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 t...

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Autores principales:	Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald, Eugenia Naro-Maciel
Formato:	article
Lenguaje:	EN
Publicado:	Pensoft Publishers 2021
Materias:	Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/e302ec4ac5b24d2a8dc0213bdef59a5a
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spelling	oai:doaj.org-article:e302ec4ac5b24d2a8dc0213bdef59a5a2021-12-02T15:13:57Z18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York10.3897/mbmg.5.696912534-9708https://doaj.org/article/e302ec4ac5b24d2a8dc0213bdef59a5a2021-09-01T00:00:00Zhttps://mbmg.pensoft.net/article/69691/download/pdf/https://mbmg.pensoft.net/article/69691/download/xml/https://mbmg.pensoft.net/article/69691/https://doaj.org/toc/2534-9708Characterising 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.Melissa R. IngalaIrena E. WernerAllison M. FitzgeraldEugenia Naro-MacielPensoft PublishersarticleEcologyQH540-549.5ENMetabarcoding and Metagenomics, Vol 5, Iss , Pp 153-162 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ecology QH540-549.5
spellingShingle	Ecology QH540-549.5 Melissa R. Ingala Irena E. Werner Allison M. Fitzgerald Eugenia Naro-Maciel 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
description	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.
format	article
author	Melissa R. Ingala Irena E. Werner Allison M. Fitzgerald Eugenia Naro-Maciel
author_facet	Melissa R. Ingala Irena E. Werner Allison M. Fitzgerald Eugenia Naro-Maciel
author_sort	Melissa R. Ingala
title	18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
title_short	18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
title_full	18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
title_fullStr	18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
title_full_unstemmed	18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York
title_sort	18s rrna amplicon sequence data (v1–v3) of the bronx river estuary, new york
publisher	Pensoft Publishers
publishDate	2021
url	https://doaj.org/article/e302ec4ac5b24d2a8dc0213bdef59a5a
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18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York

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