基于B-IBI指数的温榆河生态健康评价

基于温榆河底栖动物和水质采样数据,采用底栖动物完整性指数(B-IBI)方法,进行温榆河生态健康评价,并探求河流水质与B-IBI指数的相关性。通过分布范围、判别能力以及相关性分析等,确定研究区B-IBI指标体系,包括总分类单元数、总生物量、优势分类单元个体相对丰度、敏感类群分类单元数、生物指数和粘附者个体丰度6个指标。根据参照点25%分位数确定温榆河底栖动物完整性评价标准,即B-IBI>1.821为健康,1.366—1.821为亚健康,0.910—1.366为一般,0.455—0.910为较差,0—0.455为极差。结果表明,温榆河27.3%河段处于健康状态,9.1%河段处于亚健康状态,13.6%河段处于一般状态,50%河段处于较差和极差状态。河流水质与B-IBI指数的相关系数为-0.549,表明生物指标作为水体评价的补充指标十分必要。     

Human health risk assessment of toxic elements in fish species collected from the river Buriganga,Bangladesh

Abstract

Multielement (48) analysis was carried out of various fish species collected from river Buriganga, the most polluted river in Bangladesh to assess human health risk by toxic elements. Sixteen elements that is, Be, V, Cr, Mn, Ni, Cu, Zn, As, Se, Mo, Cd, Ba, Hg, Pb, Bi, and U, were taken into account due to their toxicities on human health. Results show that concentrations of elements in various fish species were higher in winter than those in monsoon. Among 16 elements, Mn, Cu, Zn, Cd, Ba, Pb were above Food Safety Guideline in some fishes in winter. THQ and TTHQ/HI values were less than 1 for all fishes in monsoon while THQ and TTHW/HI values were more than 1 for most of fishes in winter. These results suggesting non-carcinogenic health hazard through consumption of contaminated fishes. Only As showed low cancer risk while no cancer risk was observed for other toxic elements in monsoon. In winter, Pb showed only moderate cancer risk for Mystus vittatus (site-7) while for other fishes low cancer risk was found by Pb. It can therefore be concluded that there is human health risk in consuming of fishes collected from river Buriganga especially in winter.     

The importance of physical habitat assessment for evaluating river health

1. Physical habitat is the living space of instream biota; it is a spatially and temporally dynamic entity determined by the interaction of the structural features of the channel and the hydrological regime. 2. This paper reviews the need for physical habitat assessment and the range of physical habitat assessment methods that have been developed in recent years. These methods are needed for assessing improvements made by fishery enhancement and river restoration procedures, and as an intrinsic element of setting environmental flows using instream flow methods. Consequently, the assessment methods must be able to evaluate physical habitat over a range of scales varying from the broad river segment scale (up to hundreds of kilometres) down to the microhabitat level (a few centimetres). 3. Rapid assessment methods involve reconnaissance level surveys (such as the habitat mapping approach) identifying, mapping and measuring key habitat features over long stretches of river in a relatively short space of time. More complex appraisals, such as the Physical Habitat Simulation System (PHABSIM), require more detailed information on microhabitat variations with flow. 4. Key research issues relating to physical habitat evaluation lie in deciding which levels of detail are appropriate for worthwhile yet cost-effective assessment, and in determining those features that are biologically important and hence can be considered habitat features rather than simple geomorphic features. 5. The development of new technologies particularly relating to survey methods should help improve the speed and level of detail attainable by physical habitat assessments. These methods will provide the necessary information required for the development of the two-and three-dimensional physical and hydraulic habitat models. 6. A better understanding of the ways in which the spatial and temporal dynamics of physical habitat determine stream health, and how these elements can be incorporated into assessment methods, remains a key research goal.     

硅藻在河流健康评价中的应用研究进展

硅藻作为一种光合自养真核藻类,是水生态系统中重要的初级生产者,反映了水环境的平均状况.作为环境的指示生物,普通菱形藻、小舟形藻、极小异极藻均能指示水体富营养化状况,窄异极藻、结膜窗纹藻、念珠等片藻能反映出水体的贫营养状况;广缘小环藻、细纹长蓖藻、短缝藻能反映水体的酸度;肿节曲壳藻能指示水体中的Cu含量,肘状针杆藻能反映水体中的Zn浓度;其他硅藻种类亦能反映水体的受污染程度.本文综述了国内外对硅藻及硅藻指数的应用研究进展,指出了硅藻及硅藻指数在河流健康评价中所存在的问题,并提出了今后的研究方向:进一步完善硅藻的分类与鉴定;广泛开展不同地区及不同条件下硅藻水质监测与评价研究;注重筛选硅藻生物完整性指数并建立适宜的水质评价基准.     

Preliminary distributional analysis of US endangered bird species

A first exploration of applications of ecological niche modeling and geographic distributional prediction to endangered species protection is developed. Foci of richness of endangered bird species are identified in coastal California and along the southern fringe of the United States. Species included on the Endangered Species List on the basis of peripheral populations inflate these concentrations considerably. Species without protection in the US National Park System are focused particularly in peninsular Florida. Application of this methodology to additional taxa and regions holds promise for diverse conservation applications.     

Mapping critical areas for migratory songbirds using a fusion of remote sensing and distributional modeling techniques

Of the 338 species identified as Nearctic-Neotropical migrants occurring in North America, 98.5% have been recorded in Texas. The seasonal migration of these birds is a well-studied natural phenomenon – individuals weighing < 15 g will cross in the Gulf of Mexico approximately 965 km non-stop, completing a total distance of 1900–3200 km over the course of 26–80 h. The physiologically demanding nature of this feat makes the Texas coastline crucial to the success of these species. We used a fusion of multi-spectral remote sensing data and distributional modeling techniques to generate and evaluate predictive maps identifying critical areas for migratory passerines on the Texas coast. Imagery acquired from Landsat 8 OLI, maps provided by United States Geological Survey and the Texas Department of Transportation, and migratory bird occurrence records from the eBird citizen-contributed database were used to build predictive distribution models using three algorithms. Using the AUC to compare model performance, the Random Forest produced the most accurate distribution model, followed by MaxEnt, and Support Vector Machine (0.98, 0.81, and 0.79, respectively). We interpreted, from Boosted Regression Tree analysis, that elevation is the single most influential factor in determining migrant occupancy, with vegetative biomass the least influential predictor. Our approach here allows conservation biologists a more sophisticated approach to identifying critical areas for migratory passerines across large spatial extents in a short amount of time.     

基于底栖动物预测模型构建生物完整性指数评价河流健康

提高生物完整性指数(integrity of biotic index,IBI; 又称多参数指数multi-metric index, MMI)在时间和空间尺度的稳定性是水生态完整性评价和水环境管理实践的重要内容.本研究利用2004—2011年在浙江省多个河流采集的227个点位的底栖动物和水质理化数据,利用地理信息系统(GIS)提取样点及其对应流域的自然预测因子(如地理形态学、气候学)和土地利用数据,通过随机森林模型方法定量时间和空间尺度自然变量对生物群落的影响,构建基于预测模型控制自然因子影响方法和常规方法的MMI,并比较它们的表现力.结果表明: 基于预测模型法和基于常规方法构建的MMI的核心组成参数存在差异,随机森林模型中自然预测因子对预测模型MMI构成生物参数的解释量介于11.4%～61.2%.预测模型方法提高了MMI的精确度和准确度,但其敏感性和响应性低于常规方法的MMI.最近距离方法表明,9个评价点位和1个严重受损点位的自然属性与参照点位的自然属性存在差异性.在计算参照点位自然属性代表性范围的基础上,采用预测模型方法控制自然变量可以提高MMI的精确度和准确度,同时降低评价结果出现Ⅰ型(将健康水体误判为受损水体)或者Ⅱ型(将受损水体误判为健康水体)错误的可能性.研究结果可以为提高完整性指数评价稳定性和表现力提供方法支持.     

硅藻在河流健康评价中的应用研究进展

Diatom, as a kind of autotrophic photosynthetic eukaryotic algae, is an important primary producer in aquatic ecosystem, and can reflect the average status of water environment. As the bio-indicators of the environment, Nitzschia communis, Navicula minuscula, and Gomphonema parvulum can indicate the eutrophication of waters, whereas Gomphonema angustum, Epithemia adnata, and Diatoma moniliformis can indicate the oligotrophication of waters. Cyclotella bodanica, Neidium affine, and Eunotia exigua are all the eosinophilic species that can indicate waters acidity, Aminutissimum nodusa can indicate water’s Cu concentration, and Synedra ulna can indicate the Zn concentration in waters. Some other diatoms can also indicate water’s contamination. This paper reviewed the research progress on the applications of diatom and diatom indices in river health assessment, pointed out the related existing problems, and put forward some future research directions, e.g., further perfect the classification and identification of diatoms, broadly carry out the researches of diatom indices upon different areas and conditions, pay more attention to the screening of diatom bio integrality indices, and establish a benchmark which suits for the assessment of water quality.     

城市河流健康评价指标体系构建及其应用

健康的城市河流既能够维持其生态系统的自然运转,又能够满足城市社会经济的正常需求,还能够为人类提供休闲娱乐的场所。基于城市河流健康的内涵,构建出包含自然生态、社会经济和景观环境等3个方面24个指标的城市河流健康评价指标体系。以漓江市区段为例,通过建立基于层次分析法的模糊综合评价模型对其进行健康评价。结果表明:漓江市区段复合生态系统的评价结果为(0.2193,0.3004,0.3261,0.1137,0.0405),处于中健康状态;其自然生态子系统、社会经济子系统和景观环境子系统的健康状态分别为中、优和良;水量、防洪能力、鱼类多样性指数和底栖动物多样性是漓江市区段健康的主要影响因素。该评价指标体系可为其它城市河流的健康评价提供参考。     

River health assessment in a large river: Bioindicators of fish population

Large river systems are some of the most important aquatic resource for human beings. Unfortunately, ecological integrity of large rivers has been altered severely by human activities. To monitor and manage these ecosystems, a large number of fish-based indexes, especially at community-level have been developed in the past decades. However, community-level methods have presented unique challenges in large river assessment. Comparatively, the population-level method could not only avoid the challenges, but also show many other advantages. Therefore, the aim of this paper is to develop and validate a population-based method applicable for large river. The present study was carried out at the Dongjiang River, with Xenocypris davidi and Hemibarbus labeo being selected as the sentinel indicators. In developing our method we sought population metrics, including growth, survival and reproduction related, to reflect ecological characteristics. Candidate biological metrics were screened for stability, responsiveness and redundancy. The metrics of standard length, average age and fecundity were finally selected for X. davidi, and standard length, weight, average age, and gonadosomatic index for H. labeo. Through the relationship between biological traits and catchments human disturbance information, Xunwu and Anyuan were ultimately chosen as the reference sites for X. davidi and H. labeo, respectively. The star plot areas, representing the degree of similarity with the reference conditions, showed a large variation among different sampling sites, ranging from 0.15 to 0.94 for X. davidi and 0.13 to 1.91 for H. labeo. It was indicated that all sampling sites except for XW could be assigned to the “impaired”. The publicly available census data were used as independent data set to validate our method. The high agreement of both methods suggested that our method could provide an accurate measure for river ecosystem condition. We believe our methodology would be helpful for water resource management of large river. The methodology established here may also serve as a reference of how to develop a population-based index for similar assessments in other large river systems.     

Two-dimensional grey cloud clustering-fuzzy entropy comprehensive assessment model for river health evaluation

Abstract

The river health evaluation is typically complex non-linear system with characteristics of fuzziness and randomness. However, conventional gray clustering method has difficult to effectively describe fuzzy and random information simultaneously. For this purpose, the cloud model and fuzzy entropy theory are introduced to establish 2D gray cloud clustering-fuzzy entropy comprehensive evaluation model. Different with health level models, it reflects river health situation from aspects of health level and corresponding water body complexity simultaneously. The health level is obtained by gray cloud whitened weight function (first sub-system) and fuzzy entropy represents complexity and fuzziness of river health situation (second sub-system). Moreover, multi-level river health evaluation indicator system is constructed with dividing indicators into common and distinct sections according to differences on river characteristics. Meanwhile, indicator weights are determined by renewed combined weighting method based on minimum deviation principle. Finally, we conduct health evaluation work for rivers in the Taihu basin. The evaluation health levels and fuzzy entropy for river A–G are H3 (0.4888, relatively significant); H2 (0.5476, relatively fuzzy); H2 (0.7526, fuzzy); H2 (0.4731, relatively significant); H2 (05138, relatively fuzzy); H3 (0.5822, relatively fuzzy), and H2 (0.4064, relatively significant), respectively. Results are consistent with current river health situation and more intuitive than compared models. Furthermore, evaluation results with four different weighting methods are compared to further demonstrate rationality of the weighting method and evaluation model. Hence, the model proposed is demonstrated to provide new insight for solving river health assessment problem effectively.     

Pedigree assessment using RAPD-DGGE in cereal crop species

Summary The introduction of molecular biology methodologies to plant improvement programs offers an invaluable opportunity for extensive germplasm characterization. However, the detection of adequate DNA polymorphism in self-pollinating species remains on obstacle. We have optimized a denaturing-gradient-gel electrophoresis (DGGE) system which, when used in combination with random amplified polymorphic DNA (RAPD) analysis, greatly facilitates the detection of reproducible DNA polymorphism among closely related plant lines. We have used this approach to estimate pedigree relationships among a spectrum of plant materials in wheat, barley and oat. Based on analysis with one or two primers, we were able to distinguish soft from hard winter wheat, and 2-rowed from 6-rowed barley. Further analysis with additional primers allowed resolution of polymorpisms even among closely related lines in highly selected populations. We placed 17 cultivars of oat into two distinct clusters that differed significantly from previous oat pedigree assessments. We believe that DGGE-RAPD is a superior method for detecting DNA polymorphism when compared to RFLP, agarose-RAPD, or polyacrylamide-RAPD methods.     

Bioaccumulation of heavy metals in tissues of selected fish species from Ganga river,India, and risk assessment for human health

The study measured the concentration of Cd, Cr, Pb, Cu, and Zn in various fish tissues (muscle, gills, and liver) of 18 fish species (C. gachua, C. marulius, C. punctatus, C. nama, C. ranga, H. fossilis, C. batrachus, P. ticto, P. phutunio, L. rohita, L. calbasu, L. gonius, T. putitora, T. tor, R. rita, G. chapra, H. ilisa, and N. botia) collected from Ganga river. It is the survey regarding metal concentration in fish tissues increasing day by day. The metal concentration in different fish tissues varied on the following range: Cu (0.45–8.54 µg/g wet wt), Zn (0.07–2.2 µg/g wet wt), Pb (0.20–2.62 µg/g wet wt), Cd (0.07–2.32 µg/g wet wt), and Cr (0.09–1.74 µg/g wet wt). The results show the concentration of Pb, Cd, and Cr metals to be higher than internationally recommended standard limits (as determined by the WHO and FAO) and other similar studies. Generally, higher concentrations of metals were found in liver and gills than muscles. Despite lower estimated daily intake (EDI) of fish in the area (per recommended daily allowance guidelines), values of daily average consumption were lower than the recommended values by FAO/WHO/EFSA, and in fish samples these were below the provisional permissible levels for human consumption. The continuous exposure to heavy metals has been linked to the development of mental retardation, kidney damage, various cancers, and even death in instances of very high exposure in human body.     

Ecosystem damage assessment of land transformation using species loss

Purpose

The objectives of this study are to develop life cycle impact assessment (LCIA) methods that enable an assessment of the impact on the biodiversity by land use categorized in general land use types and to obtain the implications for an assessment of global land use impact, using the methods in the Life Cycle Impact Assessment Method based on Endpoint Modeling (LIME).

Methods

Expected Increase in Number of Extinct Species (EINES), which was calculated by summing the increments in extinction risks of each threatened vascular plant species due to land transformation, was used as an indicator of damage to biodiversity. EINES per land use category was calculated using data from the “Threatened Wildlife of Japan, Red Data Book 2nd ed. Volume 8, Vascular Plants” (hereinafter referred to as “RDB”).

Results and discussion

The EINES of wetlands and grassland was relatively high. The number of species that were assumed to exist in forestland was large; however, the EINES of forestland was relatively low. It was considered to be influenced by the huge area of forestland in Japan. EINES of other land was also relatively high, and it was considered to be the reflection of the existence of species whose habitat is peculiar, such as limestone areas or high mountains.

Conclusions

Damage factors developed for Japan in this study have broad potential application, as they have more general land use categories than those in LIME 1 and 2; however, it will be necessary to develop damage factors in other countries, taking into account threatened species categories and regional differences in the importance of various land use categories. It is also necessary to accumulate detailed data on threatened species across the planet to develop worldwide damage factors.

     

Antibody modeling assessment

A blinded study to assess the state of the art in three‐dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high‐resolution x‐ray Fab crystal structures covering a wide range of antigen‐binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x‐ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011; © 2011 Wiley‐Liss, Inc.     

着生藻类和浮游藻类在三峡库区河流健康评价中的适宜性比较研究

藻类对水体环境变化敏感,其种类和数量与环境因素有密切联系并因环境的变化而发生变化,因此藻类常作为河流健康评价的指示生物。水体中的藻类根据生活习性不同分为着生藻类和浮游藻类,在河流健康评价中,以往的工作中有的采用浮游藻类用于河流健康评价,有的采用着生藻类用于评价,但浮游藻类和着生藻类究竟何者用于河流健康评价更适宜,抑或是二者在用于评价的适宜性上没有明显差别,迄今为止未开展过深入研究。选择三峡库区内的两条河流嘉陵江和乌江作为研究对象,于2015年9月,在两条河流上共布设11个研究断面,对嘉陵江、乌江的水环境理化因子、着生藻类和浮游藻类群落进行调查研究,应用着生藻类生物完整性指数(Periphytic algal index of biological integrity,Pe-IBI)和浮游藻类生物完整性指数(Phytoplankton index of biological integrity,Ph-IBI),并结合水体综合污染指数(Comprehensive pollution index,CPI),对嘉陵江、乌江的健康状况进行评价。研究结果表明,采用着生藻类生物完整性评价(Pe-IB...     

An overview of river health assessment: philosophies, practice, problems and prognosis

1. Philosophically, the term ‘river health’ is useful because it is readily interpreted by the general public and evokes societal concern about human impacts on rivers. The common goal of achieving healthy rivers unites ecologists and the general public because the value of the ecologists’ contributions is clear (and, hence, funded). The difficulty arises in the choice of relevant symptoms because there is a wide variety that can be measured with varying accuracy at a broad range of spatial scales. These indicators may respond to impacts at different time scales, and no single indicator is a ‘silver bullet’ that reveals river health unequivocally. 2. In practice, choice of indicator often shows personal bias, technical considerations, and constraints of knowledge. Selection of appropriate spatial and temporal scales for these measures is crucial. Although most measurements are spot samples (e.g. concentration, abundance, species richness), assessment of river health based on changes in ecological processes such as post-disturbance recovery rate or nutrient spiralling lengths may be more suitable in some cases. 3. Problems include validation of the indicator, its response time at a range of scales, and the reliability of its measurement. Assessment of river health should be accurate, timely (warning of deterioration instead of waiting until the patient is terminal), rapid (so that the response is swift), and inexpensive. The connectedness of running waters with their floodplains and catchments must be explicitly recognized. Hydrological and geomorphological modifications of rivers usually affect their health by severing or impairing the linkages, and the ‘cure’ may lie in addressing these causes. Often, we need landscape-level data for management because this is the scale where cumulative effects of impacts are evident. 4. The prognosis is uncertain. We need to explore further the use of integrative measures of river health, and focus on establishing a link between the measure and impaired ecological integrity. Ecosystem-level variables (e.g. estimates of production or respiration) show promise and recent technological advances make these more accessible. Data analytical approaches (e.g. multimetric vs. predictive models) need further debate but must not overlook the importance of high quality and relevant input data. Appropriate choice of indicators, rigorous sampling and analysis, and careful data interpretation must be matched with effective communication to policy-makers and the public. When this occurs, the concept of ‘river health’ becomes more than just a rhetorical tool.‘     

Modelling distributional trends to inform conservation strategies for an endangered species

Aim Species loss has increased significantly over the last 1000 years and is ultimately attributed to the direct and indirect consequences of increased human population growth across the planet. A growing number of species are becoming endangered and require human intervention to prevent their local extirpation or complete extinction. Management strategies aimed at mitigating a species loss can benefit greatly from empirical approaches that indicate the rate of decline of a species providing objective information on the need for immediate conservation actions, e.g. captive breeding; however, this is rarely employed. The current study used a novel method to examine the distributional trends of a model endangered species, the freshwater pearl mussel, Margaritifera margaritifera (L.). Location United Kingdom and Republic of Ireland. Methods Using species presence data within 10‐km grid squares since records began three‐parameter logistic regression curves were fitted to extrapolate an estimated date of regional extinction. Results This study has shown that freshwater pearl mussel distribution has contracted since known historical records and outlier populations were lost first. Within the United Kingdom and Republic of Ireland, distribution loss has been greatest in Scotland, Northern Ireland, Wales and England, respectively, with the Republic of Ireland containing the highest relative proportion of M. margaritifera distribution, in 1998. Main conclusions This study provides empirical evidence that this species could become extinct throughout countries within the United Kingdom within 170 years under the current trends and emphasizes that regionally specific management strategies need to be implemented to prevent extirpation of this species.     

Toward a more robust assessment of intraspecies diversity, using fewer genetic markers

Phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. It remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. We show here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences. We use ANI to evaluate the phylogenetic robustness of every gene in the genome and show that almost all core genes, regardless of their functions and positions in the genome, offer robust phylogenetic reconstruction among strains that show 80 to 95% ANI (16S rRNA identity, >98.5%). Lack of elapsed time and, to a lesser extent, horizontal transfer and recombination make the selection of genes more critical for applications that target the intraspecies level, i.e., strains that show >95% ANI according to current standards. A much more accurate phylogeny for the Escherichia coli group was obtained based on just three best-performing genes according to our analysis compared to the concatenated alignment of eight genes that are commonly employed for phylogenetic purposes in this group. Our results are reproducible within the Salmonella, Burkholderia, and Shewanella groups and therefore are expected to have general applicability for microevolution studies, including metagenomic surveys.