18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York

Characterising and monitoring biological diversity to foster sustainable ecosystems is highly recommended as urban centres rapidly expand. However, much of New York City’s biodiversity remains undescribed, including in the historically degraded, but recovering Bronx River Estuary. In a pilot study to identify organisms and characterise biodiversity patterns there, 18S rRNA gene amplicons (V1–V3 region), obtained from river sediments and surface waters of Hunts Point Riverside and Soundview Parks, were sequenced. Across 48 environmental samples collected over three seasons in 2015 and 2016, following quality control and contaminant removal, 2,763 Amplicon Sequence Variants (ASVs) were identified from 1,918,463 sequences. Rarefaction analysis showed sufficient sampling depth, and community composition varied over time and by substrate at the study sites over the sampling period. Protists, plants, fungi and animals, including organisms of management concern, such as Eastern oysters (Crassostrea virginica), wildlife pathogens and groups related to Harmful Algal Blooms, were detected. The most common taxa identified in river sediments were annelid worms, nematodes and diatoms. In the water column, the most commonly observed organisms were diatoms, algae of the phylum Cryptophyceae, ciliates and dinoflagellates. The presented dataset demonstrates the reach of 18S rRNA metabarcoding for characterising biodiversity in an urban estuary.

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16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary

Microbiology Resource Announcements ◽

10.1128/mra.00182-20 ◽

2020 ◽

Vol 9 (22) ◽

Author(s):

Eugenia Naro-Maciel ◽

Melissa R. Ingala ◽

Irena E. Werner ◽

Allison M. Fitzgerald

Keyword(s):

New York ◽

16S Rrna ◽

River Estuary ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequence Variants ◽

Biodiversity Monitoring ◽

South Bronx ◽

16S Rrna Amplicon Sequencing ◽

Bronx River

ABSTRACT Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 508,352 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

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Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽

10.1017/s0031182013001960 ◽

2013 ◽

Vol 141 (5) ◽

pp. 646-651 ◽

Cited By ~ 9

Author(s):

GASTÓN MORÉ ◽

NIKOLA PANTCHEV ◽

DALAND C. HERRMANN ◽

MAJDA GLOBOKAR VRHOVEC ◽

SABINE ÖFNER ◽

...

Keyword(s):

18S Rrna ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Genes ◽

Rrna Gene ◽

Intermediate Hosts ◽

Apicomplexan Parasites ◽

Large Numbers ◽

Wide Range ◽

18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

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Morphological and molecular characterization of Mermisnigrescens Dujardin, (Nematoda: Mermithidae) parasitizing the introduced European earwig (Dermaptera: Forficulidae) in New Zealand

Journal of Helminthology ◽

10.1017/s0022149x14000017 ◽

2014 ◽

Vol 89 (3) ◽

pp. 267-276 ◽

Cited By ~ 7

Author(s):

B. Presswell ◽

S. Evans ◽

R. Poulin ◽

F. Jorge

Keyword(s):

New Zealand ◽

18S Rrna ◽

Sequence Data ◽

18S Rrna Gene ◽

Parasitic Nematodes ◽

Rrna Gene ◽

28S Rrna ◽

Forficula Auricularia ◽

Adult Females ◽

European Earwig

AbstractParasitic nematodes of the family Mermithidae were found to be infecting the introduced European earwig Forficula auricularia (Dermaptera: Forficulidae) in Dunedin, South Island, New Zealand. Adult females were later collected from various garden plants while depositing eggs. These mermithid specimens were identified morphologically as Mermis nigrescens Dujardin, 1842. A genetic distance of 0.7% between these specimens and a M. nigrescens isolate from Canada (18S rRNA gene), suggests that they have diverged genetically, but there are currently no available comparable sequences for the European M. nigrescens. Two additional nuclear fragments were also amplified, the 28S rRNA and the ribosomal DNA first internal transcribed spacer (ITS1), providing a basis for future studies. Bearing in mind the morphological similarity with other reported M. nigrescens and the lack of sequence data from other parts of the world, we retain the name M.nigrescens, and suggest that the species may be found to represent a complex of cryptic species when more worldwide data are available. Herein, we present a brief description of the post-parasitic worms and adult females, along with an inferred phylogeny using 18S rRNA gene sequences.

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Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2006.10.021 ◽

2007 ◽

Vol 43 (1) ◽

pp. 344-352 ◽

Cited By ~ 45

Author(s):

N.E. Redmond ◽

R.W.M. van Soest ◽

M. Kelly ◽

J. Raleigh ◽

S.A.A. Travers ◽

...

Keyword(s):

18S Rrna ◽

Gene Sequence ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequence Data

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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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A new species of planthopper from Costa Rica in the genus Oropuna from palms in lowland tropical rainforest

Zootaxa ◽

10.11646/zootaxa.5081.1.4 ◽

2021 ◽

Vol 5081 (1) ◽

pp. 116-130

Author(s):

BRIAN W. BAHDER ◽

MARCO A. ZUMBADO ECHAVARRIA ◽

EDWIN A. BARRANTES BARRANTES ◽

ERICKA E. HELMICK ◽

CHARLES R. BARTLETT

Keyword(s):

New Species ◽

Costa Rica ◽

18S Rrna ◽

Tropical Rainforest ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Gene ◽

The Novel ◽

Fourth Species ◽

A New Species

The derbid genus Oropuna is a small taxon of Neotropical planthoppers in the tribe Cenchreini comprised of three species. Recent survey work on palms for planthoppers in Costa Rica resulted in the discovery of a fourth species, Oropuna halo sp. n. In this study the new species is described and a key to the four species is provided along with sequence data for the cyctochrome c oxidase subunit I (COI) and 18S rRNA gene for the novel taxon.

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Description of Brooksia lacromae sp. nov. (Tunicata, Thaliacea) from the Adriatic Sea

European Journal of Taxonomy ◽

10.5852/ejt.2016.196 ◽

2016 ◽

Cited By ~ 1

Author(s):

Rade Garić ◽

Mirna Batistić

Keyword(s):

18S Rrna ◽

Adriatic Sea ◽

Sequence Data ◽

18S Rrna Gene ◽

Western Mediterranean ◽

Pairwise Distance ◽

Rrna Gene ◽

New Taxon ◽

Marine Monitoring ◽

Mediterranean Origin

Brooksia lacromae sp. nov. is described from zooplankton material collected at a marine monitoring station in the South Adriatic in the autumn of 2014. The description of both solitary and aggregate forms is given along with 18S rRNA and mitochondrial cox1 sequence data that provides strong evidence that both forms belong to the same species. The described species is morphologically markedly different from B. rostrata (Traustedt, 1893) and B. berneri van Soest, 1975, previously the only two species in the genus Brooksia. Genetic analysis based on 18S rRNA gene confirmed distinctness of B. lacromae sp. nov. from B. rostrata (1.5% uncorrected pairwise distance). The appendicularian Fritillaria helenae Bückmann, 1924, so far known from the Atlantic only, was found in the same samples as B. lacromae sp. nov. Co-occurrence of B. lacromae sp. nov. with an Atlantic appendicularian suggests an Atlantic or Western Mediterranean origin for this new taxon.

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Survey and Molecular Study of Babesia gibsoni in Dogs of Baghdad Province, Iraq

The Iraqi Journal of Veterinary Medicine ◽

10.30539/ijvm.v44i(e0).1019 ◽

2020 ◽

Vol 44 ((E0)) ◽

pp. 34-41

Author(s):

Naseir M. Badawi ◽

Afaf A. Yousif

Keyword(s):

Infection Rate ◽

18S Rrna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Clinical Signs ◽

Molecular Study ◽

18S Rrna Gene ◽

Universal Primers ◽

Rrna Gene ◽

Babesia Gibsoni

This study aimed to detect Babesia gibsoni (B. gibsoni) in dogs of different ages, sex and breeds in Baghdad province by microscopic and molecular investigations using polymerase chain reaction (PCR), sequencing, and phylogenetic analyses. The present study was investigated B. gibsoni in 310 blood samples of dogs for the period December 2018 to September 2019 in Baghdad province, Iraq. The molecular study was carried out by using universal primers of Babesia spp. (PIRO-A and PIRO-B) and specific primers of B. gibsoni (BAGIF and BAGIR) products size of 410 bp and 488 bp fragments of 18S rRNA gene respectively. The clinical signs revealed higher percentage and specific clinical signs of B. gibsoni as depression, anorexia, fever, pale mucus membrane, and ticks infestation, however icterus, and dead were low in which only occurred in two dogs out of infected dogs. The PCR assay and microscopic diagnosis revealed the infection rate of B. gibsoni 9 out of 310 (2.9%) in dogs. The sequence data analyses of nine DNA products were 98-100% similar to sequences of 18S rRNA gene of B. gibsoni data available in Gene bank. According to breed, age, and sex, the results revealed a significantly high-risk factor of infection in Husky dogs; B. gibsoni detected in females which was increased non-significantly than males; while the highest occurrence of disease was in young dogs aged three years or less in addition to the above, the infection rate of B. gibsoni was high in the spring season. In conclusion, this study was considered the first molecular record of B. gibsoni in Baghdad, Iraq documented no differences in diagnosis by blood smear and conventional PCR to amplify of 18S rRNA gene and partial sequencing of B. gibsoni with low-cost method and easily done.

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