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1.
Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization- and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in “GPR-Analyzer”, a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/edvardse/gpranalyzer.  相似文献   

2.
近年来 ,诸多国家在环境微生物领域先后开展了分子生物学研究方法的建立和生物学评价工作。一些不依靠纯培养的微生物群落的分析方法已得到广泛应用和发展。荧光原位杂交 (FISH)技术 ,具有细胞在测定过程中不被破坏、形状不改变、特异性强、能够真实反映在自然环境下微生物的情况及分布等特点 ,在环境微生物群落探测分析中已逐渐被广泛应用。该技术利用带有荧光标记的特异性寡核苷酸探针 ,与细胞内相应的靶核糖体结合 ,能将微生物探测、鉴定到属和种的水平。运用于硝化细菌、除磷细菌和丝状微生物等废水处理中常见的特征性微生物种群和群落生态学研究中 ,颇为高效。该技术的应用避免了传统培养方法进行鉴定和计数的局限性 ,在环境微生物生态学解析中具有较高应用价值。  相似文献   

3.
Monitoring of marine microalgae is important to predict and manage harmful algal blooms. Microarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a multi-species microarray as a tool to aid monitoring agencies. We tested the suitability of different prototype versions of the MIDTAL microarray for the monthly monitoring of a sampling station in outer Oslofjorden during a 1-year period. Microarray data from two different versions of the MIDTAL chip were compared to results from cell counts (several species) and quantitative real-time PCR (qPCR; only Pseudochattonella spp.). While results from generation 2.5 microarrays exhibited a high number of false positive signals, generation 3.3 microarray data generally correlated with microscopy and qPCR data, with three important limitations: (1) Pseudo-nitzschia cells were not reliably detected, possibly because cells were not sufficiently retained during filtration or lysed during the extraction, and because of low sensitivity of the probes; (2) in the case of samples with high concentrations of non-target species, the sensitivity of the arrays was decreased; (3) one occurrence of Alexandrium pseudogonyaulax was not detected due to a 1-bp mismatch with the genus probe represented on the microarray. In spite of these shortcomings our data demonstrate the overall progress made and the potential of the MIDTAL array. The case of Pseudochattonella — where two morphologically similar species impossible to separate by light microscopy were distinguished — in particular, underlines the added value of molecular methods such as microarrays in routine phytoplankton monitoring.  相似文献   

4.
Microalgae worldwide regularly cause harmful effects, considered from the human perspective, in that they cause health problems and economic damage to fisheries and tourism. Cyanobacteria cause similar problems in freshwaters. These episodes encompass a broad range of phenomena collectively referred to as “harmful algal blooms” (HABs). For adequate management of these phenomena, monitoring of microalgae is required. However, effective monitoring is time-consuming because cell morphology as determined by light microscopy may be insufficient to give definitive species and toxin attribution. In the European Union FP7 project MIDTAL (Microarrays for the Detection of Toxic Algae), we achieved rapid species identification using rRNA genes as the target. These regions can be targeted for probe design to recognise species or even strains. We also included antibody reactions to specific toxins produced by these microalgae because, even when cell numbers are low, toxins can be present and can accumulate in the shellfish. Microarrays are the state-of-the-art technology in molecular biology for the processing of bulk samples for detection of target RNA/DNA sequences. After 36 months, we have completed RNA-cell number–signal intensity calibration curves for 18 HAB species and the analysis of monthly field samples from five locations from year 1. Results from one location, Arcachon Bay (France), are reported here and compared favourably with cell counts in most cases. In general, the microarray was more sensitive than the cell counts, and this is likely a reflection in the difference in water volume analysed with the volume filtered for the microarray an order of magnitude greater.  相似文献   

5.
Harmful or nuisance algal blooms can cause economic damage to fisheries and tourism. Additionally, toxins produced by harmful algae and ingested via contaminated shellfish can be potentially fatal to humans. The seas around the Orkney Islands, UK currently hold a number of toxic algal species which cause shellfishery closures in most years. Extensive and costly monitoring programs are carried out to detect harmful microalgae before they reach action levels. However, the ability to distinguish between toxic and non-toxic strains of some algae is not possible using these methods. The microarrays for the detection of toxic algae (MIDTAL) microarray contains rRNA probes for toxic algal species/strains which have been adapted and optimized for microarray use. In order to investigate the use of the chip for monitoring in the Orkney Islands, samples were collected between 2009 and 2011 from Brings Deep, Scapa Flow, Orkney Islands, UK; RNA was extracted and hybridized with generation 2 and 3.1 of the chip. The data were then compared to cell counts performed under light microscopy and in the case of Alexandrium tamarense to qPCR data targeting the saxitoxin gene and the LSU-rRNA gene. A good agreement between cell numbers and microarray signal was found for A. tamarense, Pseudo-nitzschia sp., Dinophysis sp. (r?<?0.5, for all) in addition to this there the chip successfully detected a large bloom of Karenia mikimotoi (r?<?0.70) in August and September 2011. Overall, there was good improvement in probe signal between generation 2 and generation 3.1 of the chip with much less variability and more consistent results and better correlation between the probes. The chip performed well for A. tamarense group I signal to cell numbers in calibrations (r?>?0.9). However, in field samples, this correlation was slightly lower suggesting interactions between all species in the sample may affect signal. Overall, the chip showed it could identify the presence of target species in field samples although some work is needed to improve the quantitative nature of the chip before it would be suitable for monitoring in the Orkney Islands.  相似文献   

6.
Phytoflagellates of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta) form blooms in marine coastal waters in northern Europe, Japan, and New Zealand that at times cause fish kills with severe losses for the aquaculture industry. The aim of this study was to develop molecular probes for the detection and identification of Pseudochattonella at the genus and species level. A variety of probes were developed and applied to either dot blot hybridization, (q)PCR, or microarray format. In the dot blot hybridization assay, five different oligonucleotide probes targeting the small subunit (SSU) rDNA were tested against DNA from 18 microalgal strains and shown to be specific to the genus Pseudochattonella. A genus-specific PCR assay was developed by identifying an appropriate primer pair in the SSU—internal transcribed spacer 1 (ITS1) rDNA region. Its specificity was tested by screening against both target and non-target strains, and the assay was used to confirm the presence or absence of Pseudochattonella species in environmental samples. In order to distinguish between the two species of the genus, two PCR primer pairs each biased towards one of the species were designed in the large subunit (LSU) rDNA D1 domain and used for quantitative real-time PCR. Five selected probes (three SSU and two LSU rDNA) were adapted for the use on microarrays and included on a prototype multi-species microarray for the detection of harmful algae (http://www.midtal.com). Finally, microarrays and qPCR were used for the monthly monitoring of a sampling site in outer Oslofjorden during a 1-year period. Members of Pseudochattonella are difficult to identify by light microscopy in Lugol’s preserved samples, and the two species Pseudochattonella verruculosa and Pseudochattonella farcimen can be morphologically distinguished only by transmission electron microscopy. The molecular probes designed in this study will be a valuable asset to microscopical detection methods in the monitoring of harmful algae and for biogeographical and ecological studies of this genus.  相似文献   

7.
本文描述了海洋高技术的兴起与进展、海洋采矿对生态环境影响的案例分析。60年代以来,海洋高技术最重要的成就是深海采矿,根据当前发展动态看,深海石油和采矿技术仍是海洋高技术的主要方向,而海洋生物技术也是最有前景的高技术领域之一。对油船触礁造成的漏油事故案例分析指出海洋高技术对海洋生态环境的影响主要表现如下:1.对海洋生物资源的危害。首先,在油污染事件的短期内大量海鸟和海兽被杀死;其次,长期累积在经济鱼类内的有害物质通过食物链进入人体而对人体健康产生危害。2.对海滨环境的影响。如破坏海滨浴场水质。为了避免各种海洋高技术对海洋生态环境的影响,介绍了几点政策建议。  相似文献   

8.
Harmful algal blooms (HABs) are a global problem, which can cause economic loss to aquaculture industry's and pose a potential threat to human health. More attention must be made on the development of effective detection methods for the causative microalgae. The traditional microscopic examination has many disadvantages, such as low efficiency, inaccuracy, and requires specialized skill in identification and especially is incompetent for parallel analysis of several morphologically similar microalgae to species level at one time. This study aimed at exploring the feasibility of using membrane-based DNA array for parallel detection of several microalgae by selecting five microaglae, including Heterosigma akashiwo, Chaetoceros debilis, Skeletonema costatum, Prorocentrum donghaiense, and Nitzschia closterium as test species. Five species-specific (taxonomic) probes were designed from variable regions of the large subunit ribosomal DNA (LSU rDNA) by visualizing the alignment of LSU rDNA of related species. The specificity of the probes was confirmed by dot blot hybridization. The membrane-based DNA array was prepared by spotting the tailed taxonomic probes onto positively charged nylon membrane. Digoxigenin (Dig) labeling of target molecules was performed by multiple PCR/RT-PCR using RNA/DNA mixture of five microalgae as template. The Dig-labeled amplification products were hybridized with the membrane-based DNA array to produce visible hybridization signal indicating the presence of target algae. Detection sensitivity comparison showed that RT-PCR labeling (RPL) coupled with hybridization was tenfold more sensitive than DNA-PCR-labeling-coupled with hybridization. Finally, the effectiveness of RPL coupled with membrane-based DNA array was validated by testing with simulated and natural water samples, respectively. All of these results indicated that RPL coupled with membrane-based DNA array is specific, simple, and sensitive for parallel detection of microalgae which shows promise for monitoring natural samples in the future.  相似文献   

9.
Rapid and reliable detection of harmful algae in coastal areas and shellfish farms is an important requirement of monitoring programmes. Monitoring of toxic algae by means of traditional methods, i.e., light microscopy, can be time consuming when many samples have to be routinely analysed. Reliable species identification requires expensive equipment and trained personnel to carry out the analyses. However, all techniques for the monitoring of harmful algae usually require transportation of samples to specialised laboratories. In many monitoring laboratories, results are usually obtained within five working days after receiving the sample and therefore preventative measures are not always possible. Molecular technologies are rapidly improving the detection of phytoplankton and their toxins and the speed at which the results can be obtained. Assays are based on the discrimination of the genetic differences of the different species and species-specific probes can be designed. Such probes have been adapted to a microarray or phylochip format and assessed in several EU monitoring sites. Microarray results are presented for 1 year of field samples validated with cell counts from concentrated samples taken during toxic events from the weekly sampling of the Galician Monitoring Programme done by INTECMAR. The Galician monitoring laboratory does their own counting and their results are posted on their web site within 24 h. There was good correlation between cells present and microarray signals. In the few cases of false negatives, these can be attributed to poor RNA extraction of the target species, viz. Prorocentrum or Dinophysis. Where potential false positives were encountered, the smaller volume taken for cell counts as compared to the upto 300 times more volume taken for RNA extraction for the microarray is likely the cause for these differences, making the microarray more sensitive. The microarray was able to provide better species resolution in Alexandrium and Pseudo-nitzschia. In all cases, the toxins recovered by the toxin array were matched by target species in the array or in the cell counts.  相似文献   

10.
Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially toxic species. We designed molecular probes targeting the 18S rDNA at the family and genus levels for Dinophysis and Phalacroma and at the species level for Dinophysis acuminata, Dinophysis acuta, and Dinophysis norvegica, the most commonly occurring, potentially toxic species of these genera in Western European waters. Dot blot hybridizations with polymerase chain reaction (PCR)-amplified rDNA from 17 microalgae were used to demonstrate probe specificity. The probes were modified along with other published fluorescence in situ hybridization and PCR probes and tested for a microarray platform within the MIDTAL project (http://www.midtal.com). The microarray was applied to field samples from Norway and Spain and compared to microscopic cell counts. These probes may be useful for early warning systems and monitoring and can also be used in population dynamic studies to distinguish species and life cycle stages, such as cysts, and their distribution in time and space.  相似文献   

11.
In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.  相似文献   

12.
Human activities in river catchments interfere with natural fluxes of water and materials. Diffuse inputs and point-sources of toxicants have modified the ecological state of riverine communities considerably, and sanitation schemes are now under development for various rivers. To improve analysis, monitoring and prospecting the role of toxicants in river ecosystems a review of the available methods is undertaken. Ecotoxicological techniques are discussed in relation to basic ecological principles that are thought to regulate the functioning of communities. The response to toxicants among species is highly diverse and therefore the choice of test species (e.g. of typical riverine insects as caddisflies or mayflies) is critical, as it is the use of test-batteries. Long-term exposure may lead to developmental disturbances that may be assessed through morphometric techniques like analysis of asymmetry. Multi-generation exposure, although rarely studied, provides a useful insight into the genetic consequences of pollution. Selection for tolerant species or varieties has been experimentally assessed for smaller organisms such as insects, micro-algae, and bacteria. There is also perspective for multivariate analysis of species distribution in relation to pollutant exposure. Furthermore, a system approach to benthic ecology and sediment testing is needed. Such an approach reflects the strong linkage of ecological and ecotoxicological processes. Toxicants are transformed by biological activity; in some cases this alleviates toxicant stress, but in other cases degradation products are toxic as well. The risk of transformation to mutagenic products in the environment is indicated. The re-assessment of some of the classical ecotoxicological techniques is needed to adequately fulfil the needs of ecological recovery programs. To this purpose integration of ecotoxicological and ecological tools is needed.  相似文献   

13.

In this study, the marine microalgae Skeletonema costatum and Nitzschia closterium were exposed to different forms of copper, such as a metal salt (Cu2+), a nano-metal (nano-Cu), and nano-metal oxide (nano-CuO). During a 96-h exposure to nanoparticles (NPs) and salt, the cell number, Cu2+ concentration in the culture medium, morphology, and intracellular amino acids were measured to assess the toxicity of the copper materials and the toxicity mechanism of the NPs. As results, the toxicity of Cu2+, nano-Cu, and nano-CuO to marine phytoplankton decreased in order. The EC50 values of Cu2+ and nano-Cu for S. costatum and N. closterium ranged from 0.356 to 0.991 mg/L and 0.663 to 2.455 mg/L, respectively. Nano-Cu inhibits the growth of marine phytoplankton by releasing Cu2+; however, nano-CuO is harmful to microalgae because of the effect of NPs. The secretion of extracellular polymeric substances by microalgae could also affect the toxicity of nano-Cu and nano-CuO to microalgae. S. costatum was more sensitive to copper than N. closterium. Cu2+, nano-Cu, and nano-CuO all reduced per-cell amino acids and the total output of algae-derived amino acids by affecting the growth of the phytoplankton. This study helps to understand the risk assessment of nano-Cu and nano-CuO to marine microalgae.

  相似文献   

14.
In Mexican waters, there is no a formal and well-established monitoring program of harmful algal blooms (HAB) events. Until now, most of the work has been focused on the characterization of organisms present in certain communities. Therefore, the development of new techniques for the rapid detection of HAB species is necessary. Capillary electrophoresis finger print technique (CE-SSCP) is a fingerprinting technique based on the identification of different conformers dependent of its base composition. This technique, coupled with capillary electrophoresis, has been used to compare and identify different conformers. The aim of this study was to determine if CE-SSCP analysis of ribosomal RNA (rRNA) gene fragments could be used for a rapid identification of toxic and harmful HAB species to improve monitoring activities along the coasts of Baja California Sur, Mexico.Three different highly variable regions of the 18S and 28S rRNA genes were chosen and their suitability for the discrimination of different dinoflagellate species was assessed by CE-SSCP.The CE-SSCP results obtained for the LSU D7 fragment has demonstrated that this technique with this gene region could be useful for the identification of the ten dinoflagellates species of different genera.We have shown that this method can be used to discriminate species and the next step will be to apply it to natural samples to achieve our goal of molecular monitoring for toxic algae in Mexican waters. This strategy will offer an option to improve an early warning system of HAB events for coastal BCS, allowing the possible implementation of mitigation strategies. A monitoring program of HAB species using molecular methods will permit the analysis of several samples in a short period of time, without the pressure of counting with a taxonomic expert in phytoplankton taxonomy.  相似文献   

15.
This review article outlines harmful algal bloom (HAB) monitoring practices in New Zealand and highlights the shift from light microscope (LM)-based identification and quantification of the early 1990s to the use of molecular tools to support the HAB monitoring programmes two decades later. Published research and available client information from the monitoring programmes have been reviewed; HAB events and programme changes are highlighted. The current HAB monitoring practices allow for rapid determination of potential biotoxin issues for the shellfish industry and of potential ichthyotoxic events for finfish farmers. The use of molecular tools, including quantitative PCR, has improved risk assessments for those HAB species that are difficult to differentiate to species level using LM. This has enabled rapid feedback to aquaculture managers during HAB events. Tests for biotoxins in flesh remain the regulatory tools for commercially harvested shellfish, but this is supported by the weekly phytoplankton monitoring data. Recreational (non-commercial) shellfish harvesting and commercial finfish aquaculture rely solely on phytoplankton monitoring to assess the biotoxin risk. HAB monitoring in New Zealand continues to maintain internationally recognised standards, and the government-funded research programmes feed the latest knowledge and technical methods into the programmes. The early dependence on light microscopy continues but is now supported by molecular tools, with a view to employing multi-species detection systems in the future. The traditional mouse bioassay test has been fully replaced by chemical tests.  相似文献   

16.
Environmental monitoring faces the challenge of measuring an increasing number of analytes at ever decreasing concentrations. Since not all species of a given analyte have the same detrimental impact on the environment, new analytical devices and techniques are required to distinguish between the different species of a pollutant or different groups of pollutants. This paper describes analytical techniques based on biomaterials that are toxically sensitive to pollutants. This approach permits the biomonitoring of certain compounds by looking at their toxic properties. Although these techniques are based on a sound analytical strategy, their applications are limited because most of the interactions between the biological material and the analyte are irreversible. Additionally, the immobilised biological material has a limited stability. Several biomonitoring strategies based on electrochemical biosensing are discussed here and how to recover the bioactivity of biosensing system, both in discrete and automated procedures, is also reviewed.  相似文献   

17.
海洋环境污染监测方案是一项复杂的系统工程。中国经过20多年海洋环境污好监测的实践活动,积累了丰富的经验。但是,由于未能对海洋环境污染监测方案进行深入细致的研讨,致使今天我国海洋环境污染监测尚停留在定性或半定量描述阶段。该文第一次把有关海洋环境污染监测相结合,通过运用逻辑构思方法和监测方法学,详细分析监测方案设计中的各个阶段,监测目标的提出,到方案的实施;从监测数据的加工,到监测信息的发布都进行了辩证的分析。本文既是中国海洋环境污染监测方案的设计指南,也是中国海洋环境污染监测工作的集大成。  相似文献   

18.
Attached growth biological treatment systems are a promising solution to ammonia removal in cold-temperature climates. Environmental scanning electron microscopy (ESEM) and confocal laser scanning microscopy in combination with fluorescent in situ hybridization (FISH) was used to investigate the effects of 4 months of exposure to 4 degrees C on nitrifying biofilm and biomass. These molecular and microscopic methods were modified to minimize loss of mass and distortion of in situ perspectives. Environmental scanning electron microscopy revealed that nitrifying biofilm did not exhibit significant changes in volume with exposure to 4 degrees C. Confocal laser scanning microscopy in combination with FISH showed that the number of ammonia-oxidizing bacteria (AOB) cells present in the biofilm was statistically consistent during exposure to 4 degrees C. The RNA content of AOB cells remained sufficient for FISH enumeration. The number of nitrite-oxidizing bacteria cells remained steady during exposure to 4 degrees C; however, the RNA content of the cells appeared to decrease with exposure to 4 degrees C, thereby preventing their enumeration using FISH.  相似文献   

19.
In this era of globalization, various products and technologies are being developed by the industries. While resources and energy are utilized from processes, wastes are being excreted through water streams, air, and ground. Without realizing it, environmental pollutions increase as the country develops. Effective technology is desired to create green factories that are able to overcome these issues. Wastewater is classified as the water coming from domestic or industrial sources. Wastewater treatment includes physical, chemical, and biological treatment processes. Aerobic and anaerobic processes are utilized in biological treatment approach. However, the current biological approaches emit greenhouse gases (GHGs), methane, and carbon dioxide that contribute to global warming. Microalgae can be the alternative to treating wastewater as it is able to consume nutrients from wastewater loading and fix CO2 as it undergoes photosynthesis. The utilization of microalgae in the system will directly reduce GHG emissions with low operating cost within a short period of time. The aim of this review is to discuss the uses of native microalgae species in palm oil mill effluent (POME) and flue gas remediation. In addition, the discussion on the optimal microalgae cultivation parameter selection is included as this is significant for effective microalgae-based treatment operations.  相似文献   

20.
In this study, we compared the sensitivity of freshwater and marine organisms to two structurally similar substances, acrylic acid and methacrylic acid. Reported acute toxicity data (L(E)C50-values) for freshwater organisms range from 0.1 to 222 mg/l and 85 to >130 mg/l for acrylic acid and methacrylic acid, respectively. The large variation in toxicity data for acrylic acid is due to a specific toxicity to certain species of freshwater microalgae, with algae EC50-values being two to three orders of magnitude lower than L(E)C50-values reported for fish and invertebrates. To evaluate the sensitivity of marine organisms, ecotoxicity data was generated for ten species of microalgae, one invertebrate species and one fish species. For methacrylic acid, we found a marine acute toxicity that ranged from 110 to >1260 mg/l, which is comparable to reported data on freshwater organisms. In strong contrast, the resulting L(E)C50-values for acrylic acid ranged from 50 to >1000 mg/l, and there was no specific sensitivity of marine algae when compared to marine invertebrates and fish. For acrylic acid, therefore, use of the available freshwater toxicity data for an effects assessment for the marine environment is likely to overestimate the hazard and risk from this substance. Overall, the results of the study suggest that ecotoxicity data generated on freshwater species may not always be appropriate for the effects assessments of organic chemicals in the marine environment, thus emphasising the importance of using ecologically relevant data to assess environmental risk.  相似文献   

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