Patterns of Species Number and Abundance in Macroalgal Communities in Coastal Waters

Predictable patterns of species number have been observed in relation to habitat size, habitat heterogeneity and environmental conditions, while patterns in relative abundance of species have been examined for few communities and no assembly rules have been established. We studied communities of attached macroalgae in 61 individual sites located in four different areas; the inner, middle and outer parts of three neighbouring low-tidal estuaries and the adjacent open waters of the Kattegat, Denmark. The objectives were to determine (1) the relationships of species number and rank-abundance to the environmental conditions, and (2) the importance of scale and the consistency of species rank number at the sites for these relationships. We found that species number increased significantly from the inner estuaries to the open coastal waters along with decreasing nutrient concentrations. Turnover (β) diversity was lowest in the open waters suggesting that species composition was more similar among samples there than in the estuaries. Rank-abundance curves did not differ between depth intervals and individual sites across the environmental gradients. However, the summed rank-abundance patterns for two sites showed significantly steeper initial slopes and dominance of few species (i.e., low evenness) in the inner estuaries than in open waters. This pattern was due to high rank consistency of dominant species among sites in the inner estuaries. In open waters rank consistency was low, and the summed abundance across sites showed an even abundance of species. The results imply that the scale of the study and the community variability observed at that particular scale, is the main determinant of abundance patterns.     

卫氏并殖吸虫PCR和实时荧光PCR快速检测方法的建立

目的建立快速、灵敏、特异的分子生物学检测卫氏并殖吸虫的方法。方法根据卫氏并殖吸虫的特异性基因序列,设计适合于PCR检测的特异性引物及实时荧光PCR特异性引物和探针,并进行灵敏性和特异性试验。结果设计的引物和探针特异性强,所建立的检测方法灵敏度高。应用实时荧光PCR方法的检测灵敏度可达到0.1 pg/μL,比PCR方法的灵敏度高三个数量级。结论本研究所建立的PCR和实时荧光PCR技术检测卫氏并殖吸虫方法的特异性强,灵敏度高,为卫氏并殖吸虫感染的诊治提供了快速的检测技术手段。     

鳕鱼成分的实时荧光PCR检测方法

研究建立了鳕鱼成分的实时荧光PCR检测方法。依据鳕鱼的16S rRNA基因序列设计一对PCR引物及探针,对12种鳕鱼样品和71种非鳕鱼动植物样品进行实时荧光PCR检测,结果显示,只有12种鳕鱼样品产生荧光信号,其他非鳕鱼样品均不产生荧光信号,实验表明此方法具有特异性,其检测限为0.01 ng/μl鳕鱼DNA和0.01%鳕鱼肉粉。对市售的鳕鱼样品进行实际样品检测,均能很好地检出鳕鱼成分。此法特异性强,灵敏度高,可作为鳕鱼成分鉴定的检测方法。     

Characterization of Nontoxic and Toxin-Producing Strains of Alexandrium minutum (Dinophyceae) in Irish Coastal Waters

A comparative analysis of the morphology, toxin composition, and ribosomal DNA (rDNA) sequences was performed on a suite of clonal cultures of the potentially toxic dinoflagellate Alexandrium minutum Halim. These were established from resting cysts or vegetative cells isolated from sediment and water samples taken from the south and west coasts of Ireland. Results revealed that strains were indistinguishable, both morphologically and through the sequencing of the D1-D2 domain of the large subunit and the ITS1-5.8S-ITS2 regions of the rDNA. High-performance liquid chromatography fluorescence detection analysis, however, showed that only strains derived from retentive inlets on the southern Irish coast synthesized paralytic shellfish poisoning (PSP) toxins (GTX2 and GTX3), whereas all strains of A. minutum isolated from the west coast were nontoxic. Toxin analysis of net hauls, taken when A. minutum vegetative cells were in the water column, revealed no PSP toxins in samples from Killary Harbor (western coast), whereas GTX2 and GTX3 were detected in samples from Cork Harbor (southern coast). These results confirm the identity of A. minutum as the most probable causative organism for historical occurrences of contamination of shellfish with PSP toxins in Cork Harbor. Finally, random amplification of polymorphic DNA was carried out to determine the degree of polymorphism among strains. The analysis showed that all toxic strains from Cork Harbor clustered together and that a separate cluster grouped all nontoxic strains from the western coast.     

Quantitative PCR Method for Enumeration of Cells of Cryptic Species of the Toxic Marine Dinoflagellate Ostreopsis spp. in Coastal Waters of Japan

Monitoring of harmful algal bloom (HAB) species in coastal waters is important for assessment of environmental impacts associated with HABs. Co-occurrence of multiple cryptic species such as toxic dinoflagellate Ostreopsis species make reliable microscopic identification difficult, so the employment of molecular tools is often necessary. Here we developed new qPCR method by which cells of cryptic species can be enumerated based on actual gene number of target species. The qPCR assay targets the LSU rDNA of Ostreopsis spp. from Japan. First, we constructed standard curves with a linearized plasmid containing the target rDNA. We then determined the number of rDNA copies per cell of target species from a single cell isolated from environmental samples using the qPCR assay. Differences in the DNA recovery efficiency was calculated by adding exogenous plasmid to a portion of the sample lysate before and after DNA extraction followed by qPCR. Then, the number of cells of each species was calculated by division of the total number of rDNA copies of each species in the samples by the number of rDNA copies per cell. To test our procedure, we determined the total number of rDNA copies using environmental samples containing no target cells but spiked with cultured cells of several species of Ostreopsis. The numbers estimated by the qPCR method closely approximated total numbers of cells added. Finally, the numbers of cells of target species in environmental samples containing cryptic species were enumerated by the qPCR method and the total numbers also closely approximated the microscopy cell counts. We developed a qPCR method that provides accurate enumeration of each cryptic species in environments. This method is expected to be a powerful tool for monitoring the various HAB species that occur as cryptic species in coastal waters.     

Detection of Phytophthora nicotianae in Soil with Real-time Quantitative PCR

Phytophthora nicotianae is one of the most important soil-borne plant pathogens. A rapid, specific and sensitive real-time polymerase chain reaction (PCR) detection method for P. nicotianae was established, which used primers targeting the internal transcribed spacer (ITS) regions of rDNA genes of Phytophthora spp. Based on the nucleotide sequences of ITS2 of 15 different species of Phytophthora , the primers and probe were designed specifically to amplify DNA from P. nicotianae. With a series of 10-fold DNA dilutions extracted from P. nicotianae pure cultures, the detection limit was 10 pg/μl in conventional PCR, whereas in SYBR Green I PCR the detection limit was 0.12 fg/μl and in TaqMan PCR 1.2 fg/μl, and real-time PCR was 10⁴–10⁵ times more sensitive than conventional PCR. The simple and rapid procedures maximized the yield and quality of recovered DNA from soil and allowed the processing of many samples in a short time. The direct DNA extractions from soil were utilized to yield DNA suitable for PCR. By combining this protocol with the real-time PCR procedure it has been possible to specifically detect P. nicotianae in soil, and the degree of sensitivity was 1.0 pg/μl. The system was applied to survey soil samples from tobacco field sites in China for the presence of P. nicotianae and the analyses of naturally infested soil showed the reliability of the real-time PCR method.     

Detection of Sclerotinia sclerotiorum in Planta by a Real-time PCR Assay

Stem rot caused by Sclerotinia sclerotiorum is a very serious disease on oilseed rape worldwide. In this study, a pair of polymerase chain reaction (PCR) primers was designed based on the nucleotide sequence of a DNA region amplified by a microsatellite primer M13. The primer pair amplified a 252-bp fragment from all S. sclerotiorum isolates collected from oilseed rapes at different locations in different years, but not from any other fungus tested. Using this pair of primers, a real-time PCR assay was developed to rapidly detect early infection of S. sclerotiorum on petals of oilseed rape. The real-time PCR assay developed in this study could help growers make a timely decision on fungicide application.     

实时荧光PCR检测食品中致敏原芥末成分

对植物原料产品和植物源性食品中芥末成分的快速鉴定是避免过敏性疾病发生的重要措施。依据芥末Sin A1管家基因的核酸序列设计特异性引物和探针,对3种芥末样品和21种非芥末植物样品进行实时荧光PCR检测,结果显示,过敏原芥末管家基因的样品FAM通道有荧光信号检出,非芥末样品FAM通道均无荧光信号检出。灵敏度实验表明,植物原料产品中对芥末的检测低限可达到1 mg/kg。此外对市售的芥菜籽等样品和深加工的芥末致敏原参考物质(葡萄糖)进行实际样品的检测,均能很好检出致敏原芥末成分。     

实时荧光定量PCR检测HPV-DNA在宫颈癌筛查中应用

目的:探讨HPV感染与宫颈病变的关系。方法:对2008年2月-2009年3月期间在通山县人民医院皮肤性病科和妇科门诊就诊的1256位女性的宫颈拭子标本进行HPV DNA实时荧光定量PCR检测,比较不同宫颈病变级别组HPV的阳性率。结果:各病变组与正常组比较差异有显著性,P0.01,且随病变级别增加总阳性率逐渐上升。结论:HPV在人群具有较高的感染率,且HPV感染与宫颈病变的发生有关。实时荧光定量PCR检测HPV DNA可成为一种广泛应用的临床检验技术,作为筛查宫颈癌及癌前病变的首选方法。     

实时荧光定量PCR检测HPV—DNA在宫颈癌筛查中应用

目的：探讨HPV感染与宫颈病变的关系。方法：对2008年2月-2009年3月期间在通山县人民医院皮肤性病科和妇科门诊就诊的1256位女性的宫颈拭子标本进行HPV DNA实时荧光定量PCR检测,比较不同宫颈病变级别组HPV的阳性率。结果：各病变组与正常组比较差异有显著性,P〈0.01,且随病变级别增加总阳性率逐渐上升。结论：HPV在人群具有较高的感染率,且HPV感染与宫颈病变的发生有关。实时荧光定量PCR检测HPV DNA可成为一种广泛应用的临床检验技术,作为筛查宫颈癌及癌前病变的首选方法。     

利用实时定量PCR快速检测冷鲜猪肉新鲜度指标的方法研究

目前冷鲜猪肉新鲜度指标检测繁琐,探索快速检测冷鲜猪肉新鲜度指标新技术成为研究热点。利用国标法检测发性盐基氮(Total volatile basic n itrogen,TVB-N)含量,平板培养法和实时定量PCR技术分别检测腐败微生物数量。结果显示,冷鲜猪肉在4℃条件下,随储藏时间延长,微生物的菌落总数和TVB-N逐渐增加且呈线性相关,与猪肉品的腐败程度呈正相关;丙酮-氯仿法提取的细菌基因组条带清晰,提取效果好;基于SYBER GreenⅠ的实时定量PCR技术检测的菌落数量与平板培养测得菌落总数利用单因素方差分析结果没有显著性差异(P=0.7190),一致性较好;实时定量PCR方法缩短了检测时间,提高了检测灵敏度。微生物是冷鲜猪肉新鲜度评价的重要指标,实时定量PCR可以作为一种快速高效检测冷鲜猪肉新鲜度指标的新技术。     

Metal-Resistant Heterotrophic Bacteria in Coastal Waters of Primorye

Colony-forming heterotrophic bacteria were isolated from several locations in coastal waters of Primorye that differ in the extent and character of heavy metal pollution. Statistically significant differences in the minimum inhibitory concentrations of some metals were found for bacteria isolated from the environments with different levels of pollution. Bacterial strains that were highly tolerant of several heavy metals also showed resistance to a wide spectrum of antibiotics, and some strains bore plasmids of varying numbers and sizes. Bacteria of the family Enterobacteriaceae and the genus Pseudomonas were the dominant metal-resistant bacterial forms in the polluted coastal wasters of Primorye. No strict correlation was found between metal resistance and taxonomic identity of bacteria.Original Russian Text Copyright © 2005 by Biologiya Morya, Bezverbnaya, Buzoleva, Khristoforova.     

Real-time PCR in virology

The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5′ endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.     

Seasonal Dynamics of Mesozooplankton in Brazilian Coastal Waters

The composition, numerical abundance and seasonal distribution of mesozooplankton, in addition to copepod biomass, were studied in the São Sebastião Channel (SSC) during different seasonal periods and hydrographic regimes. Two stations were sampled every 3 months from January 1996 to July 1997 and also in July 1998 and January 1999. Temporal differences in oceanographic conditions in the SSC were observed; there was clear seasonal variation in the thermohaline structure. Phytoplankton composition, standing-stock and biomass also showed consistent seasonal variation, peaking during summer due to advection of cold and nutrient-rich South Atlantic Central Water (SACW). Sixty-nine mesozooplankton taxa were identified and counted. Mesozooplankton density also increased during summer, ranging from 93 to 12,774 ind  m^?3. In contrast, a unimodal peak of copepod biomass was recorded during winter and under the influence of the oligotrophic Coastal Water (CW), suggesting that copepod biomass at SSC is driven by resource control. There was no significant evidence of seasonal pattern in overall community composition or evidence of changes due to water mass advection. The mesozooplankton community was continuously dominated by coastal and warm-water species, particularly the copepods Acartia lilljeborgi, Paracalanus aculeatus, P. quasimodo, Parvocalanus crassirostris, Corycaeus giesbrechti and Oithona oswaldocruzi, the cladocerans Penilia avirostris and Evadne tergestina, in addition to the appendicularians Oikopleura longicauda and O. dioica, all of which are perennial species in the SSC. This taxonomic composition may represent an efficient biotic structure for rapid recycling of primary production during periods of SACW influence.     

Genetic Diversity and Temporal Variation in the Cyanophage Community Infecting Marine Synechococcus Species in Rhode Island's Coastal Waters

The cyanophage community in Rhode Island's coastal waters is genetically diverse and dynamic. Cyanophage abundance ranged from over 10⁴ phage ml⁻¹ in the summer months to less then 10² phage ml⁻¹ during the winter months. Thirty-six distinct cyanomyovirus g20 genotypes were identified over a 3-year sampling period; however, only one to nine g20 genotypes were detected at any one sampling date. Phylogenetic analyses of g20 sequences revealed that the Rhode Island cyanomyoviral isolates fall into three main clades and are closely related to other known viral isolates of Synechococcus spp. Extinction dilution enrichment followed by host range tests and PCR restriction fragment length polymorphism analysis was used to detect changes in the relative abundance of cyanophage types in June, July, and August 2002. Temporal changes in both the overall composition of the cyanophage community and the relative abundance of specific cyanophage g20 genotypes were observed. In some seawater samples, the g20 gene from over 50% of isolated cyanophages could not be amplified by using the PCR primer pairs specific for cyanomyoviruses, which suggested that cyanophages in other viral families (e.g., Podoviridae or Siphoviridae) may be important components of the Rhode Island cyanophage community.     

实时荧光定量PCR在猪肺炎支原体检测中的应用

实时荧光定量PCR技术是一种利用荧光检测方法来定量核酸的技术,具有高度的灵敏性、特异性和精确性.综述了荧光定量PCR技术的基本原理及其在猪肺炎支原体检测中的应用.     

Detection of Campylobacter jejuni and Campylobacter coli in Environmental Waters by PCR Enzyme-Linked Immunosorbent Assay

A PCR enzyme-linked immunosorbent assay (ELISA) assay was applied to the detection of Campylobacter jejuni and Campylobacter coli in environmental water samples after enrichment culture. Bacterial cells were concentrated from 69 environmental water samples by using filtration, and the filtrates were cultured in Campylobacter blood-free broth. After enrichment culture, DNA was extracted from the samples by using a rapid-boiling method, and the DNA extracts were used as a template in a PCR ELISA assay. A total of 51 samples were positive by either PCR ELISA or culture; of these, 43 were found to be positive by PCR ELISA and 43 were found to be positive by culture. Overall, including positive and negative results, 59 samples were concordant in both methods. Several samples were positive in the PCR ELISA assay but were culture negative; therefore, this assay may be able to detect sublethally damaged or viable nonculturable forms of campylobacters. The method is rapid and sensitive, and it significantly reduces the time needed for the detection of these important pathogens by 2 to 3 days.     

Use of PCR for Direct Detection of Campylobacter Species in Bovine Feces

This study reports on the use of PCR to directly detect and distinguish Campylobacter species in bovine feces without enrichment. Inhibitors present in feces are a major obstacle to using PCR to detect microorganisms. The QIAamp DNA stool minikit was found to be an efficacious extraction method, as determined by the positive amplification of internal control DNA added to bovine feces before extraction. With nested or seminested multiplex PCR, Campylobacter coli, C. fetus, C. hyointestinalis, and C. jejuni were detected in all fecal samples inoculated at ≈10⁴ CFU g⁻¹, and 50 to 83% of the samples inoculated at ≈10³ CFU g⁻¹ were positive. At ≈10² CFU g⁻¹, C. fetus, C. hyointestinalis, and C. jejuni (17 to 50% of the samples) but not C. coli were detected by PCR. From uninoculated bovine feces, a total of 198 arbitrarily selected isolates of Campylobacter were recovered on four commonly used isolation media incubated at three temperatures. The most frequently isolated taxa were C. jejuni (152 isolates) and C. lanienae (42 isolates), but isolates of C. fetus subsp. fetus, Arcobacter butzleri, and A. skirrowii also were recovered (≤2 isolates per taxon). Considerable variability was observed in the frequency of isolation of campylobacters among the four media and three incubation temperatures tested. With genus-specific primers, Campylobacter DNA was detected in 75% of the fecal samples, representing an 8% increase in sensitivity relative to that obtained with microbiological isolation across the four media and three incubation temperatures tested. With nested primers, C. jejuni and C. lanienae were detected in 25 and 67% of the samples, respectively. In no instance was DNA from either C. coli, C. fetus, or C. hyointestinalis detected in uninoculated bovine feces. PCR was more sensitive than isolation on microbiological media for detecting C. lanienae (17%) but not C. jejuni. Campylobacters are a diverse and fastidious group of bacteria, and the development of direct PCR not only will increase the understanding of Campylobacter species diversity and their frequency of occurrence in feces but also will enhance the knowledge of their role in the gastrointestinal tract of livestock and of the factors that influence shedding.     

Real-Time PCR for Detection and Quantification of the Protistan Parasite Perkinsus marinus in Environmental Waters

The protistan parasite Perkinsus marinus is a severe pathogen of the oyster Crassostrea virginica along the east coast of the United States. Very few data have been collected, however, on the abundance of the parasite in environmental waters, limiting our understanding of P. marinus transmission dynamics. Real-time PCR assays with SybrGreen I as a label for detection were developed in this study for quantification of P. marinus in environmental waters with P. marinus species-specific primers and of Perkinsus spp. with Perkinsus genus-specific primers. Detection of DNA concentrations as low as the equivalent of 3.3 × 10⁻² cell per 10-μl reaction mixture was obtained by targeting the multicopy internal transcribed spacer region of the genome. To obtain reliable target quantification from environmental water samples, removal of PCR inhibitors and efficient DNA recovery were two major concerns. A DNA extraction kit designed for tissues and another designed for stool samples were tested on environmental and artificial seawater (ASW) samples spiked with P. marinus cultured cells. The stool kit was significantly more efficient than the tissue kit at removing inhibitors from environmental water samples. With the stool kit, no significant difference in the quantified target concentrations was observed between the environmental and ASW samples. However, with the spiked ASW samples, the tissue kit demonstrated more efficient DNA recovery. Finally, by performing three elutions of DNA from the spin columns, which were combined prior to target quantification, variability of DNA recovery from different samples was minimized and more reliable real-time PCR quantification was accomplished.