Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon

ABSTRACT The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible...

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Autores principales:	Bruno S. de O. Silva, Felipe H. Coutinho, Gustavo B. Gregoracci, Luciana Leomil, Louisi S. de Oliveira, Adriana Fróes, Diogo Tschoeke, Ana Carolina Soares, Anderson S. Cabral, Nicholas D. Ward, Jeffrey E. Richey, Alex V. Krusche, Patricia L. Yager, Carlos Eduardo de Rezende, Cristiane C. Thompson, Fabiano L. Thompson
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Amazon River microbial communities next-generation sequencing river ecology river plume virome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/8d3b03b7492a45eb86a6053f3af171e8
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spelling	oai:doaj.org-article:8d3b03b7492a45eb86a6053f3af171e82021-11-15T15:22:05ZVirioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon10.1128/mSphere.00366-172379-5042https://doaj.org/article/8d3b03b7492a45eb86a6053f3af171e82017-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00366-17https://doaj.org/toc/2379-5042ABSTRACT The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.Bruno S. de O. SilvaFelipe H. CoutinhoGustavo B. GregoracciLuciana LeomilLouisi S. de OliveiraAdriana FróesDiogo TschoekeAna Carolina SoaresAnderson S. CabralNicholas D. WardJeffrey E. RicheyAlex V. KruschePatricia L. YagerCarlos Eduardo de RezendeCristiane C. ThompsonFabiano L. ThompsonAmerican Society for MicrobiologyarticleAmazon Rivermicrobial communitiesnext-generation sequencingriver ecologyriver plumeviromeMicrobiologyQR1-502ENmSphere, Vol 2, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Amazon River microbial communities next-generation sequencing river ecology river plume virome Microbiology QR1-502
spellingShingle	Amazon River microbial communities next-generation sequencing river ecology river plume virome Microbiology QR1-502 Bruno S. de O. Silva Felipe H. Coutinho Gustavo B. Gregoracci Luciana Leomil Louisi S. de Oliveira Adriana Fróes Diogo Tschoeke Ana Carolina Soares Anderson S. Cabral Nicholas D. Ward Jeffrey E. Richey Alex V. Krusche Patricia L. Yager Carlos Eduardo de Rezende Cristiane C. Thompson Fabiano L. Thompson Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
description	ABSTRACT The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.
format	article
author	Bruno S. de O. Silva Felipe H. Coutinho Gustavo B. Gregoracci Luciana Leomil Louisi S. de Oliveira Adriana Fróes Diogo Tschoeke Ana Carolina Soares Anderson S. Cabral Nicholas D. Ward Jeffrey E. Richey Alex V. Krusche Patricia L. Yager Carlos Eduardo de Rezende Cristiane C. Thompson Fabiano L. Thompson
author_facet	Bruno S. de O. Silva Felipe H. Coutinho Gustavo B. Gregoracci Luciana Leomil Louisi S. de Oliveira Adriana Fróes Diogo Tschoeke Ana Carolina Soares Anderson S. Cabral Nicholas D. Ward Jeffrey E. Richey Alex V. Krusche Patricia L. Yager Carlos Eduardo de Rezende Cristiane C. Thompson Fabiano L. Thompson
author_sort	Bruno S. de O. Silva
title	Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
title_short	Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
title_full	Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
title_fullStr	Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
title_full_unstemmed	Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon
title_sort	virioplankton assemblage structure in the lower river and ocean continuum of the amazon
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/8d3b03b7492a45eb86a6053f3af171e8
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Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon

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