Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.     

从旱生植物叶结构探讨其生态适应的多样性

以西北地区６２种旱生植物的叶器官为研究对象,通过切片显微观察、生物学统计及模糊数学分析,探讨旱生植物生态适应的多样性,获得如下结果：①旱生植物依叶肉组成和细胞排列可划分为正常型、双栅型、环栅型、全栅型、不规则型,折迭和和无叶肉型;②叶肉类型的演化是以正常型与不规则型两条路线呈树枝状发展。深化较原始的偏向于中生,演化层次较高的更具适应旱生环境的能力;③进生植物的叶肉类型与生活型具有相关性,与环境具有     

The genetics and ecology of sympatric speciation: A case study

Mating occurs on the larval host plant in allRhagoletis species (Diptera: Tephritidae). We show how this attribute, when coupled with certain differences in other biological traits, strongly influences the mode of speciation. In species of thesuavis species group, host shifts have never occurred during speciation, and larvae feed in the husks of any walnut species(Juglans spp.), which are highly toxic. Taxa are allopatric or parapatric and exhibit deep phylogenetic nodes suggesting relatively ancient speciation events. Traits responsible for species and mate recognition, particularly in parapatric species, are morphologically distinct and strongly sexually dimorphic. All aspects of their biology, genetics and distribution are consistent with a slow rate of allopatric speciation followed by morphological divergence in secondary contact. In contrast, speciation in thepomonella species group has always involved a shift to a new, usually unrelated, non-toxic host, and all taxa within these groups are sympatric, monophagous and morphologically indistinguishable from one another. Phylogenetic nodes are very shallow, indicating recent sympatric speciation. Sympatric divergence is promoted by genetic variation which allows a portion of the original species to shift to a new habitat or host. Evidence suggests that changes in a few key loci responsible for host selection and fitness on a new host may initiate host shifts. By exploiting different habitats, competition for resources between diverging populations is reduced or avoided. We provide evidence that in phytophagous and parasitic insects sufficient intrinsic barriers to gene flow can evolve between sister populations as they adapt to different habitats or hosts to allow each population to establish independent evolutionary lineages in sympatry.     

能值生态足迹模型的改进——以海南为例

通过对比总结现有能值生态足迹模型研究成果,从能值密度、能值生态承载力、能值生态指标分类和整合等方面分析了模型存在的问题,在此基础上,构建了消费端和供给端构建足迹账户体系,并提出能值生态足迹和能值生态承载力模型的改进和优化。利用改进模型,实证分析了2000—2016年海南生态经济系统的变化特征。结果表明:(1)能源账户和生物产品账户足迹大幅增加。污染账户和建设用地账户足迹状态稳定。(2)生产承载力随着技术进步不断提高,而环境承载力随着人类对环境资源的占用强度增加不断下降。(3)海南生态环境整体表现为生态盈余,但污染账户、能源账户盈余缩减,2011年能源账户开始出现生态赤字。通过足迹账户的构建,能够更清晰地追踪各账户和各类土地能值生态足迹、能值生态承载力以及能值生态盈余/赤字产生的变化,能值生态足迹模型改进之后能够更客观反映区域生态经济系统状况,为地区有针对性开展环境管理和保护提供依据。     

Uranium concentrates bioproduction in Spain: A case study

Abstract: ENUSA mines an ore-body in the 'Schisto-greywacke complex' near Ciudad Rodrigo, close to the Portuguesc border. The uranium ore (pitchblende) is associated with sulphide minerals (pyrite, chalcopyrite). The whole Spanish yellow cake production (250 t U∼Os/year) is obtained from this mine (MINA FE) by bioleaching, although at the beginning, in 1973. it was an acid heap-leaching operation.     

Global microbial ecology: biogeography and diversity of Vibrios as a model

An environmental source of cholera was hypothesized as early as the late nineteenth century by Robert Koch, but not proven because of the ability of Vibrio cholera, the causative agent of cholera, to enter a dormant phase between epidemics. Standard bacteriological procedures for isolation of the vibrios from the environmental samples, including water, between epidemics generally were unsuccessful. Vibrio cholera, a marine vibrio requiring salt for growth, enters into a dormant 'viable but non-culturable' stage when conditions are unfavourable for growth and reproduction. The association of V. cholera with plankton, notably copepods, provides evidence for the environmental origin of cholera, as well as an explanation for the sporadic and erratic nature of cholera epidemics. Thus, the association of V. cholera with plankton was established only recently, allowing analysis of epidemic patterns of cholera, especially in those countries where cholera is endemic. The sporadic and erratic nature of cholera epidemics can now be related to climate and climate events, such as El Ni?o. Since zooplankton have been shown to harbour the bacterium and zooplankton blooms follow phytoplankton blooms, remote sensing can be employed to determine the relationship of cases of cholera with chlorophyll, as well as sea surface temperature (SST), ocean height, and turbidity. Cholera occurs seasonally in Bangladesh with two annual peaks in the number of cases occurring each year. From the data obtained and analysed to date, when the height of the ocean is high and sea surface temperature is also elevated, cholera cases are numerous. When the height is low and sea surface temperature is also low, little or no cholera is recorded. From the examination of data for the 1992-1993 cholera epidemic in India, preliminary comparisons of cholera data for Calcutta show a similar relationship between cholera cases, ocean height and SST. In conclusion, from results of studies of SST, phytoplankton and zooplankton, and their relationships to incidence of cholera, correlation of selected climatological factors and incidence of V. cholera appears to be significant, bringing the potential of predicting conditions conducive to cholera outbreaks closer to reality.     

Mathematical conservation ecology: A one-predator-two-prey system as case study

A method is presented to analyse the long-term stochastic dynamics of a biological population that is at risk of extinction. From the full ecosystem the method extracts the minimal information to describe the long-term dynamics of that population by a stochastic logistic system. The method is applied to a one-predator-two-prey model. The choice of this example is motivated by a study on the near-extinction of a porcupine population by mountain lions whose presence is facilitated by mule deer taking advantage of a change in land use. The risk of extinction is quantified by the expected time of extinction of the population.     

Contribution to the aeromycological study in the atmosphere of the city of Granada (South of Spain): seasonal and daily variations.

The seasonal and daily variations in the concentrations of certain fungal spores in the atmosphere of the city of Granada (South of Spain) have been studied. Sampling was carried out in 1994 using a Hirst-type volumetric spore trap. The spores analysed correspond to the genera Alternaria, Cladosporium (Cladosporium cladosporioides and Cladosporium herbarum), Fusarium, Stemphylium and Ustilago. The seasonal-variation data obtained indicate that most of these spores are abundant throughout the year, with the exception of Fusarium, which was only present in trace amounts. The maximum concentrations of Alternaria, Cladosporium and Stemphylium are obtained during two sharp peaks in spring and autumn, with the minimum values being recorded during the summer and winter months; Fusarium and Ustilago spores are most abundant in autumn and winter. Although intradiurnal-variation models vary from one taxon to the next, the highest levels are generally recorded after 12:00 hours, with maximum levels being obtained in the afternoon.     

EDENetworks: A user‐friendly software to build and analyse networks in biogeography,ecology and population genetics

The recent application of graph‐based network theory analysis to biogeography, community ecology and population genetics has created a need for user‐friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy‐to‐use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray‐Curtis or Sorensen distance, or population genetic metrics such as F_ST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.     

Undaria pinnatifida: A case study to highlight challenges in marine invasion ecology and management

Marine invasion ecology and management have progressed significantly over the last 30 years although many knowledge gaps and challenges remain. The kelp Undaria pinnatifida, or “Wakame,” has a global non‐native range and is considered one of the world's “worst” invasive species. Since its first recorded introduction in 1971, numerous studies have been conducted on its ecology, invasive characteristics, and impacts, yet a general consensus on the best approach to its management has not yet been reached. Here, we synthesize current understanding of this highly invasive species and adopt Undaria as a case study to highlight challenges in wider marine invasion ecology and management. Invasive species such as Undaria are likely to continue to spread and become conspicuous, prominent components of coastal marine communities. While in many cases, marine invasive species have detectable deleterious impacts on recipient communities, in many others their influence is often limited and location specific. Although not yet conclusive, Undaria may cause some ecological impact, but it does not appear to drive ecosystem change in most invaded regions. Targeted management actions have also had minimal success. Further research is needed before well‐considered, evidence‐based management decisions can be made. However, if Undaria was to become officially unmanaged in parts of its non‐native range, the presence of a highly productive, habitat former with commercial value and a broad ecological niche, could have significant economic and even environmental benefit. How science and policy reacts to the continued invasion of Undaria may influence how similar marine invasive species are handled in the future.     

广西南丹县生物多样性和文化多样性与生态旅游的关系

南丹县地处广西西北边陲 ,与贵州接壤 ,为多民族聚居地 ,是大西南出海铁路和高速公路通道的咽喉要地。全县总面积 3916ｋｍ2 ,人口 2 7.6万 ,全国第二大水电站———龙滩水电站距县城 76ｋｍ ,是一个具有交通枢纽和商贸物资集散功能的地方。矿产资源丰富 ,目前已查明的有锡、锑、铅、铜、银和铟等 2 0多种有色金属 ,储量超过 10 0 0× 10 4 ｔ,是罕见的富矿区 ,有“有色金属之乡”之称。其中 ,锡的储量 144× 10 4 ｔ,随着云南固旧锡都的衰落 ,南丹县将成为中国新的锡都。该县农业资源也很丰富 ,有许多著名的土特产品 ,例如黄蜡李、瑶鸡、魔…     

Banana and plantain production systems in Benin: ethnobotanical investigation,varietal diversity,pests, and implications for better production

Background

The cultivated banana and plantain (Musa spp.) are valuable for nutritional and socio-economic security for millions of people worldwide. In Benin, banana and plantain are among the most produced, consumed, and traded commodities. Its production is mainly for local consumption and remains insufficient to the demand. However, the varietal diversity of banana and plantain cultivated in Benin is not documented. This study aims at characterizing the banana and plantain cropping systems, genetic diversity, and production constraints as a baseline to the full utilization of this resource in crop improvement and to identify the potential production and agronomic qualities.

Methods

A baseline investigation of ethnobotanical attributes of banana cultivars was done in 51 randomly chosen villages in southern Benin. Interviews with randomly selected representative farmers were carried out. Key informant interviews and focus group discussions were used for global confirmatory investigation of survey data. Socio-demographic data and indigenous knowledge on the farmer uses of banana and plantain diversity, such as cultural practices, origin, and availability of banana and plantain planting materials, and the constraints and criteria of varietal preference cited by farmers were ranked.

Results

Eighty-seven locally recognized cultivars were found: 73 of banana and 14 of plantain groups. The most popular cultivars were Sotoumon (banana) (52.94%), Aloga (plantain) (41.17%), Planta (banana) (33.33%), and Adjangan (plantain) (27.45%). Of the eleven production constraints identified, the main biotic challenges were banana weevil Cosmopolites sordidus Germar and banana bunchy top virus (BBTV), while abiotic problems were drought and the wind. Some local varieties like Amandan, Assonwonnou, Coleti, and Ninkouin are extremely rare owing to agronomic and economic preference perceptions.

Conclusion and implications

This study provides a baseline for banana diversity in Benin and the West African region and entry points for biological characterization and production improvement. This would enable the exploitation of this resource for plant breeding towards biotic and abiotic challenges facing banana production.

     

A mathematical model for animal ecology with special reference to the ecology of the Tribolium beetle

An axiomatic model, originally developed for evolutionary theory, is adapted to describe animal ecology. A matrix representation of the present simulation of Tribolium castaneum, genetic strain c-IVa, is incorporated in the general system. The “weal” of a population is introduced as part of the general system and specified in more detail for Tribolium. The application of the model to the principle of competitive displacement is discussed.     

Herbivorous insects: model systems for the comparative study of speciation ecology

Does ecological divergence drive species-level evolutionary diversification? How so and to what degree? These questions were central to the thinking of the evolutionary synthesis. Only recently, however, has the ecology of speciation become an important focus of empirical study. Here, we argue that ecologically specialized, phylogenetically diverse, and experimentally tractable herbivorous insect taxa offer great opportunities to study the myriad mechanisms by which ecology may cause reproductive isolation and promote speciation. We call for the development and integrated experimental study of a taxonomic diversity of herbivore model systems and discuss the availability and recent evaluation of suitable taxa. Most importantly, we describe a general comparative framework that can be used to rigorously test a variety of hypotheses about the relative contributions and the macroevolutionary generality of particular mechanisms. Finally, we illustrate important issues for the experimental analysis of speciation ecology by demonstrating the consequences of specialized host associations for ecological divergence and premating isolation in Neochlamisus bebbianae leaf beetles.     

A population study of the Rook Corvus frugilegus in Leon Province, northwest Spain

A resident population of Kooks Corvus frugilegus in Leon, Spain, decreased by 247; from 197679. Migrant Rooks appear not to enter the range of this population which is unique in the Iberian Peninsula. During the breeding seasons colonies are attacked by man: 17–19% of birds failed to breed and only 0.5-0.7 young per nest survived to fly. The trees chosen for nesting are in plantations subject to regular cropping, after which colonies are scattered. Adult mortality was 16–26% annually. Young formed 17.6–23% of the population in June; 11–15.6% of birds in March were in their first year and many of these bred successfully. Communal roosts were used only from mid-July to mid-October.