Optimal colonization and growth of marine benthic diatoms on artificial substrata: protocol for a routine use in bioindication

Benthic diatoms growing on hard substrata are used for their bioindication ability in freshwater quality monitoring. Artificial substrata are needed in cases where any natural substrate is present or to achieve similar sampling conditions between sites. Prior to use marine benthic diatoms for monitoring, a standardized protocol for sampling on artificial substrata must be set up. Two major types of information are required: (1) the time needed for a diatom community to be well developed and mature (climax stage); (2) the optimal growth conditions, given that the substrataum nature and texture are important parameters for the initial phase of biofilm development and can influence the future diatom assemblage. Three substrataum types were tested: frosted Plexiglass®, frosted glass, and rough enameled tiles. They were submerged for 8 weeks and sampled weekly. The experiment was conducted at five sites of distinct morphology and water chemistry, along the coastal area of Martinique Island, French West Indies. Development of diatom community was studied through biofilm dry weight, valve density, species richness, and species relative abundances. Globally, substratum type had no significant effect on any parameter. Frosted Plexiglass® was found to be the most interesting substratum because of higher valve densities and practical use. The asymptotic phase of biofilm development was encountered between 5 and 8 weeks depending on site and parameter. A compromise between community development and vandalism or loss through time was fixed to 5 weeks. This period is longer than for stream environments and is valid for tropical oligotrophic marine environments.     

Efficient sampling methodologies for lake littoral invertebrates in compliance with the European Water Framework Directive

Lake shores are characterised by a high natural variability, which is increasingly threatened by a multitude of anthropogenic disturbances including morphological alterations to the littoral zone. The European Water Framework Directive (EU WFD) calls for the assessment of lake ecological status by monitoring biological quality elements including benthic macroinvertebrates. To identify cost- and time-efficient sampling strategies for routine lake monitoring, we sampled littoral invertebrates in 32 lakes located in different geographical regions in Europe. We compared the efficiency of two sampling methodologies, defined as habitat-specific and pooled composite sampling protocols. Benthic samples were collected from unmodified and morphologically altered shorelines. Variability within macroinvertebrate communities did not differ significantly between sampling protocols across alteration types, lake types and geographical regions. Community composition showed no significant differences between field composite samples and artificially generated composite samples, and correlation coefficients between macroinvertebrate metrics calculated with both methods and a predefined morphological stressor index were similar. We conclude that proportional composite sampling represents a time- and cost-efficient method for routine lake monitoring as requested under the EU WFD, and may be applied across various European geographical regions.     

生物物种资源监测原则与指标及抽样设计方法

生物物种资源监测是了解生物物种资源现状、开展生物物种资源保护与管理的基础工作和重要手段.阐述了生物物种资源监测的科学性原则、可操作性原则和持续性原则.提出了监测计划的制定程序;监测计划应充分考虑所具有的人力、资金和后勤保障等条件,并进行定期评估.分析了指示物种在物种资源监测中的作用与不足;认为应选择具有不同生态需求和生活史的生物类群作为监测对象.讨论了监测指标的选取方法;监测指标应可测量、有科学基础、易被公众接受、低成本和高效益;监测方法应具有科学性,能检测到相应的变化,应采用高效率、低成本的标准化监测方法.分析了现有监测计划在抽样设计方面存在的问题,探讨了空间变异性和可检测率对监测数据误差的影响及其处理方式,讨论了样本量确定和监测样地的大小、形状及位置设计.监测样地要有较好的代表性,能在有限的监测面积中较好地反映监测区域内群落种类组成与数量特征.最后,讨论了生物物种资源监测的尺度和标准化问题.     

An efficient and quantitative aquatic benthos sampler for use in diverse habitats with variable flow regimes

A suction sampler designed to minimize sampling error, and quantitatively collect benthic macroinvertebrates from coarse substrata under various flow regimes is described. This sampler uses a 12 V bilge pump (capacity 4400 1 h^–1) to suck animals into a collecting net from substrata disturbed by a single operator. Macroinvertebrates were collected more rapidly by this sampler than by a Surber sampler or a Boulton suction sampler. Sources of sampling error are discussed for all three samplers. The electric pump sampler described here is suitable for sampling habitats where depth and velocity vary spatially and with time.     

Artificial substrata in a shallow sublittoral habitat: do they adequately represent natural habitats or the local species pool?

Artificial substrata have been advocated as tools which have considerable potential for monitoring both natural and anthropogenic effects on invertebrate communities of shallow coastal environments. In this experiment, community structure was compared between two dominant natural algal habitats (kelp holdfasts and algal turf) and artificial substratum units (ASUs; nests of pan scourers) deployed in close contact with, and 20 cm above the substratum. Univariate and multivariate statistical analyses were applied to the data to determine the similarity of community structure between the four different habitats. In addition, recently developed measures of taxonomic distinctness were applied to the data from both sets of artificial substrata to determine if they provided a representative sample of the local epifaunal species pool and thus have the potential to be used as surrogate samples for this important faunal group. There were marked differences between community structure in each of the habitats. Both sets of artificial substrata were dominated by tubicolous polychaetes with abundances that were more than an order of magnitude greater than in the holdfast and turf samples. The fauna recruiting to the artificial substrata deployed above the substratum showed the lowest values in the univariate summaries of diversity and evenness and were unrepresentative of the local species pool. Artificial samples deployed in contact with the substratum showed greater diversity and evenness but were still mostly unrepresentative of the local species pool. The tendency for both sets of artificial substrata to under-sample amphipods and to be dominated by suspension-feeding polychaetes suggests that methods using these units may be relatively insensitive to the effects of anthropogenic impacts (e.g. sewage outfalls) where shifts in community structure including increased dominance of suspension-feeders and polychaetes and a reduced dominance of amphipods have been observed. Further studies, including the evaluation of temporal variation in community structure related to the time at which the ASUs are deployed and duration of deployment, are needed to test the wider utility of artificial substrata as tools for monitoring shallow, sublittoral, epifaunal communities.     

Comparative algological and bacteriological examinations on biofilms developed on different substrata in a shallow soda lake

According to the European Water Framework Directives, benthic diatoms of lakes are a tool for ecological status assessment. In this study, we followed an integrative sample analysis approach, in order to find an appropriate substratum for the water qualification-oriented biomonitoring of a shallow soda lake, Lake Velencei. Six types of substrata (five artificial and one natural), i.e., andesite, granite, polycarbonate, old reed stems, Plexiglass discs and green reed, were sampled in May and in November. We analysed total alga and diatom composition, chlorophyll a content of the periphyton, surface tension and roughness of the substrata and carbon source utilisation of microbial communities. Water quality index was calculated based on diatom composition. Moreover, using a novel statistical tool, a self-organising map, we related algal composition to substratum types. Biofilms on plastic substrates deviated to a great extent from the stone and reed substrata, with regard to the parameters measured, whereas the biofilms developing on reed and stone substrata were quite similar. We conclude that for water quality monitoring purposes, sampling from green reed during springtime is not recommended, since this is the colonization time of periphyton on the newly growing reed, but it may be appropriate from the second half of the vegetation period. Stone and artificially placed old reed substrata may be appropriate for biomonitoring of shallow soda lakes in both spring and autumn since they showed in both seasons similar results regarding all measured features.     

Six recommendations for improving monitoring of diseases shared with wildlife: examples regarding mycobacterial infections in Spain

Monitoring is needed to identify changes in disease occurrence and to measure the impact of intervention. Using mycobacterial diseases as an example, we discuss herein the pros and cons of the current Spanish Wildlife Disease Surveillance Scheme providing suggestions for monitoring relevant diseases shared with wildlife in other regions facing similar challenges. Six points should be considered. This includes: (1) making sure the disease is properly monitored in the relevant domestic animals or even in humans; (2) also making sure that background information on wildlife population ecology is available to maximize the benefits of the monitoring effort; (3) selecting the appropriate wildlife hosts for monitoring, while being flexible enough to incorporate new ones if research suggests their participation; (4) selecting the appropriate methods for diagnosis and for time and space trend analysis; (5) deciding which parameters to target for monitoring; and finally (6) establishing a reasonable sampling effort and a suitable sampling stratification to ensure detecting changes over time and changes in response to management actions. Wildlife disease monitoring produces knowledge that benefits at least three different agencies, namely, animal health, public health and conservation, and these should combine efforts and resources. Setting up stable, comprehensive and accurate schemes at different spatial scales should become a priority. Resources are always a limiting factor, but experience shows that combined, cross-collaborative efforts allow establishing acceptable schemes with a low enough cost to be sustainable over time. These six steps for monitoring relevant shared diseases can be adapted to many other geographical settings and different disease situations.     

Recommendations for sampling littoral diatoms in lakes for ecological status assessments

This review summarises the existing literature and outlines the theoretical basis for using standard methods for sampling diatoms from rivers to sample littoral diatoms and other phytobenthos from standing waters. The European Union's Water Framework Directive has created a statutory obligation for EU Member States to monitor macrophytes and phytobenthos in lakes. Although there has been a considerable amount of work using phytobenthos (especially diatoms) to monitor river water quality in Europe, there are fewer studies on the use of phytobenthos for monitoring in lakes. European standard methods for sampling diatoms from rivers should be suitable, with only minor modifications, for sampling littoral diatoms from lakes and other standing water bodies. These recommendations should be applicable to all temperate regions.     

典型河床底质组成中底栖动物群落及多样性

底栖动物是河流生态系统中食物链的重要环节。通过对长江、黄河、东江和拒马河等河流野外调查和采样分析研究了河床底质组成对底栖动物群落结构的影响规律。研究结果发现,不同河床底质组成中的底栖动物结构差别很大,不同地理位置而相同底质条件和水力条件的河流底栖动物群落组成相似,说明河床底质是影响河流底栖动物群落结构的关键因素,受地理位置和大气候的影响不大;利用多项生物指标分析了不同河床底质组成中底栖动物群落的多样性,卵石河床且有水生植物生长的河流底栖动物物种组成最丰富,大河中沙质河床不稳定,未采集到底栖动物;不同底质类型河床中的优势种群亦不同。并分析了采样所得底栖动物物种数与采样面积之间的关系,符合前者随后者呈幂指数增加的规律,当实测采样面积为1～2m^2时物种数变化不大,建议一般情况下最小采样面积应为1m^2。     

Are unmanned aircraft systems (UASs) the future of wildlife monitoring? A review of accomplishments and challenges

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Reintroduction as a tool for population recovery of farmland birds

Conservation efforts in the United Kingdom have increasingly sought to restore the populations and ranges of birds affected by changes to their habitat or by direct human persecution. One approach is reintroduction, although this is likely to be appropriate in only a limited set of circumstances, involving a small number of species. This paper reviews the use of reintroduction as a tool for conserving birds associated with lowland farmland, highlighting the benefits of this approach to conservation, as well as the potential dangers. Two case studies are presented to illustrate how different reintroduction techniques are required, depending on the species involved and the donor stock available. The internationally agreed, though not legally binding, IUCN guidelines for reintroduction projects are summarized, together with the requirements of The Wildlife & Countryside Act (1981) in relation to the release of birds into the wild in Britain. Potential changes to current legislation are suggested, to prevent inappropriate and potentially damaging reintroduction projects from being carried out in the future.     

Line transect methods for plant surveys

Interest in surveys for monitoring plant abundance is increasing, due in part to the need to quantify the rate of loss of biodiversity. Line transect sampling offers an efficient way to monitor many species. However, the method does not work well in some circumstances, for example on small survey plots, when the plant species has a strongly aggregated distribution, or when plants that are on the line are not easily detected. We develop a crossed design, together with methods that exploit the additional information from such a design, to address these problems. The methods are illustrated using data on a colony of cowslips.     

cfRNAs as biomarkers in oncology – still experimental or applied tool for personalized medicine already?

Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods.In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.     

Neurite extension by neuroblastoma cells on substratum-bound fibronectin''s cell-binding fragment but not on the heparan sulfate-binding protein, platelet factor-4

Human and rat neuroblastoma cells extend neurites over plasma fibronectin (pFN)-coated substrata. For resolution of which fibronectin binding activities (the cell-binding domain (CBD), the heparan sulfate-binding domains, or a combination of the two) are responsible for neurite outgrowth, CBD was prepared free of heparan sulfate-binding activity as described by Pierschbacher et al. (Cell 26 (1981) 259-267). Neuroblastoma cells attached and extended neurites as stably and as effectively on CBD-coated substrata as on intact pFN, while cytoplasmic spreading was more extensive on pFN-coated substrata. The structures of growth cones on CBD or pFN were virtually identical. On substrata coated with the model heparan sulfate-binding protein, platelet factor 4 (PF4), cells attached and spread somewhat but never extended neurites. When cells were challenged with substrata coated with various ratios of CBD and PF4, PF4 was found to be an effective inhibitor of CBD-mediated neurite extension. Similarly, cells grown on substrata coated at different locations with CBD or PF4 in order to evaluate topographical dependence of growth cone formation extended neurites only onto the CBD-coated region or along the interface between these two proteins, but never onto the PF4 side of cells that bridged the interface. These studies indicate that (a) the CBD activity of pFN, and not its heparan sulfate-binding activity, is the critical determinant in neurite extension of these neural tumor cells from the central nervous system; (b) under some circumstances, heparan sulfate-binding activity can be antagonistic to neurite extension; (c) the chemical nature of the substratum controls the direction of neurite extension; (d) these neuroblastoma cells respond to these binding proteins very differently than fibroblasts or neurons from the peripheral nervous system.     

Analysis of Methods for Growth Detection in the Search for Extraterrestrial Life

In the search for life on other planets, experiments designed to detect the growth of microorganisms may prove to be definitive when coupled with chemical characterization and metabolic experiments. If organisms are not abundant, growth provides the only means for obtaining a large mass of biological material suitable for chemical compositional analyses and metabolic assays. Several methods of monitoring growth are described. Of these, optical monitoring in a unique system free of soil particles is advanced as the most appropriate. Theoretical problems related to the formulation of culture media are discussed, and several possible solutions are proposed. The sampling system, the type of monitoring, the size and placement of inoculum, and the medium volume and composition are contingent upon one another and must be integrated without sacrifice to the biological demands.     

A Comparison of Remote Sensing and Ground-Based Methods for Monitoring Wetland Restoration Success

Abstract Efficient and accurate vegetation sampling techniques are essential for the assessment of wetland restoration success. Remotely acquired data, used extensively in many locations, have not been widely used to monitor restored wetlands. We compared three different vegetation sampling techniques to determine the accuracy associated with each method when used to determine species composition and cover in restored Pacific coast wetlands dominated by Salicornia virginica (perennial pickleweed). Two ground‐based techniques, using quadrat and line intercept sampling, and a remote sensing technique, using low altitude, high resolution, color and color infrared photographs, were applied to estimate cover in three small restoration sites. The remote technique provided an accurate and efficient means of sampling vegetation cover, but individual species could not be identified, precluding estimates of species density and distribution. Aerial photography was determined to be an effective tool for vegetation monitoring of simple (i.e., single‐species) habitat types or when species identities are not important (e.g., when vegetation is developing on a new restoration site). The efficiency associated with these vegetation sampling techniques was dependent on the scale of the assessment, with aerial photography more efficient than ground‐based sampling methods for assessing large areas. However, the inability of aerial photography to identify individual species, especially mixed‐species stands common in southern California salt marshes, limits its usefulness for monitoring restoration success. A combination of aerial photography and ground‐based methods may be the most effective means of monitoring the success of large wetland restoration projects.     

The inference of stepwise changes in substitution rates using serial sequence samples.

It is frequently true that molecular sequences do not evolve in a strictly clocklike manner. Instead, substitution rate may vary for a number of reasons, including changes in selection pressure and effective population size, as well as changes in mean generation time. Here we present two new methods for estimating stepwise changes in substitution rates when serially sampled molecular sequences are available. These methods are based on multiple rates with dated tips (MRDT) models and allow different rates to be estimated for different intervals of time. These intervals may correspond to the sampling intervals or to a priori--defined intervals that are not coincident with the times the serial samples are obtained. Two methods for obtaining estimates of multiple rates are described. The first is an extension of the phylogeny-based maximum-likelihood estimation procedure introduced by Rambaut. The second is a new parameterization of the pairwise distance least-squares procedure used by Drummond and Rodrigo. The utility of these methods is demonstrated on a genealogy of HIV sequences obtained at five different sampling times from a single patient over a period of 34 months.     

Intercalibration and comparison – major results and conclusions from the STAR project

The main results of the STAR project on the intercalibration of boundaries of European assessment systems and comparison between assessment methods are summarized here. The main findings are outlined in the context of the Water Framework Directive that requires reliable instructions to be set up on how to use and harmonise assessment systems and methods for European rivers. The main papers published on these subjects by STAR partners are reviewed, with focus on major questions addressed and approaches used for investigation. The need for broad coverage of geographic ranges and pressure gradients, together with the goal of providing outcomes appropriate to the effective application of the WFD are emphasized. Extensive datasets from a wide range of countries, stream types and sites and a large number of methods, metrics and approaches are compared and tested and various cross-cutting themes emerged. Among these, the value of the use of benchmarking systems for comparison and intercalibration is highlighted. Two ways of looking for comparability of assessment systems results were analyzed: a) by adopting identical sampling techniques across Europe and b) by harmonizing the classification results of the national assessment systems. In addition, the need, in the intercalibration process, for a proper definition of the criteria for reference conditions is underlined. This is because their imprecision now represents one of the major weaknesses of the whole intercalibration process. Direct and indirect approaches to intercalibration are considered and commented on for their potential use in distinct circumstances. Finally, the use common metrics for the intercalibration process, which make comparability across Europe valid, is tested and indeed encouraged.     

Understanding of Aquifer Microbiology is Tightly Linked to Sampling Approaches

Primary samples of groundwater or core are collected and analyzed to characterize the microbiology of aquifers and to predict biogeochemical transformations. Alternative sampling devices have been developed that are incubated for some length of time in the aquifer to accrue biomass for analysis. Considering data generated from different types of aquifer samples, it appears that the type of sample collected and analyzed may strongly influence the resulting view of aquifer microbiology. Borehole artifacts need to be rigorously considered when incubated substrata are used. The indigenous attached populations in deeper, fractured rock aquifers remain understudied and await new sampling approaches.