DNA条形码技术在林业科学研究中的应用

DNA条形码是利用生物体内普遍存在的一个或几个、较短的且标准化的基因片段作为通用片段,通过碱基序列差异来实现物种水平准确鉴定的工具。相对于传统的分类学,DNA条形码技术具有不依赖形态特征和发育阶段、鉴定数字化、快速准确、操作简单规范等优势。已成功应用在生物多样性监控、海关、中药材真伪鉴定、法医鉴定、动植物检疫、生物入侵、食品和药物市场监督等诸多领域。经过15年时间发展,DNA条形码研究已基本确定针对不同生物类群使用不同的通用片段,同时构建了标准的全球生命条形码数字化数据库。目前DNA条形码研究主要集中在如何提高近缘类群物种分辨率和构建区域条形码数据库两个方向。在林业科学研究中,DNA条形码在木材识别、森林群落生态和生物多样性监控与评估等领域发展迅猛,但同时也面临一些问题,如木材DNA降解、整条片段的扩增等,需要在条形码片段选择、数据库构建、数据库与高通量测序技术结合、分析方法改进等进一步深入研究。未来DNA条形码将在林业资源评价、保护和可持续利用等方向具有广阔的应用前景。     

中科院北京植物园壳斗科植物鉴定

利用DNA条形码技术对中科院北京植物园壳斗科专类园的23份植物材料进行鉴定,从Genebank中获得相关数据,选择matK、rbcL、trnH-psbA序列引物对样本材料进行PCR扩增和测序,通过比较各序列的扩增效率、有效片段获得率,用PAUP4.0 b10建物种关系树评价不同序列的鉴定能力。本研究认为,matK序列物种鉴别能力最高,种间变异差异最大的为trnH-psbA序列,rbcL相对保守。     

植物DNA条形码研究进展

DNA条形码技术是利用标准的、具有足够变异的、易扩增且相对较短的DNA片段在物种内的特异性和种间的多样性而创建的一种新的生物身份识别系统,从而实现对物种的快速自动鉴定。本文从植物DNA条形码的开发、应用、国内研究现状、植物DNA条形码面临的挑战以及发展前景等进行了综合分析,以期推动我国植物DNA条形码和分类学研究的发展。     

A synthesis on the impact of non-native conifer plantations on ant and beetle diversity in north-western Patagonia

Softwood forestry with non-native tree species is increasing worldwide and especially in many developing countries of the Southern Hemisphere. Tree plantations are beneficial in environmental and socioeconomic aspects, but at the same time there are recognised costs associated with afforestation. Our aim was to revise the existing information on the impact of exotic conifer plantations in north-western Patagonia on insect biodiversity. A total of five studies were selected and, in these, not every insect group responded in a similar manner to the habitat replacement. There was a tendency towards a reduction in abundance and species richness of several insects inside pine plantations. This change in abundance and richness was especially evident for ant assemblages and when pine plantations were dense. Beetle assemblages, in turn, showed diverse responses to the replacement of native vegetation with forests depending on the native habitat matrix. Our findings confirm that practices that reduce tree density (via thinning or during plantation) should be recommended to minimise their impact on insect biodiversity in north-western Patagonia. The consistent behaviour of ant assemblages, coupled with their abundance, ease to sample and unambiguous taxonomy make them reliable candidates for long-term monitoring of the impact conifer forestation in north-western Patagonia, as well as probably in other regions of the world in which non-native pines replace natural environments.     

融合遗传、形态和环境信息的植物智能识别

以植物DNA条形码为代表的新兴生物技术逐渐推广应用于林业科学研究领域。文中介绍了美国科研机构和高校联合开发的Leafsnap可视化植物识别软件的应用情况,根据当前已开展的植物DNA测序和数据库平台构建情况,初步提出一个综合植物DNA条形码、形态和环境信息的智能识别系统,以期为将来改进或开发出更准确、更快捷、更有趣且能进行公众参与的植物识别应用软件提供一些思路,为森林生物多样性研究和应用提供帮助。     

木材DNA条形码鉴定研究进展

木材种属鉴定具备显著的生物学与经济意义, 但传统的以显微特征观察为主的方法已不能适应高通量和精细化鉴别的需要。DNA条形码是根据特定基因片段的序列差异, 利用生物信息学技术对生物物种进行快速分类与鉴别的方法。近年来, DNA条形码技术已被陆续应用于木本植物及相应木材的种质鉴定, 在目标基因选择、木材DNA提取及生物信息学分析等方面均取得显著进展。在使用优化的微量DNA提取技术的前提下, 干燥木材中也可提取出满足扩增要求的DNA。经过生命条形码联盟等国际机构的长期努力, 确定了rbcL+ matK组合等通用植物条形码标记及ITS2等补充标记, 并建立了BOLD等数据库系统。传统的条形码序列分析主要通过BLAST比对、遗传距离分析及系统进化分析来实现, 近年来随着生物信息学的发展, DNA条码数据库不断完善, 新的数据分析方法和软件正不断涌现。文中在总结现有研究成果和实施规范的基础上, 综述国内外应用DNA条形码技术进行木材鉴别的新进展, 并着重阐述新型序列分析方法和相应的生物信息学工具。     

森林生物多样性保护原理概述

热点地区的分析,为我们确定生物多样性保护的策略和优先等级提供了依据;由于人类的剧烈干扰,现在地球上有许多物种和生态系统都处于濒危的境地,热带雨林的生物多样性丧失最为严重;热点地区虽然在地球上所占的面积很小,但却拥有大量的物种,这些地区的生物多样性丧失应特别引起我们注意;每个物种灭绝的难易程度不同,稀有种和长寿命种特别易于灭绝,而关键种一旦受到威胁,依赖于其生存的许多物种也会有灭绝的危险。遗传多样性的丧失也是生物多样性丧失的重要方面,种群内遗传多样性的丧失主要来源于奠基者效应、统计瓶颈效应、遗传漂变和近亲交配４种因素。物种的概念影响到对物种的保护,物种保护应包括物种内遗传多样性的保护;种群的动态调节机制和源—汇种群动态对于生物多样性保护具有重要的意义。种群生存力分析是了解物种濒危机制的崭新手段。群落中的种间关系和自然干扰体系是生物多样性保护中应考虑的重要方面。人为的生境破碎与自然景观的异质性不同,生境破碎会造成边缘效应和拥挤效应等一系列的生物学后果。     

Degradation of chloroplast DNA during natural senescence of maple leaves

The fate of chloroplast DNA (cpDNA) during plastid development and conversion between various plastid types is still not very well understood. This is especially true for the cpDNA found in plastids of naturally senescing leaves. Here, we describe changes in plastid nucleoid structure accompanied with cpDNA degradation occurring during natural senescence of the free-growing deciduous woody species Acer pseudoplatanus L. Natural senescence was investigated using three types of senescing leaves: green (G), yellow-green (YG) and yellow (Y). The extent of senescence was evaluated at the level of photosynthetic pigment degradation, accumulation of starch and plastid ultrastructure. Determination of cpDNA amount was carried out by in planta visualization with 4,6-diamidino-2-phenylindole, by Southern hybridization, and by dot-blot using an rbcL gene probe. During natural senescence, plastid nucleoids undergo structural rearrangements accompanied by an almost complete loss of cpDNA. Furthermore, senescence-associated protein components exhibiting strong binding to an ～10kbp rbcL-containg cpDNA fragment were identified. This interaction might be important for rbcL expression and Rubisco degradation during the course of natural senescence in trees.     

Variation in post-wildfire regeneration of boreal mixedwood forests: underlying factors and implications for natural disturbance-based management

To test the direct regeneration hypothesis and support natural disturbance-based forest management we characterized the structure and composition of boreal mixedwood forests regenerating after large wildfires and examined the influence of pre-fire stand composition and post-fire competing vegetation. In stands which had been deciduous (Populus sp.)-dominated, conifer (white spruce)-dominated, or mixed pre-fire we measured regeneration stocking (presence in 10 m² plots), density and height 10–20 years post-burn in five wildfires in Alberta, Canada. Most plots regenerated to the deciduous or mixed stocking types; plots in the older fire and in stands that were pure conifer pre-fire had higher amounts of conifer regeneration. Surprisingly, regeneration in pre-fire ‘pure’ white spruce stands was most often to pine, although these had not been recorded in the pre-fire inventory. Pre-fire deciduous stands were the most resilient in that poplar species dominated their post-fire regeneration in terms of stocking, density and height. These stands also had the highest diversity of regenerating tree species and the most unstocked plots. High grass cover negatively affected regeneration density of both deciduous and conifer trees. Our results demonstrate the natural occurrence of regeneration gaps, pre- to post-fire changes in forest composition, and high variation in post-fire regeneration composition. These should be taken into consideration when developing goals for post-harvest regeneration mimicking natural disturbance.     

Effects of thinning intensity on species diversity and timber production in a conifer (Cryptomeria japonica) plantation in Japan

In conifer plantations, enhancement of species diversity has become an important management goal. Although thinning is a useful method to enhance diversity, determining optimum thinning intensities may be rather complicated because of potential trade-offs among a broad array of management goals (e.g., recovery of biodiversity, increasing individual tree sizes, increasing net primary production, saving management costs). To evaluate the optimum thinning intensity by analyzing these relationships, we conducted a thinning experiment with three different thinning intensities—unthinned, 33% thinned, and 67% thinned—in a Cryptomeria japonica plantation in 2003, and investigated the number, diameter at breast height (DBH), and diversity of hardwoods (height?>?1.5?m) in 2008, and the growth of conifers over five?years. In hardwoods, the number of individuals, number of species, mean DBH, and total basal area were greatest in the 67% thinned treatment, irrespective of successional status. However, Shannon’s diversity index did not differ among the three treatments due to a disproportionate increase with thinning intensity in the abundance of a mid-successional species, Cornus controversa. Diameter growth of conifers was also highest in the 67% thinned and lowest in the unthinned treatment, whereas the reverse was true for stand volume increment. These results suggest that intensive thinning is a reliable method to convert conifer plantations into conifer–hardwood mixed forests at canopy level much more quickly and consistently than weak thinning, although primary production is to some extent reduced. If forest managers prefer sustainable timber production of conifers rather than full recovery of diversity, weak thinning may be suitable.     

Associations between Forest Type and Invertebrates: Ground Beetle Community Patterns in a Natural Oakwood and Juxtaposed Conifer Plantations

The character of carabid communities in juxtaposed conifer plantationand natural oak woodland was assessed and each found to be quitedistinctive. Distinctions arose from the differential abundanceof species and a lower species number in the natural oak woodland.Species at sample sites in the oak woodland, occurred with atleast equal frequency at sites in the conifer plantations. Therelatively species rich communities of ground beetles in areasafforested with conifers may have been derived partly from uplandblanket peat and heath, and partly from older woodland. At thetransition zone between the two main woodland types there wasan abrupt change in community character but none of the changesin species abundance could be interpreted as being detrimentalto the quality of carabid fauna in the oak woodland.     

Community structure and biodiversity in plantations and natural forests of seabuckthorn in southern Ningxia, China

Two types of sampling plots of seabuckthorn (Hippophae rhamnoides) communities were investigated in Pengyang County of Ningxia region by a typical sampling method to study the characteristics of community structure and biodiversity. Composition and dominant species of each community were analyzed by the importance value of species as an index. The number of individuals and the importance value, as well as Sorensen’s similarity coefficient, Shannon-Wiener diversity index, Pielou’s evenness index and Simpson’s dominance index, were used as indices to compare characteristics of community structure, similarity and biodiversity between plantations and natural forests of seabuckthorn. The results indicate that the importance values of species of natural seabuckthorn communities were dispersed and the difference between dominant species was not statistically significant. Diversity indices of natural seabuckthorn communities reflected by species richness and evenness were higher than that of plantations. Com-munity structure of natural seabuckthorn forests is more complex. We propose that natural forest can be used as sample to guide se-lection of plant species in silviculture in order to improve biodiversity of plantation.     

Nature vs. nurture: managing relationships between forests,agroforestry and wild biodiversity

Many agroforestry systems are found in places that otherwise would be appropriate for natural forests, and often have replaced them. Humans have had a profound influence on forests virtually everywhere they both are found. Thus ‘natural’ defined as ‘without human influence’ is a hypothetical construct, though one that has assumed mythological value among many conservationists. Biodiversity is a forest value that does not carry a market price. It is the foundation, however, upon which productive systems depend. The relationship between agroforestry and the wild biodiversity contained in more natural forests is a complicated one, depending on the composition of the agroforestry system itself and the way it is managed. Complex forest gardens are more supportive of biodiversity than monocrop systems, shade coffee more than sun coffee, and systems using native plants tend to be more biologically diverse. Nonnative plants, especially potentially invasive alien species, threaten biodiversity and need to be avoided. The relationship between forests, agroforestry and wild biodiversity can be made most productive through applying adaptive management approaches that incorporate ongoing research and monitoring in order to feed information back into the management system. Maintaining diversity in approaches to management of agroforestry systems will provide humanity with the widest range of options for adapting to changing conditions. Clear government policy frameworks are needed that support alliances among the many interest groups involved in forest biodiversity.

     

Tree regeneration in partially cut conifer–hardwood mixed forests in northern Japan: roles of establishment substrate and dwarf bamboo

We assessed the relationship of the regeneration (seedling and sapling) densities of seven representative tall-tree species to the past partial cutting and current stand structure. We also determined if differences in tree regeneration were associated to establishment substrates (coarse woody debris (CWD) and root throws) and understory inhibitor vegetation (the dwarf bamboo species: Sasa senanensis). The study was conducted in 17 conifer–hardwood mixed stands in a heavy snowfall region in Hokkaido, northern Japan. The results suggest that stand structure, rather than logging intensity, is the primary factor influencing regeneration densities. Total conifer basal area was positively correlated with the regeneration density of individual tree species, including two conifers and three hardwoods. These patterns differ from those observed in old-growth stands in the region. A negative correlation between total conifer basal area and dwarf bamboo coverage suggests that the presence of dense conifer canopies causes an increase in regeneration density of tall-tree species by preventing domination of dwarf bamboo. Picea glehnii, a species that depends for its establishment strongly on CWD, has lower seedling and sapling density in stands with higher logging intensity. This seems to be a result of the decrease in the volume of CWD with increasing logging intensity in these stands. We suggest that both reducing logging intensity and retaining overstory conifers should be considered to develop a sustainable silvicultural system in this region. Providing sufficient CWD and root throws may also be important to ensure natural regeneration of tree species that require these as an establishment substrate.     

Sustainability and Biodiversity

Abstract

The implementation of the Rio protocol and the preservation of biodiversity at the national and regional levels is an important step in achieving sustainable forestry. This is indeed a challenging task since our knowledge of the ecology and habitat demands for but a few species is severely restricted. Research in the last years shows that forest species have very different qualitative and spatial demands on their environment, which require complex and broad solutions. This poses a great problem for conservation and often forces societies/decision-makers to make decisions based on assumptions rather than on empirical data. With assumptions follow uncertainty, a factor that is necessary to control. We identify and discuss the uncertainties of steps that are considered to be important for preserving biodiversity on a regional level and exemplify this with cases from southern Sweden. We argue that there is no universal solution for the conservation of biodiversity. In strongly fragmented and transformed regions like southern Sweden, a mix of species approaches and ecosystem approaches is necessary for biodiversity conservation. Programs for preserving biodiversity should be flexible, not rigid, allowing for modifications due to a constantly increasing body of knowledge and environmental changes. Prominent gaps in our knowledge include species dispersal ability and propensity, extinction rates and the species dependence on fragmentation and landscape history. It is possible that the question of responsibility species (a species for which a region has an explicit conservational responsibility) may gain in importance, an issue with far-reaching implications for economy and inter-regional compensatory systems.     

人工林生物多样性研究的现状及展望

叙述了人工林生物多样性的研究现状,分析了影响人工林生物多样性的因素,并提出了人工林生物多样性的评价标准、提高途径及未来的研究方向.     

秃杉的物种确立、天然林种群特征、保护、引种和种源选择研究

根据秃杉有关的研究文献,对秃杉物种的确立,天然林的生物多样性、空间分布、动态和更新演替等种群特征,原生地保护与迁地保护,引种地气候和立地的适应性,速生性,抗寒、耐高温干旱、耐萌、抗风和抗病虫害能力等抗逆性,种源的遗传多样性,种源地理变异和生态适应性,种子、苗期及林木生长的变异,不同年龄林木生长性状的相关性,优良种源选择和种源区划等的研究进行了综合评述。     

Regional impact assessment on forest structure and functions under climate change—the Brandenburg case study

A forest simulation model has been applied in a regional impact assessment to investigate impacts of climate change on forest structure and function in the Federal state of Brandenburg, Germany. The forest model FORSKA-M was linked to a GIS that included soil, groundwater table and land-use maps. Two climate scenarios (current climate and a climate change of 1.5 K temperature increase which is combined with a precipitation decrease of 10–20% on average) for 40 meteorological stations in and around Brandenburg were used to assess the sensitivity of species composition to climate change. Furthermore, the implications of vegetation changes for other forest functions were analysed by means of several indicators. To evaluate the impacts of climate change on biodiversity, measures of species diversity (Shannon’s and Simpson’s index) and habitat and structural diversity (Seibert’s index) were applied. The evaluation of impacts on groundwater recharge of natural and managed forests was carried out using the soil water balance model of FORSKA-M.At first, model simulations of the potential natural vegetation (PNV) on the whole area of Brandenburg with different climate scenarios were analysed. The results indicated that climatic warming would lead to a shift in the natural species composition in Brandenburg towards more drought tolerant species. The simulated diversity of the forests would be reduced, and groundwater recharge would be decreased.The majority of forests in the state of Brandenburg have been managed intensively in the past. At present, large areas of Brandenburg’s forests are dominated by pure stands of Scots pine, but current forest management practice aims at increasing the share of deciduous and mixed forests. In order to analyse the possible consequences of climate change on forest management, forest inventory data were used to initialise FORSKA-M with representative forest stands. Simulation experiments with three different management scenarios showed that the short to mid-term effects of climatic change in terms of species composition were not as severe as expected. However, the comparison of different diversity measures indicates a decrease in the species diversity in contrast to an increase in habitat diversity under climate warming. Furthermore, a decrease in productivity and groundwater recharge was simulated under the climate change scenario.The regional impact assessment corroborated the high sensitivity of natural forests in the region to the projected climatic change and it underlined the importance of adaptive management strategies to help forestry to cope with climatic change.     

The Effect of the Surrounding Landscape and Socioeconomic characteristics on Woody Species Diversity in Homegardens of Shewarobit District,Northeast Ethiopia

Although homegardens are most often suggested as the refuges for biodiversity in human-dominated landscapes, how the surrounding landscape and socioeconomic characteristics affect this diversity in the tropics has received little research attention. Hence, this study has examined how these factors affect woody species diversity in homegardens of northeast Ethiopia. Three landscapes which are similar in agroecology were selected and in total 54 households were used for both a survey and a woody species inventory in respondents’ homegardens. The homegardens were stratified based on their locations in relation to crop fields and natural vegetation using satellite images from Google Earth. The variation in Shannon–Wiener diversity index among homegardens and the effect of the socioeconomic factors including household wealth status, homegarden area and the households’ types of uses of woody plants on species diversity were analyzed using one-way ANOVA. Altogether 53 woody plant species belonging to 35 botanical families were identified. Survey results indicated that the woody species diversity was higher in homegardens situated close to crop land as compared with the diversity in homegardens close to natural vegetation. Higher woody species diversity was recorded in homegardens which are larger in area and where the households’ types of uses of woody plants is higher. Moreover, the woody species diversity was found to be higher in homegardens of the high and medium income households when compared with that of poor households. Overall, results suggest that the concurrent ecological and socioeconomic studies are needed to design conservation strategy and policy for plant biodiversity in agricultural landscapes.     

Identification of two thaumatin-like proteins (TLPs) in the pollination drop of hybrid yew that may play a role in pathogen defence during pollen collection

We describe the proteomic identification of two pathogenesis-related group 5 (PR-5) proteins, an acidic thaumatin-like protein (TLP) and a basic TLP isolated from the pollination drop of hybrid yew (Taxus x media Rehder). The basic TLP (TxmTLPb) was the most abundant protein in the yew pollination drop based on protein spot size after two-dimensional electrophoresis. The acidic TLP (TxmTLPa) is also a major protein component of the yew ovular secretion and appears to be encoded by a number of mRNAs transcribed from a TLP gene family that has undergone limited sequence divergence. We have sequenced five acidic TLP-encoding cDNAs (TxmTLPa-1,2,3,4 and 5) isolated from the yew ovule that vary from each other by no more than five out of 233 amino acid residues in their predicted protein sequences. All of the cDNA variants encode TLPs possessing the 16 conserved cysteine residues and five charged amino acid side chains associated with antifungal activity. Amplification of genomic DNA with TxmTLPa primers indicated that at least 11 acidic TLPs with highly similar amino acid sequences may be expressed in yew tissues. Antibodies against TLPs confirmed the identity of TxmTLPa and TxmTLPb in the yew pollination drop and detected TLPs in the ovular secretions of four other species from three other conifer families. Our results suggest that TLPs are a conserved component of conifer ovular secretions and are involved in broad spectrum pathogen defence of ovules.