Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray

ABSTRACT The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.

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Fungi found in Mediterranean and North Sea sponges: how specific are they?

PeerJ ◽

10.7717/peerj.3722 ◽

2017 ◽

Vol 5 ◽

pp. e3722 ◽

Cited By ~ 9

Author(s):

Mohd Azrul Naim ◽

Hauke Smidt ◽

Detmer Sipkema

Keyword(s):

North Sea ◽

Ribosomal Rna ◽

18S Rrna Gene ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Operational Taxonomic Units ◽

The North ◽

Hypervariable Regions ◽

The North Sea ◽

Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

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Fungi found in Mediterranean and North Sea sponges: How specific are they?

10.7287/peerj.preprints.3049 ◽

2017 ◽

Cited By ~ 1

Author(s):

Mohd Azrul Naim ◽

Hauke Smidt ◽

Detmer Sipkema

Keyword(s):

North Sea ◽

Ribosomal Rna ◽

18S Rrna Gene ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Operational Taxonomic Units ◽

The North ◽

Hypervariable Regions ◽

The North Sea ◽

Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point into the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

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Fungi found in Mediterranean and North Sea sponges: How specific are they?

10.7287/peerj.preprints.3049v1 ◽

2017 ◽

Author(s):

Mohd Azrul Naim ◽

Hauke Smidt ◽

Detmer Sipkema

Keyword(s):

North Sea ◽

Ribosomal Rna ◽

18S Rrna Gene ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Operational Taxonomic Units ◽

The North ◽

Hypervariable Regions ◽

The North Sea ◽

Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point into the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

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A century of change in North Sea plankton communities explored through integrating historical datasets

ICES Journal of Marine Science ◽

10.1093/icesjms/fsy148 ◽

2018 ◽

Vol 76 (1) ◽

pp. 104-112 ◽

Cited By ~ 1

Author(s):

Jacob Bedford ◽

David Johns ◽

Abigail McQuatters-Gollop

Keyword(s):

Community Composition ◽

North Sea ◽

Large Scale ◽

Plankton Community ◽

Temporal Scale ◽

Series Data ◽

The North ◽

Time Period ◽

The North Sea ◽

Plankton Communities

Abstract Plankton communities make useful ecosystem indicators, and taking a historical perspective on plankton community composition provides insights into large-scale environmental change. Much of our understanding of long temporal-scale change in plankton communities in the North Sea has been provided by the Continuous Plankton Recorder (CPR) survey, operating since 1931, with consistent time-series data available since 1958. This article further increases the temporal scale of our understanding of community change in the North Sea by combining the CPR dataset with a digitized collection of plankton surveys undertaken by ICES from 1902 to 1912. After steps taken to integrate the two disparate datasets, differences in overall community composition between time periods suggest that the multidecadal changes observed through the CPR survey time period may have occurred from a non-stable baseline that was already on a trajectory of change. Therefore, a stable historical time period in which plankton communities are assessed against for any impact of human pressures may be hard to define for the North Sea and instead underlying variation needs to be encompassed within any baseline chosen. Further evidence for the influence of large-scale changes in sea surface temperature driving change in plankton community composition was found using the extended dataset.

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Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting

10.1101/2021.05.05.442872 ◽

2021 ◽

Author(s):

Jasmine Heyse ◽

Florian Schattenberg ◽

Peter Rubbens ◽

Susann Müller ◽

Willem Waegeman ◽

...

Keyword(s):

Flow Cytometry ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Time Series Data ◽

Temporal Dynamics ◽

Marker Gene ◽

Amplicon Sequencing ◽

Series Data ◽

Rrna Gene

Microbiome management research and applications rely on temporally-resolved measurements of community composition. Current technologies to assess community composition either make use of cultivation or sequencing of genomic material, which can become time consuming and/or laborious in case high-throughput measurements are required. Here, using data from a shrimp hatchery as an economically relevant case study, we combined 16S rRNA gene amplicon sequencing and flow cytometry data to develop a computational workflow that allows the prediction of taxon abundances based on flow cytometry measurements. The first stage of our pipeline consists of a classifier to predict the presence or absence of the taxon of interest, with yields an average accuracy of 88.13±4.78 % across the top 50 OTUs of our dataset. In the second stage, this classifier was combined with a regression model to predict the relative abundances of the taxon of interest, which yields an average R2 of 0.35±0.24 across the top 50 OTUs of our dataset. Application of the models on flow cytometry time series data showed that the generated models can predict the temporal dynamics of a large fraction of the investigated taxa. Using cell-sorting we validated that the model correctly associates taxa to regions in the cytometric fingerprint where they are detected using 16S rRNA gene amplicon sequencing. Finally, we applied the approach of our pipeline on two other datasets of microbial ecosystems. This pipeline represents an addition to the expanding toolbox for flow cytometry-based monitoring of bacterial communities and complements the current plating- and marker gene-based methods.

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Phosphorus and land-use changes are significant drivers of cladoceran community composition and diversity: an analysis over spatial and temporal scales

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f10-058 ◽

2010 ◽

Vol 67 (8) ◽

pp. 1262-1273 ◽

Cited By ~ 11

Author(s):

Marc Richard Albert ◽

Guangjie Chen ◽

Graham K. MacDonald ◽

Jesse C. Vermaire ◽

Elena M. Bennett ◽

...

Keyword(s):

Land Use ◽

Community Composition ◽

Time Series Data ◽

Temporal Analysis ◽

Phosphorus Loading ◽

Series Data ◽

Phosphorus Concentration ◽

Total Phosphorus Concentration ◽

Watershed Disturbance ◽

Subfossil Cladoceran

We conducted paleolimnological studies over spatial and temporal gradients to define the responses of subfossil cladoceran community composition and diversity to changes in land use and phosphorus concentrations in shallow lakes. We predicted that watershed disturbance by humans, through its impact on water quality, would explain significant variation in cladoceran diversity and composition. Across lakes, water-column total phosphorus concentration was a significant (p < 0.05) predictor of the subfossil cladoceran community composition. Chydorid diversity was also found to be related significantly to phosphorus concentration (r = –0.55, p < 0.05) and the proportion of disturbed land in the watershed (r = –0.47, p < 0.05). However, net load of phosphorus to the watershed rather than proportion of watershed disturbance was a significant predictor of chydorid diversity (r = –0.86, p < 0.001) in our temporal analysis of an eutrophying lake. Given that phosphorus loading to surface waters is often related to phosphorus concentrations in soils, we suggest that the net phosphorus load to the watershed is a more sensitive metric of land-use change and necessary for detecting ecological responses in time series data.

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Moderate-Intensity Physical Exercise Affects the Exercise Performance and Gut Microbiota of Mice

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.712381 ◽

2021 ◽

Vol 11 ◽

Author(s):

Wenqian Yang ◽

Yuqian Liu ◽

Guang Yang ◽

Binglin Meng ◽

Zhicheng Yi ◽

...

Keyword(s):

Gut Microbiota ◽

Exercise Performance ◽

Exercise Intervention ◽

Time Series Data ◽

Shannon Index ◽

Series Data ◽

Moderate Intensity ◽

Rrna Gene ◽

Exercise Tests ◽

Significant Difference

The gut microbiota is closely associated with the health of the host and is affected by many factors, including exercise. In this study, we compared the gut microbial changes and exercise performance over a 14-week period in mice that performed exercise (NE; n = 15) and mice that did not perform exercise (NC; n = 15). Mice were subjected to stool collection and exercise tests one week prior to adaptive training and after 2, 6, 10, and 14 weeks of exercise. Bacteria associated with the stool samples were assessed via Illumina-based 16S rRNA gene sequencing. While there was no significant difference in body weight between the groups (p > 0.05), the NE group had a significantly higher exercise performance from weeks 2–14 (p < 0.01) and lower fat coefficient (p < 0.01) compared with the NC group. The Shannon index of the gut microbiota in the NC group was higher than that in the NE group at weeks 6 and 10, and the Chao1 index was higher than that in the NE group at week 14. Exercise performance positively correlated with the relative abundance of Phascolarctobacterium. Grouped time series data analysis demonstrated that Bifidobacteria, Coprococcus, and one unnamed genus in the Clostridiales order were significantly increased in the NE group, which correlated with increased glucose, flavonoid, arginine, and proline metabolism. In conclusion, moderate-intensity treadmill exercise significantly increased the exercise performance of mice and changed the core bacteria and bacterial metabolic activity. These results provide a reference for studying the effects of exercise intervention and exercise performance on the gut microbiota of mice.

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Phylogeny and Synonymy of Gyrodinium heterostriatum comb. nov. (Dinophyceae), a Common Unarmored Dinoflagellate in the World Oceans [plus supplementary materials]

Acta Protozoologica ◽

10.4467/16890027ap.20.007.12675 ◽

2020 ◽

Vol 59 (2) ◽

pp. 77-87

Author(s):

Fernando Gómez ◽

Luis F. Artigas ◽

Rebecca J. Gast

Keyword(s):

North Sea ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Morphological Plasticity ◽

Sister Group ◽

Rrna Gene ◽

Microbial World ◽

The North ◽

The North Sea ◽

Environmental Sequences

The North Sea and the English Channel are regions with a long tradition of plankton studies, where the colony-forming haptophyte Phaeocystis globosa dominates the spring phytoplankton blooms. Among its predators, we investigated an abundant unarmored dinoflagellate (~3000 cells per liter) in the North Sea in May 2019. It has been reported in the literature as Gymnodinium heterostriatum or G. striatissimum, and often identified as Gyrodinium spirale. Phylogenetic analyses using the small-, large subunit- and Internal Transcriber Spacers of the ribosomal RNA (SSU-, LSU-, ITS rRNA) gene sequences indicate that our isolates clustered within the Gyrodinium clade. The new sequences formed a sister group with sequences of the freshwater taxon Gyrodinium helveticum, being one of the infrequent marine-freshwater transitions in the microbial world. This isolate is the first characterized member of a clade of numerous environmental sequences widely distributed from cold to tropical seas. This common and abundant taxon has received several names due to its morphological plasticity (changes of size and shape, often deformed after engulfing prey) and the difficulty in discerning surface striation. We conclude that the priority is for the species name Gymnodinium heterostriatum Kofoid & Swezy 1921, a new name that was proposed for Gymnodinium spirale var. obtusum sensu Dogiel 1906. The species Gyrodinium striatissimum (Hulburt 1957) Gert Hansen & Moestrup 2000 and Gymnodinium lucidum D. Ballantine in Parke & Dixon 1964 (=G. hyalinum M. Lebour 1925) are posterior synonyms. We propose Gyrodinium heterostriatum comb. nov. for Gymnodinium heterostriatum.

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Parameter uncertainty of a dynamic multispecies size spectrum model

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0022 ◽

2016 ◽

Vol 73 (4) ◽

pp. 589-597 ◽

Cited By ~ 14

Author(s):

Michael A. Spence ◽

Paul G. Blackwell ◽

Julia L. Blanchard

Keyword(s):

Time Series ◽

Time Series Data ◽

Size Structure ◽

Management Strategies ◽

Optimization Methods ◽

Series Data ◽

Size Spectrum ◽

Aquatic Communities ◽

The North ◽

Spectrum Model

Dynamic size spectrum models have been recognized as an effective way of describing how size-based interactions can give rise to the size structure of aquatic communities. They are intermediate-complexity ecological models that are solutions to partial differential equations driven by the size-dependent processes of predation, growth, mortality, and reproduction in a community of interacting species and sizes. To be useful for quantitative fisheries management these models need to be developed further in a formal statistical framework. Previous work has used time-averaged data to “calibrate” the model using optimization methods with the disadvantage of losing detailed time-series information. Using a published multispecies size spectrum model parameterized for the North Sea comprising 12 interacting fish species and a background resource, we fit the model to time-series data using a Bayesian framework for the first time. We capture the 1967–2010 period using annual estimates of fishing mortality rates as input to the model and time series of fisheries landings data to fit the model to output. We estimate 38 key parameters representing the carrying capacity of each species and background resource, as well as initial inputs of the dynamical system and errors on the model output. We then forecast the model forward to evaluate how uncertainty propagates through to population- and community-level indicators under alternative management strategies.

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Municipal changes in Slovakia. The evidence from spatial data.

European Journal of Geography ◽

10.48088/ejg.m.mar.11.1.58.72 ◽

2020 ◽

Vol 11 (1) ◽

pp. 58-72

Author(s):

Martin MARIS

Keyword(s):

Spatial Data ◽

Time Series Data ◽

Population Sample ◽

Series Data ◽

Annual Growth Rate ◽

The West ◽

Compound Annual Growth Rate ◽

Fast Growing ◽

The North ◽

Statistical Criteria

The main objective of the paper is to examine the evolution of spatial patterns of settlement network in Slovakia as a result of population rearrangement among municipalities based on time series data of 1993 - 2017. The objects of the research are municipalities, which during the searched period recorded unusual fast population growth or decline, far exceeding the chosen parameter of the population sample. The primary population sample consists of 2919 municipalities. The experimental samples consist of 563 of fast-growing municipalities and 413 of fast-declining municipalities, based on the chosen statistical criteria, what is the compound annual growth rate. The results have shown that fast-growing municipalities are predominantly situated on the West, surrounding the Bratislava agglomeration, on the North and the East surrounding the Kosice metropolis. Generally, they tend to cluster around the cities on the district and regional levels. Fast-declining municipalities predominantly situated in the Middle, along the Hungarian, Polish, and Ukrainian border on the South and the East of the country, respectively.

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