Picoeukaryotic Plankton Diversity at the Helgoland Time Series Site as Assessed by Three Molecular Methods

We analyzed picoeukaryote assemblages in the German Bight at the Helgoland time series site by sequencing cloned eukaryotic 18S rRNA genes in six genetic libraries plus one library from the Orkney Islands from a cruise of opportunity. The libraries were constructed from environmental samples collected at different periods of the year. The same samples were also analyzed using a fingerprinting technique, single-strand conformational polymorphism (SSCP), and DNA microarrays with class-level oligonucleotide probes. One hundred unique clones were analyzed from each library, thus insuring over 85% coverage of the library. The V4 region of the 18S rRNA gene was sequenced from each of these clones, thus providing the most discrimination among the clones. The nonphotosynthetic picoeukaryotic component dominated over the photosynthetic one and was represented by the ciliates at 45% and group II alveolates at 42%. Prasinophytes dominated the photosynthetic group at 40%, but other picoplankton groups, such as bolidomonads and chrysophytes, were also present. Totally novel groups were found in the cryptomonads and in the dinoflagellates. A new algal group sister to the cryptophyte nuclear gene and the glaucocystophytes was also found. These three groups have been found in other picoeukaryotic planktonic clone libraries. SSCP analyses at closer time intervals suggest that clone libraries should be made at weekly intervals if succession in the picoeukaryotic plankton community is to be monitored accurately. A comparison of annual samples suggests thatthere appears to be an annual cycle with regard to species composition. Microarray analysis supported the clone library data and offered a faster means of community analysis, which can be performed with similar accuracy and with higher throughput for a more in-depth analysis.     

Genetic Diversity of Plankton Community as Depicted by PCR-DGGE Fingerprinting and its Relation to Morphological Composition and Environmental Factors in Lake Donghu

To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.     

Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy

Protist community composition and seasonal dynamics are of major importance for the production of higher trophic levels, such as zooplankton and fish. Our aim was to reveal how the protist community in the Skagerrak changes through the seasons by combining high‐throughput sequencing and microscopy of plankton collected monthly over two years. The V4 region of the 18S rRNA gene was amplified by eukaryote universal primers from the total RNA/cDNA. We found a strong seasonal variation in protist composition and proportional abundances, and a difference between two depths within the euphotic zone. Highest protist richness was found in late summer‐early autumn, and lowest in winter. Temperature was the abiotic factor explaining most of the variation in diversity. Dinoflagellates was the most abundant and diverse group followed by ciliates and diatoms. We found about 70 new taxa recorded for the first time in the Skagerrak. The seasonal pattern in relative read abundance of major phytoplankton groups was well in accordance with microscopical biovolumes. This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.     

Stimulation of Alexandrium fundyense growth by bacterial assemblages from the Bay of Fundy

AIMS: To evaluate the influence of marine bacterial assemblages from the Bay of Fundy on Alexandrium fundyense str. CB301 growth. METHODS AND RESULTS: Bacterial assemblages were collected from the Bay of Fundy during an Alexandrium spp. bloom, serially diluted to extinction and inoculated into axenic CB301 cultures. Bacterial assemblages dramatically enhanced CB301 growth. Retrieval and analysis of 16S rDNA fragments revealed an Alteromonas sp. strain to be the only detectable bacterium in all assemblages that promoted A. fundyense and the sole bacterium found in the most dilute inoculum that promoted A. fundyense. While this bacterium has not yet been isolated, other isolates obtained from the assemblages did not stimulate A. fundyense, indicating that the observed stimulation was not a general effect of marine bacteria. CONCLUSIONS: Bay of Fundy marine bacterial assemblages dominated by a member of the family Alteromonadaceae were found to dramatically stimulate growth of A. fundyense. SIGNIFICANCE AND IMPACT OF THE STUDY: These results show that native bacteria have the potential to dramatically promote the growth of A. fundyense and may play an important role in influencing A. fundyense dynamics in the Bay of Fundy.     

A Comparison of Morphological and Molecular-Based Surveys to Estimate the Species Richness of Chaetoceros and Thalassiosira (Bacillariophyta), in the Bay of Fundy

The goal of this study was to compare the ability of morphology and molecular-based surveys to estimate species richness for two species-rich diatom genera, Chaetoceros Ehrenb. and Thalassiosira Cleve, in the Bay of Fundy. Phytoplankton tows were collected from two sites at intervals over two years and subsampled for morphology-based surveys (2010, 2011), a culture-based DNA reference library (DRL; 2010), and a molecular-based survey (2011). The DRL and molecular-based survey utilized the 3′ end of the RUBISCO large subunit (rbcL-3P) to identify genetic species groups (based on 0.1% divergence in rbcL-3P), which were subsequently identified morphologically to allow comparisons to the morphology-based survey. Comparisons were compiled for the year (2011) by site (n = 2) and by season (n = 3). Of the 34 taxa included in the comparisons, 50% of taxa were common to both methods, 35% were unique to the molecular-based survey, and 12% were unique to the morphology-based survey, while the remaining 3% of taxa were unidentified genetic species groups. The morphology-based survey excelled at identifying rare taxa in individual tow subsamples, which were occasionally missed with the molecular approach used here, while the molecular methods (the DRL and molecular-based survey), uncovered nine cryptic species pairs and four previously overlooked species. The last mentioned were typically difficult to identify and were generically assigned to Thalassiosira spp. during the morphology-based survey. Therefore, for now we suggest a combined approach encompassing routine morphology-based surveys accompanied by periodic molecular-based surveys to monitor for cryptic and difficult to identify taxa. As sequencing technologies improve, molecular-based surveys should become routine, leading to a more accurate representation of species composition and richness in monitoring programs.     

不同种源乌拉尔甘草形态和ISSR遗传多样性研究

利用形态学指标对34份乌拉尔甘草种质资源进行遗传多样性分析,结果表明,34份甘草在7个性状上差异均达到了极显著水平,主要是由以内蒙古和新疆种源为主的两大组群之间形态特性差异明显。在分子标记中,从100条核甘酸序列中筛选出18条ISSR多态性引物,对46份乌拉尔甘草种质资源进行了遗传多样性分析,研究结果表明:①我国乌拉尔甘草种质资源遗传变异十分丰富,18条引物共扩增出210条多态性带,分布在150~3000bp之间,平均每个引物扩增出11.67条;②新疆地区乌拉尔甘草遗传变异最为丰富,其次是西北地区,东北地区遗传变异最低;③基于ISSR分子标记划分的组群与地域性没有明显关系。     

Modeling spring migration patterns of scoters and loons in the Bay of Fundy

Populations of scoter and loon species that winter in the Atlantic are understudied in North America, but coastal observatories may provide the data required to fill some of the knowledge gaps. The migration of scoters and loons has been monitored at the Point Lepreau Bird Observatory (PLBO) in the Bay of Fundy every spring since 1996, but little peer-reviewed research based on the resultant database has been published. Using data collected over 18 years at the Bay of Fundy (2000–2017), our objectives were to (1) determine the most accurate method of modeling hourly migration rates for Surf (Melanitta perspicillata), White-winged (M. deglandi), and Black (M. americana) scoters, and Red-throated (Gavia stellata) and Common (G. immer) loons, and (2) assess trends in hourly migration rates for our five focal species to determine if the numbers of migrants passing PLBO have changed over time. We calculated hourly migration rates for each of our five focal species and evaluated drivers (i.e., timing and environmental conditions) of migration and annual trends using zero-inflated generalized linear mixed models (GLMMs). We found that drivers of migration differed among species. Specifically, hourly migration rates decreased with increasing tide height for all species except Red-throated Loons. In addition, hourly migration rates increased with increasing wind vector (i.e., a tailwind) for the three scoter species, but decreased with increasing wind vector for the two loon species. Scoter migration rates peaked daily between 11:00 and 13:00 UTC, but we found no daily peak for either loon species. Peak hourly migration rates of Black and Surf scoters occurred from 12 to 26 April, but migration rates of White-winged Scoters and both loon species continued to increase throughout our migration-monitoring window. Finally, we found no changes in hourly migration rates over time for any of our focal species, suggesting no changes in abundance over the 18 years of data collection. Our study reveals the importance and utility of long-term, coastal observation stations, and we recommend their continued funding and use as valuable sources of monitoring data.     

Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers

Switchgrass (Panicum virgatum L.) is a warm season, C₄ perennial grass native to most of North America with numerous applications, including use as a bioenergy feedstock species. To date, no studies on genetic diversity in switchgrass have been conducted that use both molecular and morphological markers. The objectives of this study were to assess genetic diversity and determine differences among and between 12 switchgrass populations grown in New Jersey by examining both morphological and molecular characteristics, and to determine whether morphological, molecular, and/or combined data sets can detect ecotype and/or geographical differences at the population level. Twelve plants from each population were characterized with 16 switchgrass expressed sequence tag-simple sequence repeat markers (EST-SSRs) and seven morphological characters. Data was analyzed using GenAlEx and Unweighted Pair-Group Method of Averages (UPGMA) cluster analysis. Most (64%) of the molecular variation in switchgrass populations exists among individuals within populations, with lesser amounts between populations (36%). Upland and lowland populations were distinguished in all three data sets. Some eastern US and midwestern US populations were distinct in all three data sets. Similarities were observed between all three data sets indicating molecular markers may be useful for identifying morphological differences or other adaptive traits. The combined data set was the most useful in differentiating populations based on geography and found separation between midwestern and eastern upland populations. The results indicate that the combination of morphological and molecular markers may be useful in future applications such as genetic diversity studies, plant variety protection, cultivar identification, and/or identifying geographic origin.     

Zooplankton Communities of a Dammed Estuary in the Bay of Fundy,Canada

The upper estuary of the macrotidal Petitcodiac River, New Brunswick, Canada, was converted to a freshwater impoundment by construction of a causeway in 1968. Thirty years later, zooplankton community structure in the impoundment was characteristic of a disturbed ecosystem. The depauperate zooplankton consisted of a mixture of freshwater and marine/brackish taxa, but was not typical of regional estuaries or lakes. The causeway dam was an obstacle to fish migration, and several anadromous species that would formerly have been represented in the ichthyoplankton were absent. The invertebrate plankton community was dominated by rotifers, likely as a result of frequent water level fluctuations, and highly suspended sediment levels in the water column. Estuarine/marine calanoids (Eurytemora affinis, Temora longicornis, Centropages typicus, Tortanus discaudatus), the mysid Neomysis americana, and Cancer crab zoeae were collected in fresh water up to 14 km upstream of the causeway.     

Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods

There is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. For this purpose the soil microbial community of a wheat field on an experimental farm in The Netherlands was studied by using both cultivation-based and molecule-based methods. Samples were taken in the different seasons over a 1-year period. Fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacteria, and only a few isolates appeared to belong to the Proteobacteria and green sulfur bacteria. Some genera, such as Micrococcus, Arthrobacter, and Corynebacterium were detected throughout the year, while Bacillus was found only in July. Isolate diversity was lowest in July, and the most abundant species, Arthrobacter oxydans, and members of the genus Pseudomonas were found in reduced numbers in July. Analysis by molecular techniques showed that diversity of cloned 16S ribosomal DNA (rDNA) sequences was greater than the diversity among cultured isolates. Moreover, based on analysis of 16S rDNA sequences, there was a more even distribution among five main divisions, Acidobacterium, Proteobacteria, Nitrospira, cyanobacteria, and green sulfur bacteria. No clones were found belonging to the gram-positive bacteria, which dominated the cultured isolates. Seasonal fluctuations were assessed by denaturing gradient gel electrophoresis. Statistical analysis of the banding patterns revealed significant differences between samples taken in different seasons. Cluster analysis of the patterns revealed that the bacterial community in July clearly differed from those in the other months. Although the molecule- and cultivation-based methods allowed the detection of different parts of the bacterial community, results from both methods indicated that the community present in July showed the largest difference from the communities of the other months. Efforts were made to use the sequence data for providing insight into more general ecological relationships. Based on the distribution of 16S rDNA sequences among the bacterial divisions found in this work and in literature, it is suggested that the ratio between the number of Proteobacteria and Acidobacterium organisms might be indicative of the trophic level of the soil.     

Pseudo-nitzschia species population dynamics in the Quoddy Region, Bay of Fundy

The population dynamics of Pseudo-nitzschia species from the Quoddy Region of the Bay of Fundy was examined in a field-based study. Five stations were sampled over a period of 11 weeks during the course of one discrete bloom episode in 2003 with seven species of Pseudo-nitzschia found and enumerated: P. americana, P. delicatissima, P. pseudodelicatissima, P. fraudulenta, P. pungens, P. seriata and P. subpacifica. We related species abundance to physical and chemical properties of seawater (transparency, fluorescence, silicate, phosphate, nitrite + nitrate, ammonia, nitrite, oxygen, sigma-t, tidal level, tidal state and total depth of water column) using canonical correspondence analysis (CCA) to identify factors explaining the greatest amount of variance in their temporal and spatial distribution patterns. Our results indicate that abundance of species and groups of species correlated well with certain specific chemical and physical properties of seawater. P. pseudodelicatissima and P. delicatissima abundance was positively correlated with nitrates and P. americana with depth of the water column. P. pungens was more abundant in samples with higher concentrations of phosphates and lower concentrations of nitrates. P. seriata abundance was negatively associated with total fluorescence. P. subpacifica and P. fraudulenta abundances were not statistically related to any of the variables examined. Our data therefore provides direction for testable, hypothesis driven experiments that could provide predictive insights into the occurrence of certain harmful algal bloom (HAB) species should specific environmental variables be further affected along the gradients extracted in this study.     

用形态与分子标记研究石刁柏种质资源遗传多样性

采用RAPD分子标记结合形态学指标对43份石刁柏种质资源的遗传多样性进行评价。田间试验相关分析表明,茎粗、林高、茎数与产量呈极显著正相关,三者是影响石刁柏产量的主要因素。茎粗、株高、产量与一级笋率呈显著正相关。花梗全紫的石刁柏一级笋率相对较高。根据形态学指标将材料分为7大类。在分子标记中,从60个随机引物中筛选出12个能产生清晰、稳定可重复DNA片段的引物,对供试材料进行RAPD扩增。在供试材料中共获得183条扩增产物,产生的DNA片段大小主要分布在200～1600bp之间,其中170条具有遗传多态性,约占总数的92．92％。各基因型间的Nei氏相似性系数分布在0．407～0．931之间,平均相似性为0．765,可见石刁柏各基因型之间的遗传多态性较为丰富。经UPGMA方法建立的树状图,可将参试品种划分为8大类群。形态学指标与遗传多样性指标的相关分析结果显示：分枝节间距、花梗颜色、每簇拟叶数、最长分枝长度、茎粗5个形态学指标与遗传多样性指标之间存在一定的相关性。     

Reproductive bionomics of two sublittoral amphipods in a Bay of Fundy estuary

The reproductive bionomics of two Canadian sublittoral amphipods, Casco bigelowi and Leptocheirus pinguis, are compared in a Bay of Fundy estuary. Casco is semelparous and Leptocheirus iteroparous, although both have a biannual life history. The relatively high reproductive potential of each species, Casco with a reproductive potential of 12.5 and Leptocheirus with 25.5 young per year, is dictated by a combination of wave-caused sediment washout and prédation within the estuary.     

Molecular Weight of Sindbis Virus Ribonucleic Acid as Measured by Polyacrylamide Gel Electrophoresis

The molecular weight (MW) of Sindbis virion ribonucleic acid (RNA) determined by gel electrophoresis was in a range of 3.89 x 10(6) to 4.45 x 10(6) daltons. Upon denaturation with urea, it separated into fragments having an MW of 1.76 x 10(6) daltons. Viral-specific Sindbis 26S RNA contained a major species having an MW of 1.76 x 10(6) daltons.     

Intertidal ecology and potential power impacts, Bay of Fundy, Canada

A large-scale tidal power project in the upper reaches of the Bay of Fundy would cause major changes in the tidal elevations of the headpond which would have a pronounced effect on intertidal ecology. The new mean low water level would be, on average, slightly above the present mean sea level whilst the new mean high water level would drop about 0.7 m. This would result in a much compressed intertidal zone. Mud and sand flats, below the present mean sea level, would be converted to sub-tidal habitat, whilst the high saltmarsh, flooded at present only on the highest spring tides, would become colonized by terrestrial vegetation. There would be major shifts in the relative importance of primary production by saltmarshes, intertidal microalgae and phytopiankton, but overall, it is likely that production would increase. Changes in both primary food sources and habitat area would affect the abundance of intertidal invertebrate organisms and the fish and migratory shorebirds that feed upon them.     

The Recent Terebratulina Community in the rocky subtidal zone of the Bay of Fundy, Canada

A distinctive rocky subtidal benthic community (the Terebratulina Community) is described from the Bay of Fundy, Canada. It is shown to consist of three closely intcrspersed sub-communities: a cavity sub-community, characterised by chitons, coelenterates, brachiopods, bryozoans, chordates and annelids; a rock-face subcommunity, similar in composition but enriched in brachiopods and sponges; and an upper-surface subcommunity, dominated by algae, chitons, bivalves and echinoids.
Comparison with recently described Jurassic, Cretaceous and Recent (Mediterranean) hard-ground communities suggests a relative constancy in composition, in terms of higher taxa, since the Mesozoic. Development of these (sub-)communities occurs wherever crevice or cavity systems on hard substrates lead to microenvironments differentiated mainly on the basis of water energy and light.
The composition and trophic structure of the community and the life habits of Terebratulina septentrionalis (Couthouy) are related to aspects of the environment. Marked differences in composition between the living cavity sub-community and the death assemblage in the sediments are shown to be due to differential preservation, fragmentation, population dynamics and limited local transportation.     

Diatoms from two macro-tidal mudflats in Chignecto Bay,Upper Bay of Fundy,New Brunswick,Canada

Mudflat research is dispersed among several fields (ecology, sedimentology), each with its own focus and methodology. Consequently, although the volume of mudflat literature is considerable, our understanding of mudflat ecology remains fragmented. For example, little is known about the structure of microbial communities outside Western Europe. Here we present the first North American specific composition and densities of live mudflat diatoms and relate them to properties of their environment on two closely located flats. The two flats (Daniel’s and Buck’s) were similar until the mid–1980s. After this time the biological and sedimentary environment on Buck’s Flats began to change and resulted in a precipitous decline of the keystone invertebrate Corophium volutator (Pallas). The specific diatom composition on each of the two flats examined was still very similar. Tychoplanktonic diatoms were numerically dominant on both flats. The flats differed significantly in the relative contribution of epipelic diatoms, which were about an order of magnitude greater on Buck’s Flats. CCA analysis suggests that very few of these species exist within their optimal habitat. Some of the differences appeared small, but were statistically and biologically significant. Daniel’s Flats sediments had a 30% larger mean grain size, less water and organic carbon compared to Buck’s Flats sediments. Buck’s Flats had more variable depths of the oxygenated layer, often with anoxic inclusions throughout. Daniel’s Flats supported more C. volutator, while Buck’s Flats contained greater densities of diatoms. The importance of preserving environmental conditions (sedimentary and biotic) prevailing on flats such as Danielȁ9s Flat in order to foster populations of Corophium at a level necessary to support foraging migratory shorebirds is also discussed.