Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples — first record of Gammarus fossarum in the UK

Abstract. Within the context of the UK Ocean Acidification project, Emiliania huxleyi (type A) coccolith morphology was examined from samples collected during cruise D366. In particular, a morphometric study of coccolith size and degree of calcification was made on scanning electron microscope images of samples from shipboard CO2 perturbation experiments and from a set of environmental samples with significant variation in calcite saturation state (Ωcalcite). One bioassay in particular (E4 from the southern North Sea) yielded unambiguous results – in this bioassay exponential growth from a low level occurred with no artificial stimulation and coccosphere numbers increased ten-fold during the experiment. The samples with elevated CO2 saw significantly reduced coccolithophore growth. However, coccolithophore morphology was not significantly affected by the changing CO2 conditions even under the highest levels of perturbation (1000 μatm). Environmental samples similarly showed no correlation of coccolithophore morphology with calcite saturation state. Some variation in coccolith size and degree of calcification does occur but this seems to be predominantly due to genotypic differentiation between populations on the shelf and in the open ocean.

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PIMBA: a PIpeline for MetaBarcoding Analysis

10.1101/2021.03.23.436646 ◽

2021 ◽

Author(s):

Renato R. M. Oliveira ◽

Raissa L S Silva ◽

Gisele L. Nunes ◽

Guilherme Oliveira

Keyword(s):

Environmental Samples ◽

Next Generation Sequencing Data ◽

Ecological Studies ◽

Sequencing Data ◽

Monitoring Method ◽

Computational Tools ◽

Dna Metabarcoding ◽

Reference Databases ◽

User Friendly ◽

Generation Sequencing

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, and mBRAVE have been widely used in ecological studies. However, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the softwares mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines.

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First record of Neoxysomatium brevicaudatum through the non-invasive sampling of Anguis fragilis: complementary morphological and molecular detection

Journal of Helminthology ◽

10.1017/s0022149x11000174 ◽

2011 ◽

Vol 86 (1) ◽

pp. 125-129 ◽

Cited By ~ 7

Author(s):

R. Jones ◽

D.S. Brown ◽

E. Harris ◽

J. Jones ◽

W.O.C. Symondson ◽

...

Keyword(s):

Mitochondrial Gene ◽

Nematode Species ◽

First Record ◽

Parasite Fauna ◽

Ribosomal Gene ◽

Morphological Identification ◽

Morphological Examination ◽

Mean Intensity ◽

Anguis Fragilis ◽

The Uk

AbstractRelatively few studies have examined the parasite fauna of British reptiles, partly due to the cryptic nature and low population density of these hosts. Here we examined 12 populations of the slow worm Anguis fragilis which, unlike other UK lizards, occurs at locally high population densities. Morphological examination of non-invasively collected faecal samples revealed the presence of Neoxysomatium brevicaudatum and a second unidentified nematode species. Although previously unrecorded from slow worms in the UK, N. brevicaudatum was present in 38% of animals (mean intensity 70.9, range 1–686). Morphological identification was confirmed by sequencing the 18S ribosomal gene. The use of the species-specific, cytochrome oxidase I mitochondrial gene primers proved an efficient alternative to conventional, microscope screening for parasites, although the original identification of N. brevicaudatum was dependent upon morphological characters. Sequencing also identified the second, smaller nematode as belonging to the Rhabdiasidae family: this species was even more common at a prevalence of 83% (mean intensity 102.8, range 1–2000). While increasing our knowledge of the UK macroparasite fauna, this work demonstrates the benefits of a combined morphological–molecular approach.

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First record of Cylindrocladium pauciramosum on Ceanothus in the UK

Plant Pathology ◽

10.1111/j.1365-3059.2006.01363.x ◽

2006 ◽

Vol 55 (4) ◽

pp. 582-582 ◽

Cited By ~ 6

Author(s):

C. R. Lane ◽

P. A. Beales ◽

B. Henricot ◽

A. Holden

Keyword(s):

First Record ◽

The Uk

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Taxonomic identification of airborne pollen from complex environmental samples by DNA metabarcoding: a methodological study for optimizing protocols

10.1101/099481 ◽

2017 ◽

Cited By ~ 1

Author(s):

Kleopatra Leontidou ◽

Cristiano Vernesi ◽

Johannes De Groeve ◽

Fabiana Cristofolini ◽

Despoina Vokou ◽

...

Keyword(s):

Sample Preparation ◽

Chloroplast Dna ◽

Dna Extraction ◽

Environmental Samples ◽

Airborne Pollen ◽

Reference Database ◽

Taxonomic Assignment ◽

Spore Trap ◽

Custom Made ◽

Dna Metabarcoding

AbstractMetabarcoding is a promising DNA-based method for identifying airborne pollen from environmental samples with advantages over microscopic methods. This method requires several preparatory steps of the samples, with the extraction protocol being of fundamental importance to obtain an optimal DNA yield. Currently, there is no consensus in sample preparation and DNA extraction, especially for gravimetric pollen samplers. Therefore, the aim of this study was to develop protocols to process environmental samples for pollen DNA extraction and further metabarcoding analysis, and to assess the efficacy of these protocols for the taxonomic assignment of airborne pollen, collected by gravimetric (Tauber trap) and volumetric samplers (Burkard spore trap). Protocols were tested across an increasing complexity of samples, from single-species pure pollen to environmental samples. A short fragment (about 150 base pair) of chloroplast DNA was amplified by universal primers for plants (trnL). After PCR amplification, amplicons were Sanger-sequenced and taxonomic assignment was accomplished by comparison to a custom-made reference database including chloroplast DNA sequences of 46 plant families, including most of the anemophilous taxa occurring in the study area (Trentino, Italy, Eastern Italian Alps). Using as a benchmark the classical morphological pollen analysis, it emerged that DNA metabarcoding is applicable efficiently across a complexity of samples, provided that sample preparation, DNA extraction and amplification protocols are specifically optimized.

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First record of downy mildew, caused byPeronospora belbahrii, onSolenostemon scutellarioidesin the UK

New Disease Reports ◽

10.5197/j.2044-0588.2015.031.014 ◽

2015 ◽

Vol 31 ◽

pp. 14 ◽

Cited By ~ 5

Author(s):

G.J. Denton ◽

E. Beal ◽

J.O. Denton ◽

G. Clover

Keyword(s):

Downy Mildew ◽

First Record ◽

The Uk

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First record of verticillium wilt (Verticillium longisporum) in winter oilseed rape in the UK

New Disease Reports ◽

10.5197/j.2044-0588.2011.023.008 ◽

2011 ◽

Vol 23 ◽

pp. 8 ◽

Cited By ~ 13

Author(s):

P. Gladders ◽

J.A. Smith ◽

L. Kirkpatrick ◽

E. Clewes ◽

C. Grant ◽

...

Keyword(s):

Oilseed Rape ◽

Verticillium Wilt ◽

First Record ◽

Winter Oilseed Rape ◽

Verticillium Longisporum ◽

The Uk

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New palaeodictyopterans from the Late Carboniferous of the UK (Insecta: Palaeodictyopterida)

Earth and Environmental Science Transactions of the Royal Society of Edinburgh ◽

10.1017/s1755691017000408 ◽

2016 ◽

Vol 107 (2-3) ◽

pp. 99-107 ◽

Cited By ~ 2

Author(s):

Jakub Prokop ◽

Martina Pecharová ◽

Edmund A. Jarzembowski ◽

Andrew J. Ross

Keyword(s):

Abdominal Segment ◽

First Record ◽

Late Carboniferous ◽

The Uk ◽

Tracheal Gills

ABSTRACTNew palaeodictyopterans, Vernooijia sassoonae gen. et sp. nov. (Breyeriidae) and Mazonopterumcooperi sp. nov. (Homoiopteridae) are described from the Middle Pennsylvanian (Westphalian D/Late Asturian) of Writhlington, near Radstock (UK). Based on the re-examination of venation in Breyeriaharlemensis, we propose the transfer of this species to the genus Vernooijia as V.harlemensis (Brauckmann & Gröning, 1996) comb. nov. We report the first record of Homaloneura sp. (Spilapteridae) from the Langsettian to Duckmantian of Coseley, Staffordshire. Additionally, we report a fragmentary wing from the Middle Pennsylvanian (late Westphalian D/early Cantabrian) of the Forest of Dean, Gloucestershire, tentatively belonging to the Lycocercidae. Our re-examination of a putative blattodean nymph described by Rolfe (1967) allows re-assignment to Palaeodictyoptera, as it has well-developed wing pads with a corrugated pattern of probably original tracheation and lacunal channels, identified as presumably nymphal exuvia of Idoptilus sp. Surprisingly, our study reveals the presence of three triangular caudal appendages bearing prominent lateral lamellae emerging from the terminal abdominal segment, previously unknown in other nymphs of Palaeodictyoptera. We assume that these lamellae were originally covered with dense setae and possibly represent modified caudal appendages in the form of tracheal gills, as known in the nymphs of damselflies (Odonata: Zygoptera). Thus, the scenario of a possible aquatic lifestyle for nymphs of at least some members of Palaeodictyoptera, as considered by Brongniart (1885, 1893) and Handlirsch (1906), cannot be definitely excluded.

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First record of the fungus Blumeriella kerriae in the UK

New Disease Reports ◽

10.5197/j.2044-0588.2017.035.034 ◽

2017 ◽

Vol 35 ◽

pp. 34

Author(s):

R.J. Robinson ◽

K. Könyves ◽

J. Scrace

Keyword(s):

First Record ◽

The Uk

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The Blattodea (cockroaches), Mantodea (praying mantises) and Dermaptera (earwigs) of the Insect Limestone (late Eocene), Isle of Wight, including the first record of Mantodea from the UK

Earth and Environmental Science Transactions of the Royal Society of Edinburgh ◽

10.1017/s1755691018000440 ◽

2019 ◽

Vol 110 (3-4) ◽

pp. 301-311 ◽

Cited By ~ 2

Author(s):

Andrew J. ROSS

Keyword(s):

New Species ◽

First Record ◽

Late Eocene ◽

Praying Mantis ◽

Isle Of Wight ◽

Southern England ◽

The Family ◽

Three New Species ◽

The Uk

ABSTRACTThe fossil cockroaches (Blattodea), praying mantises (Mantodea) and earwigs (Demaptera) are described from the Insect Limestone (Priabonian) of the Isle of Wight, southern England. Three new species of cockroach are described in the family Ectobiidae – Phyllodromica protosardea sp. nov., Balta protosimilis sp. nov. and Malaccina? wightensis sp. nov. – and a further nine indeterminate species are presented (based on ten specimens). The only known specimen of praying mantis is described as Protohierodula crabbi gen. et sp. nov. in the family Manteidae, which constitutes the first record of Mantodea from the UK. The only known specimen of earwig is an incomplete juvenile belonging to the superfamily Forficuloidea.

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