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

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

Applied and Environmental Microbiology ◽

10.1128/aem.01271-08 ◽

2008 ◽

Vol 74 (17) ◽

pp. 5305-5316 ◽

Cited By ~ 33

Author(s):

Christine Gescher ◽

Katja Metfies ◽

Stephan Frickenhaus ◽

Britta Knefelkamp ◽

Karen H. Wiltshire ◽

...

Keyword(s):

Community Composition ◽

Dna Microarrays ◽

Time Series Data ◽

Sampling Site ◽

18S Rrna Gene ◽

Series Data ◽

Rrna Gene ◽

The North ◽

Algal Group ◽

The North Sea

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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Constitutive Expression of the Proteorhodopsin Gene by a Flavobacterium Strain Representative of the Proteorhodopsin-Producing Microbial Community in the North Sea

Applied and Environmental Microbiology ◽

10.1128/aem.02971-09 ◽

2010 ◽

Vol 76 (10) ◽

pp. 3187-3197 ◽

Cited By ~ 39

Author(s):

Thomas Riedel ◽

Jürgen Tomasch ◽

Ina Buchholz ◽

Jenny Jacobs ◽

Mario Kollenberg ◽

...

Keyword(s):

Water Sample ◽

North Sea ◽

Sea Water ◽

Constitutive Expression ◽

Physiological Role ◽

Rrna Gene ◽

Bacterial Strains ◽

Degenerate Primers ◽

The North ◽

The North Sea

ABSTRACT Proteorhodopsin (PR), a photoactive proton pump containing retinal, is present in approximately half of all bacteria in the ocean, but its physiological role is still unclear, since very few strains carrying the PR gene have been cultured. The aim of this work was to characterize PR diversity in a North Sea water sample, cultivate a strain representative of North Sea PR clusters, and study the effects of light and carbon concentration on the expression of the PR gene. A total of 117 PR sequences, of which 101 were unique, were obtained from a clone library of PCR-amplified PR gene fragments. Of the North Sea PRs, 97% were green light absorbing, as inferred from the amino acid at position 105; 67% of the PR protein fragments showed closest similarity to PRs from Alphaproteobacteria, 4% showed closest similarity to PRs from Gammaproteobacteria, and 29% showed closest similarity to PRs from “Bacteroidetes”/Flavobacteria. The dominant PR cluster (comprising 18% of all PRs) showed a high degree of similarity to the PR from the cultivated Roseobacter strain HTCC2255. The relative abundances of the North Sea PR clusters were confirmed by quantitative PCR. They were detected in metagenomic fragments from coastal oceans worldwide with various degrees of abundance. Several hundred bacterial strains from the North Sea water sample were cultivated on oligocarbophilic media. By screening with degenerate primers, two strains carrying the PR gene were identified. Their 16S rRNA gene sequences were identical and affiliated with a Bacteroidetes subcluster from the North Sea. The PR sequence of isolate PRO95 was completed by chromosomal walking. It was 76% identical to that of Dokdonia donghaensis MED134 and was functional, as indicated by the signature amino acids. PRO95 expressed its PR gene in liquid media containing between 9.7 and 121 mM carbon, both in the light and in the dark. Growth was not enhanced by light. Thus, the detection of the physiological role of PR may require more sensitive methods.

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