Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer

Abstract. During the MALINA cruise (summer 2009) an extensive effort was undertaken to isolate phytoplankton strains from the North East (NE) Pacific Ocean, the Bering Strait, and the Beaufort Sea. Strains were isolated by flow cytometry sorting (FCS) and pipetting before or after phytoplankton enrichment of seawater samples. Strains were isolated both onboard and back in the laboratory and cultured at 4 °C under light/dark conditions. Overall, we isolated and characterised by light microscopy and 18S rRNA gene sequencing 104 strains of photosynthetic flagellates which grouped into 21 genotypes (defined by 99.5% 18S rRNA gene sequence similarity) mainly affiliated to Chlorophyta and Heterokontophyta. The taxon most frequently isolated was an Arctic ecotype of the green algal genus Micromonas (Arctic Micromonas) which was almost the only phytoplankter recovered within picoplankton (≤ 2 μm) size range. Strains of Arctic Micromonas as well as three unidentified strains related to the same genus were identified in further details by sequencing the Internal Transcribed Spacer (ITS) region of the rRNA operon. The MALINA Micromonas strains share identical 18S rRNA and ITS sequences suggesting high genetic homogeneity within Arctic Micromonas. The unidentified strains form a genotype likely belonging to a new genus within the family Mamiellaceae to which Micromonas belongs. Other green algae genotypes from the genera Nephroselmis, Chlamydomonas, Pyramimonas were also isolated whereas Heterokontophyta included Pelagophyceae, Dictyochophyceae and Chrysophyceae. Dictyochophyceae included Pedinellales which could not be identified to the genus level whereas Chrysophyceae comprised Dinobryon faculiferum. Moreover, we isolated Rhodomonas sp. as well as a few Haptophyta and dinoflagellates. We identified the dinoflagellate Woloszynskia cincta by Scanning Electron Microscopy (SEM) and 28S rRNA gene sequencing. Our morphological analyses show that this species possess the diagnostic features of the genus Biecheleria, and the 28S rRNA gene topology corroborates this affiliation. We thus propose the transfer of W. cincta to the genus Biecheleria and its recombination as Biecheleria cincta.

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Eukaryotic Community in UASB Reactor Treating Domestic Sewage Based on 18S rRNA Gene Sequencing

Lecture Notes in Civil Engineering - Frontiers in Wastewater Treatment and Modelling ◽

10.1007/978-3-319-58421-8_34 ◽

2017 ◽

pp. 218-224 ◽

Cited By ~ 2

Author(s):

Y. Hirakata ◽

M. Hatamoto ◽

M. Oshiki ◽

N. Araki ◽

T. Yamaguchi

Keyword(s):

18S Rrna ◽

Gene Sequencing ◽

18S Rrna Gene ◽

Domestic Sewage ◽

Uasb Reactor ◽

Rrna Gene ◽

Eukaryotic Community ◽

Rrna Gene Sequencing

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Ecological assessment of phytoplankton community via microscopic method and 18S rRNA gene sequencing in Pearl River Estuary

E3S Web of Conferences ◽

10.1051/e3sconf/201913101043 ◽

2019 ◽

Vol 131 ◽

pp. 01043 ◽

Cited By ~ 1

Author(s):

Bo Peng ◽

Yuannan Wang ◽

Hengjun Zhang ◽

Chen Chen ◽

Hailin Luo ◽

...

Keyword(s):

18S Rrna ◽

Phytoplankton Community ◽

Diversity Index ◽

River Estuary ◽

Gene Sequencing ◽

Pearl River Estuary ◽

Ecological Assessment ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequencing

Monitoring phytoplankton community underpins our understanding of water quality and ecological functions. In this study, we approached phytoplankton abundance, community composition, and diversity by both microscopy and 18S rRNA gene sequencing. Environmental variances influencing the phytoplankton were evaluated as well. There were 6 phyla and 62 species identified by microscopy, and the diversity index Shannon-Wiener and evenness index Pielou index indicated phytoplankton community had high diversity; however, the high density of dominance genus suggested that our research region had potential red tide effects. The canonical correspondence analysis illustrated that suspended solids, phosphate and temperature were three major factors that affected the distribution and components of phytoplankton community. The DNA barcoding sequencing of 18S rRNA gene supported the main results via microscopic methods while providing more identified community components, which implied that 18S rRNA gene sequencing can be used as a supplemental method for fast ecological assessment of phytoplankton community.

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Association between diet and rumen microbiota in wild roe deer

FEMS Microbiology Letters ◽

10.1093/femsle/fnz060 ◽

2019 ◽

Vol 366 (6) ◽

Cited By ~ 1

Author(s):

Robert Wilson ◽

Kjartan Østbye ◽

Inga Leena Angell ◽

Knut Rudi

Keyword(s):

18S Rrna ◽

Roe Deer ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rumen Microbiota ◽

Dietary Components ◽

Rrna Gene Sequencing ◽

Insight Into

ABSTRACT The association between diet and the rumen microbiota for wild animals remains largely unexplored. Here, we explored this association using a combination of 16S rRNA gene sequencing to determine the prokaryote microbiota and 18S rRNA gene sequencing to determine the dietary components for wild roe deer. These analyses revealed a wide diversity of dietary components, with over-representation of Bacteroidetes for the diet-correlating bacteria. Ruminococcus, on the other hand, dominated the stable diet-independent part of the microbiota. Taken together, the combination of 16S and 18S rRNA gene analyses provide novel insight into rumen microbiota ecology.

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Diversity and distribution of nematodes associated with terrestrial slugs in the Western Cape Province of South Africa

Journal of Helminthology ◽

10.1017/s0022149x11000277 ◽

2011 ◽

Vol 86 (2) ◽

pp. 215-221 ◽

Cited By ~ 16

Author(s):

J.L. Ross ◽

E.S. Ivanova ◽

W.F. Sirgel ◽

A.P. Malan ◽

M.J. Wilson

Keyword(s):

South Africa ◽

18S Rrna ◽

Parasitic Nematode ◽

Gene Sequencing ◽

18S Rrna Gene ◽

Rrna Gene ◽

Western Cape ◽

Western Cape Province ◽

Rrna Gene Sequencing ◽

Three New Species

AbstractA survey of nematodes associated with native and introduced species of terrestrial slugs was conducted in the Western Cape Province of South Africa, in order to gather new data regarding diversity and distribution. A total of 521 terrestrial slugs were collected from 35 localities throughout the Western Cape. All slugs were dissected and examined for the presence of internal nematodes. Extracted nematodes were identified using a combination of molecular (18S rRNA gene sequencing) and morphological techniques. Nematodes were found parasitizing slugs at 14 of the 35 sites examined, amounting to 40% of sample sites. Of all slugs, 6% were infected with nematodes. A total of seven species of nematode were identified in the province, includingAgfa flexilis,Angiostomasp.,Phasmarhabditissp. SA1,Phasmarhabditissp. SA2,Caenorhabditis elegans,Panagrolaimussp. andRhabditissp. Of these species, four were thought to be parasitic to slugs (A. flexilis, Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2), as opposed to forming necromenic or phoretic associations. Three new species of slug-parasitic nematode were identified during this study (Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2).

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18S rRNA gene sequencing identifies a novel species of Henneguya parasitizing the gills of the channel catfish (Ictaluridae)

Parasitology Research ◽

10.1007/s00436-014-4156-6 ◽

2014 ◽

Vol 113 (12) ◽

pp. 4651-4658 ◽

Cited By ~ 11

Author(s):

Thomas G. Rosser ◽

Matt J. Griffin ◽

Sylvie M. A. Quiniou ◽

Lester H. Khoo ◽

Linda M. Pote

Keyword(s):

Channel Catfish ◽

18S Rrna ◽

Novel Species ◽

Gene Sequencing ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequencing

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Sequencing and Analysis of Fungal rRNA Operons for Development of Broad-Range Fungal PCR Assays

Applied and Environmental Microbiology ◽

10.1128/aem.02383-08 ◽

2009 ◽

Vol 75 (6) ◽

pp. 1559-1565 ◽

Cited By ~ 52

Author(s):

Prasanna D. Khot ◽

Daisy L. Ko ◽

David N. Fredricks

Keyword(s):

Fungal Pathogens ◽

18S Rrna ◽

18S Rrna Gene ◽

Internal Transcribed Spacers ◽

Rrna Gene ◽

28S Rrna ◽

28S Rrna Gene ◽

Fungal Dna ◽

Pcr Assays ◽

Distance Matrices

ABSTRACT rRNA genes are attractive targets for developing PCR assays targeting human fungal pathogens. Most studies have focused on the 18S rRNA gene, internal transcribed spacers, and the 5′ end of the 28S rRNA gene. An approximately 2,900-bp region of the 28S rRNA gene remains largely unexplored because sequences of many medically relevant fungi are either unavailable or undefined in genomic databases. The internal transcribed spacers and 28S rRNA gene of nine medically and phylogenetically important fungi were sequenced. In addition, 42 sequences from this region were acquired from public databases, resulting in an alignment of 51 fungal sequences spanning 30 fungal genera. For the nearly 3,950-bp region from the 3′ end of 18S rRNA gene to the 3′ end of the 28S rRNA gene, 27 broad-range PCR primers were designed such that their sequence homology with the human rRNA gene was minimal. All 62 possible amplicons in the size range from 75 to 400 bp from 27 primers were screened using fungal genomic DNA from 26 species spanning 14 genera. Eleven of the 62 amplicons did not cross-react with 1 μg/PCR human DNA but simultaneously amplified 10 fg of fungal DNA. Phylogenetic distance matrices were calculated for regions covered by these 11 amplicons based on 51 fungi. Two of these 11 amplicons successfully amplified 30 fg of fungal DNA from 25 of 26 fungi and provided the most phylogenetic information for species identification based on the distance matrices. These PCR assays hold promise for detection and identification of fungal pathogens in human tissues.

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