity and productivity. The positive role of biodiversity in facilitating forest productivity was confirmed at the smaller scales. Our findings emphasize the fundamental role of environmental conditions in determining forest ecosystem performances. The results of this study provide a better understanding of the underlying ecological processes that influence specific forest biodiversity and productivity relationships.     

Functional traits explain ecosystem function through opposing mechanisms

The ability to explain why multispecies assemblages produce greater biomass compared to monocultures, has been a central goal in the quest to understand biodiversity effects on ecosystem function. Species contributions to ecosystem function can be driven by two processes: niche complementarity and a selection effect that is influenced by fitness (competitive) differences, and both can be approximated with measures of species’ traits. It has been hypothesised that fitness differences are associated with few, singular traits while complementarity requires multidimensional trait measures. Here, using experimental data from plant assemblages, I show that the selection effect was strongest when trait dissimilarity was low, while complementarity was greatest with high trait dissimilarity. Selection effects were best explained by a single trait, plant height. Complementarity was correlated with dissimilarity across multiple traits, representing above and below ground processes. By identifying the relevant traits linked to ecosystem function, we obtain the ability to predict combinations of species that will maximise ecosystem function.