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Geospatial distribution of viromes in tropical freshwater ecosystems
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier Ltd.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112100/ https://www.ncbi.nlm.nih.gov/pubmed/29550725 http://dx.doi.org/10.1016/j.watres.2018.03.017 |
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author | Gu, Xiaoqiong Tay, Qi Xiang Martin Te, Shu Harn Saeidi, Nazanin Goh, Shin Giek Kushmaro, Ariel Thompson, Janelle R. Gin, Karina Yew-Hoong |
author_facet | Gu, Xiaoqiong Tay, Qi Xiang Martin Te, Shu Harn Saeidi, Nazanin Goh, Shin Giek Kushmaro, Ariel Thompson, Janelle R. Gin, Karina Yew-Hoong |
author_sort | Gu, Xiaoqiong |
collection | PubMed |
description | This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. |
format | Online Article Text |
id | pubmed-7112100 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Elsevier Ltd. |
record_format | MEDLINE/PubMed |
spelling | pubmed-71121002020-04-02 Geospatial distribution of viromes in tropical freshwater ecosystems Gu, Xiaoqiong Tay, Qi Xiang Martin Te, Shu Harn Saeidi, Nazanin Goh, Shin Giek Kushmaro, Ariel Thompson, Janelle R. Gin, Karina Yew-Hoong Water Res Article This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. Elsevier Ltd. 2018-06-15 2018-03-08 /pmc/articles/PMC7112100/ /pubmed/29550725 http://dx.doi.org/10.1016/j.watres.2018.03.017 Text en © 2018 Elsevier Ltd. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Gu, Xiaoqiong Tay, Qi Xiang Martin Te, Shu Harn Saeidi, Nazanin Goh, Shin Giek Kushmaro, Ariel Thompson, Janelle R. Gin, Karina Yew-Hoong Geospatial distribution of viromes in tropical freshwater ecosystems |
title | Geospatial distribution of viromes in tropical freshwater ecosystems |
title_full | Geospatial distribution of viromes in tropical freshwater ecosystems |
title_fullStr | Geospatial distribution of viromes in tropical freshwater ecosystems |
title_full_unstemmed | Geospatial distribution of viromes in tropical freshwater ecosystems |
title_short | Geospatial distribution of viromes in tropical freshwater ecosystems |
title_sort | geospatial distribution of viromes in tropical freshwater ecosystems |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112100/ https://www.ncbi.nlm.nih.gov/pubmed/29550725 http://dx.doi.org/10.1016/j.watres.2018.03.017 |
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