微生物系统发育多样性及其保护生物学意义

近年来,分子系统发育分析方法,特别是rBNA基因同源性分析方法,在微生物多样性的研究中发挥着越来越重要的作用．它克服了传统的微生物分离培养方法的限制,极大地促进了人们对微生物多样性的理解．在遗传信息同源性分析基础上得出的微生物系统发育多样性为多样性的保护提供了新的视点．它不但可以作为微生物多样性评价的手段,而且为多样性保护中优先秩序的确定提供了依据．同时也为生物多样性保护确定了目标,即最大程度地保护系统发育关系中所包含的信息．本文对微生物系统发育多样性的特点及其保护生物学意义进行了简要评述．     

Resemblance in phylogenetic diversity among ecological assemblages

Questions: How can a resemblance (similarity or dissimilarity) measure be formulated to include information on both the evolutionary relationships and abundances of organisms, and how does it compare to measures lacking such information? Methods: We extend the family of Phylogenetic Diversity (PD) measures to include a generalized method for calculating pair‐wise resemblance of ecological assemblages. Building on previous work, we calculate the matching/mismatching components of the 2 × 2 contingency table so as to incorporate information on both phylogeny and abundance. We refer to the class of measures so defined as “PD resemblance” and use the term “SD resemblance” for the traditional class of measures based on species diversity alone. As an illustration, we employ data on the diversity and stem density of shrubs of Toohey Forest, Australia, to compare PD resemblance to its SD resemblance equivalent for both incidence and abundance data. Results: While highly correlated, PD resemblance consistently measures assemblages as more similar than does SD resemblance, and tends to “smooth out” the otherwise skewed and truncated distribution of pair‐wise resemblance indices of our high‐turnover data set, resulting in nMDS ordinations with lower stress. Randomization of species distributions across assemblages indicates that phylogeny has made a significant contribution to the ordination pattern. Conclusions: PD resemblance measures, in addition to providing an evolutionary perspective, have great potential to improve distance‐based analyses of community patterns, particularly if species responses to ecological gradients are unimodal and phylogenetically conserved.     

Invasive alien plants in China: diversity and ecological insights

China’s current invasive alien plant species were analyzed with regard to their floristic status, biological attributes and invasion status elsewhere. Most of the 270 species identified were annuals, followed by perennial herbs. Woody perennials made only about 10% of the species. The invasives were comprised of 59 families, the largest being Asteraceae, Poaceae, and Brassicaceae. The genera with most invasive species were Amaranthus, Ipomoea, and Solanum. Most of the species originated from the New World, notably from South America. About one-third of the species were serious invaders of natural habitats in countries other than China. The proportion of invasive alien plants in province floras ranged from 0.5 to 3.8%, absolute numbers from nine to 117 species per province. Density of invasive species was correlated positively with native species density at provincial scale. The results demonstrate that in China invasive plants are present throughout the country, with a particularly high species richness in the Southeast. The ecological diversity of invasive plants suggests wide ranging impacts which need to be assessed.     

云南被子植物菊类分支的系统发育多样性及其分布格局

全球气候变化与人为活动等因素导致的生物多样性丧失,引起了全球各界对生物多样性保护的高度关注。传统生物多样性保护主要对物种、特有种、受威胁物种的种类组成及其分布模式开展研究,忽视了进化历史在生物多样性保护中的作用。云南是全球生物多样性热点地区的交汇区,生物多样性的保护历来受到广泛关注,为了更好地探讨云南生物多样性的保护措施,该研究以云南被子植物菊类分支物种为研究对象,基于物种间的演化关系,结合其地理分布,从进化历史的角度探讨物种、特有种、受威胁物种的种类组成及系统发育组成的分布格局,并整合自然保护地的空间分布,识别生物多样性的重点保护区域。结果表明：云南被子植物菊类分支的物种、特有种及受威胁物种的物种密度与系统发育多样性均显著正相关;通过零模型分析发现,由南向北标准化系统发育多样性逐渐降低;云南南部、东南部、西北部是云南被子植物菊类分支的重点保护区域,加强这些区域的保护,将最大化地保护生物多样性的进化历史和进化潜能。由此可见,融合进化历史信息的植物多样性格局分析不仅有助于更加深入地理解植物多样性的形成与演变,也为生物多样性保护策略的制定提供更多的思路。     

Phylogenetic and functional diversity of bacterioplankton during Alexandrium spp. blooms

The phylogenetic and functional diversity of the bacterioplankton assemblage associated with blooms of toxic Alexandrium spp. was studied in three harbours of the NW Mediterranean. Denaturing gradient gel electrophoresis and DNA sequence analysis revealed the presence of a bacterium within the Roseobacter clade related to the presence of Alexandrium cells. Phylogenetic diversity was affected by the presence of Alexandrium spp., geographic situation and seasonality. In contrast, functional diversity, assessed with Biolog plates, was clearly affected by seasonality, but not by the presence of Alexandrium, indicating that the presence of the bacterium associated with the blooms was not enough to modify the metabolic pattern of the bacterioplankton assemblage.     

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.     

Phylogenetic skew: an index of community diversity

The distribution of divergence times between member species of a community reflects the pattern of species composition. In this study, we contrast the species composition of a community against the meta‐community, which we define as the species composition of a set of target communities. We regard the collection of species that comprise a community as a sample from the set of member species of the meta‐community, and interpret the pattern of the community species composition in terms of the type of species sampled from the meta‐community. A newly defined effective species sampling proportion explains the amount of the difference between the divergence time distributions of the community and that of the meta‐community, assuming random sampling. We propose a new index of phylogenetic skew (PS), as the ratio of the maximum‐likelihood estimate of the effective species sampling proportion to the observed sampling proportion. A PS value of 1 is interpreted as random sampling. If the value is >1, the sampling is suspected to be phylogenetically skewed. If it is <1, systematic thinning of species is likely. Unlike other indices, the PS does not depend on species richness as long as the community has more than a few members of a species. Because it is possible to compare partially observed communities, the index may be effectively used in exploratory analysis to detect candidate communities with unique species compositions from a large number of communities.     

Genetic diversity and geographic distribution of Bemisia tabaci species complex in Nepal

Bemisia tabaci species complex comprises at least 44 cryptic species worldwide. Here, we analyze the nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) gene obtained from 76 samples of B. tabaci collected from 23 districts in Nepal. This is the first genetic and geographic study of B. tabaci species complex in Nepal. Our phylogenetic study identified the presence of three cryptic species—Asia I, Asia II 1, and Asia II 5—with high interspecific but low intraspecific variations. Among the three cryptic species, Asia II 5 was the most prevalent in Nepal, constituting 64.47% of all the sequenced samples. Based on haplotype network analysis of COI sequences, Asia II 1 was more genetically diversified than the other two cryptic species. Our results provided useful information on the genetic diversity and geographic distribution of B. tabaci in Nepal, which help monitor population changes of B. tabaci at cryptic species level and develop sustainable management strategies for its control.     

Tropical rain forest fragmentation and its ecological and species diversity changes in southern Yunnan

Three fragmented rain forests and one primary forest in southern Yunnan were plotted. The microclimate and soil conditions of these forests were also studied. The following conclusions were drawn: (1) The microclimatic differences between inside and outside forest are less in the fragmented forests than in the primary forest, which indicates that the buffer effects to climatic change have been reduced in the fragmented forests. The soil has deteriorated to some extent due to forest fragmentation. (2) In species composition, especially the abundance of some species and the dominant ranks of some families have changed with fragmentation. Barringtonia macrostachya, the most dominant species in the control primary forest, disappeared from the fragmented forests, while Antiaris toxicaria, which is a characteristic but not dominant species in the primary forest, is dominant in fragmented forests. (3) The total number of species per plot was reduced in the fragmented forests and the more seriously disturbed the fragment was, the more the species richness diminished. (4) In life form spectra, the liana and microphanerophyte species increased, but epiphyte, megaphanerophyte, mesophanerophyte and chamaephyte species decreased in the fragmented forests. (5) The plant species diversity is generally lower in the fragmented forests than in the primary forest, although for some life forms it could be higher. (6) The tree species with small populations could be lost first in the process of rain forest fragmentation. (7) The heliophilous or pioneer tree species increased and the shade-tolerant species were reduced in the fragmented forests.     

Cryptic diversity within the harmful dinoflagellate Akashiwo sanguinea in coastal Chinese waters is related to differentiated ecological niches

Blooms of the harmful dinoflagellate Akashiwo sanguinea are responsible for the mass mortality of fish and invertebrates in coastal waters. This cosmopolitan species includes several genetically differentiated clades. Four clonal cultures were established by isolating single cells from Xiamen Harbour (the East China Sea) for morphological and genetic analyses. The cultures displayed identical morphology but were genetically different, thus revealing presence of cryptic diversity in the study area. New details of the apical structure complex of Akashiwo sanguinea were also found. To investigate whether the observed cryptic diversity was related to environmental differentiation, 634 cells were obtained from seasonal water samples collected from 2008 to 2012. These cells were sequenced by single-cell PCR. For comparison with Chinese material, additional large subunit ribosomal DNA sequences were obtained for three established strains from Malaysian and French waters. To examine potential ecological differentiation of the distinct genotypes, growth responses of the studied strains were tested under laboratory conditions at temperatures of 12 °C to 33 °C. These experiments showed four distinct ribotypes of A. sanguinea globally, with the ribotypes A and B co-occuring in Xiamen Harbour. Ribotype A of A. sanguinea was present year-round in Xiamen Harbour, but it only bloomed in the winter and spring, thus corresponding to the winter type. In contrast, A. sanguinea ribotype B bloomed only in the summer, corresponding to the summer type. This differentiation supports the temperature optimum conditions that were established for these two ribotypes in the laboratory. Ribotype A grew better at lower temperatures compared to ribotype B which preferred higher temperatures. These findings support the idea that various ribotypes of A. sanguinea correspond to distinct ecotypes and allopatric speciation occurred in different climatic regions followed by dispersal.     

Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea

To examine the diversity and structure of archaeal communities in the Yangtze River estuarine region of East China Sea (ECS), the 16S rRNA gene clone libraries of two typical sites were constructed with the archaea-specific primers. In total, 71 clones randomly selected were screened by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and 21 clones with unique RFLP pattern were sequenced. All the sequences are clustered into the two groups of Marine Group I (MGI) and Marine Group II (MGII) which are affiliated with the phyla Crenarchaeota and Euryarchaeota, respectively. MGI clones dominate both libraries with 20 MGI sequences obtained. The majority of sequences are closely related to uncultured marine archaea except for two sequences of which the nearest neighbor is a newly identified isolate of nitrifying marine archaeon Nitrosopumilus maritimus (98% identity). The results indicate that ECS coastal waters are inhabited by archaeal community with low dominance and high diversity corresponding to the complex estuarine environments, suggesting that archaea may perform an important role in the estuarine ecosystem.     

应用糖皮质激素进行鼻腔冲洗对慢性鼻窦炎患者鼻腔菌群多样性和生物膜的影响

目的 分析应用糖皮质激素进行鼻腔冲洗对慢性鼻窦炎(CRS)患者鼻腔菌群多样性及生物膜的影响。 方法 将2018年1月至2018年6月于我院治疗的40例慢性鼻窦炎患者随机分成两组,每组各20例,一组给予0.9%氯化钠注射液进行鼻腔冲洗(NS组),另一组给予0.9%氯化钠注射液及布地奈德进行鼻腔冲洗(NS+BUD组),对两组患者治疗前后的菌群结构差异、多样性及细菌生物膜生成情况进行比较。 结果 治疗前两组患者菌群多样性指标(Chao1指数、Ace指数、Simpson指数及Shannon指数)比较,差异均无统计学意义(均P>0.05),治疗后两组患者的Chao1指数、Ace指数及Shannon指数均明显下降(均P结论 应用糖皮质激素对慢性鼻窦炎患者进行鼻腔冲洗可降低患者鼻腔微生物多样性,减少菌群的异常增殖,降低主要致病菌的生物膜表达,提高临床疗效。     

不同生态环境中中国猪种的遗传多样性研究

采用最小二乘法研究了中国部分地方猪种血液蛋白质Tf、Am、Pa和Cp位点基因频率与生态环境之间的关系及其变化规律。结果表明,Tf、Am和Cp位点分别被检测出存在3个等位基因,而Pa位点存在2个等位基因。4个位点的各种基因频率在不同猪种类型和生态区域之间均表现出显着差异(P<0.05),显示出地理区域和生态类型对4个位点的基因频率和杂合度有明显的影响。洞庭-洪湖区-新安江-鄱阳湖区-太湖流域是各位点基因频率高低变化的起点.     

极小种群植物水松群落系统发育多样性分析

极小种群植物水松（Glyptostrobus pensilis（Staunton ex D.Don）K.Koch）是著名的孑遗植物,被列为我国Ⅰ级重点保护和极小种群野生植物,在IUCN红色名录中被评估为"极危"等级,且种群数量仍在继续减少。水松主要分布于我国华南和东南地区以及越南和老挝。本研究对我国42个水松种群周边植被、种群健康状况、群落干扰类型、外来植物入侵状况等进行了调查,采用系统发育多样性相关指数对该物种所在群落进行了研究。结果显示,系统发育多样性指数对水松种群状况具有一定的指示性,人为干扰对所在群落的影响越严重,种群的健康状况愈差;具有较高系统发育多样性水平（PD值）的群落内水松种群状况良好;入侵物种的存在会使群落系统发育结构聚集,系统发育多样性水平降低。因此,在对水松种群进行保护时,要尽量减少群落中人为恶性干扰因素和外来植物的入侵威胁,以增强水松种群和个体的健康水平,维持群落系统发育的多样性,从而提高水松种群抵抗力和恢复力的稳定性。     

土壤微生物生态过程与微生物功能基因多样性

土壤微生物在陆地生态系统中具有重要的生态功能,包括参与地球化学物质循环、污染物降解、环境剧烈变化的缓冲等.土壤微生物的生态功能与土壤功能联系密切,微生物群落结构与组成变化会直接影响土壤功能的发挥.土壤微生物通过具有生物活性的酶参与一系列的代谢活动,编码酶的功能基因成为微生物功能标记物.近10年中,以功能基因多样性为核心的分子生态学研究迅速发展,为从功能基因角度了解土壤微生物的生态功能提供了一个新的切入点.本文综述了与土壤微生物生态功能相关的功能基因多样性研究进展,并对该领域的发展前景提出展望.     

中国外来陆生草本植物: 多样性和生态学特性

构建包含基本生物学和生态学信息的外来物种数据库不仅对理解生物入侵分布格局至关重要, 同时也是制定外来种管理策略和解释生物入侵过程的重要一步。作者在前人研究的基础上构建了中国外来陆生草本植物数据库, 共收集到中国外来陆生草本植物800种, 分属37目72科; 其中约有60%集中在菊科、豆科、仙人掌科、禾本科、十字花科等10个优势科。中国外来陆生草本植物主要来源于美洲(407种, 占总数的47%), 主要分布在南亚热带—热带区(46%, 密度为4种/10⁴km²), 其次为温带湿润区(26%, 密度约2种/10⁴km²)和亚热带区(23%, 密度约2种/10⁴km²), 旱—寒区(5%, 密度小于1种/10⁴km²)分布较少。从生活型上看, 以多年生 (293种, 40%)和一年生 (272种, 37%)为主; 而从生境类型来看, 约有一半(46%)分布于“高养分高干扰”类型的生境。约有80%的物种属有意引入, 因此有意引入是陆生外来草本植物进入中国的主要途径。近2个世纪来, 外来陆生草本植物进入中国的速度快速增加, 约90%的物种在这个时期进入; 而近半个世纪以来, 外来陆生草本植物进入中国的速度快速增长, 约60%的物种在这个时期进入中国。本文所提供的中国外来陆生草本植物的生物学和生态学特征, 可以为管理层制定外来种相关管理和控制策略提供参考信息。     

Phylogenetic diversity of Bradyrhizobium strains isolated from root nodules of Lupinus angustifolius grown wild in the North East of Algeria

From a total of 80 bacterial strains isolated from root nodules of Lupinus angustifolius grown wild in the North-Eastern Algerian region of El Tarf, 64 plant host-nodulating strains clustered into 17 random amplified polymorphic DNA (RAPD) fingerprinting groups. The nearly complete 16S rRNA gene sequence from the representative strain of each group revealed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but their affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis, showed that 12 strains belong to B. lupini, other 2 strains affiliated with B. diazoefficiens and that 1 strain was closely related to B. japonicum. The remaining two strains showed similarity values ≤95% with B. cytisi and could represent new lineages within the genus Bradyrhizobium. Sequencing of the symbiotic nodC gene from 4 selected bradyrhizobial strains showed they were all similar to those of the species included in symbiovar genistearum.