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

Abstract

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 familiesMicroviridaeandMyoviridaewere 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 levelsmore » 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. IMPORTANCEThe 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.« less

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1406752
Report Number(s):
PNNL-SA-128630
Journal ID: ISSN 2379-5042
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: mSphere; Journal Volume: 2; Journal Issue: 5
Country of Publication:
United States
Language:
English
Subject:
Amazon; aquatic; bacteria; virus; viral; plankton; virioplankton; biogeochemistry; biology; carbon cycling; coastal; continuum; ecosystem; ecotone; estuarine; exchange; export; gene expression; gradients; genomic; interface; marine; metagenome; microbes; microbial; organic matter; river; terrestial aquatic interface; terrestrial; tidal river; tidal; transition

Citation Formats

Silva, Bruno S. de O., Coutinho, Felipe H., Gregoracci, Gustavo B., Leomil, Luciana, de Oliveira, Louisi S., Fróes, Adriana, Tschoeke, Diogo, Soares, Ana Carolina, Cabral, Anderson S., Ward, Nicholas D., Richey, Jeffrey E., Krusche, Alex V., Yager, Patricia L., de Rezende, Carlos Eduardo, Thompson, Cristiane C., Thompson, Fabiano L., and Imperiale, Michael J. Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. United States: N. p., 2017. Web. doi:10.1128/mSphere.00366-17.
Silva, Bruno S. de O., Coutinho, Felipe H., Gregoracci, Gustavo B., Leomil, Luciana, de Oliveira, Louisi S., Fróes, Adriana, Tschoeke, Diogo, Soares, Ana Carolina, Cabral, Anderson S., Ward, Nicholas D., Richey, Jeffrey E., Krusche, Alex V., Yager, Patricia L., de Rezende, Carlos Eduardo, Thompson, Cristiane C., Thompson, Fabiano L., & Imperiale, Michael J. Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. United States. doi:10.1128/mSphere.00366-17.
Silva, Bruno S. de O., Coutinho, Felipe H., Gregoracci, Gustavo B., Leomil, Luciana, de Oliveira, Louisi S., Fróes, Adriana, Tschoeke, Diogo, Soares, Ana Carolina, Cabral, Anderson S., Ward, Nicholas D., Richey, Jeffrey E., Krusche, Alex V., Yager, Patricia L., de Rezende, Carlos Eduardo, Thompson, Cristiane C., Thompson, Fabiano L., and Imperiale, Michael J. Wed . "Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon". United States. doi:10.1128/mSphere.00366-17.
@article{osti_1406752,
title = {Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon},
author = {Silva, Bruno S. de O. and Coutinho, Felipe H. and Gregoracci, Gustavo B. and Leomil, Luciana and de Oliveira, Louisi S. and Fróes, Adriana and Tschoeke, Diogo and Soares, Ana Carolina and Cabral, Anderson S. and Ward, Nicholas D. and Richey, Jeffrey E. and Krusche, Alex V. and Yager, Patricia L. and de Rezende, Carlos Eduardo and Thompson, Cristiane C. and Thompson, Fabiano L. and Imperiale, Michael J.},
abstractNote = {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 familiesMicroviridaeandMyoviridaewere 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. IMPORTANCEThe 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.},
doi = {10.1128/mSphere.00366-17},
journal = {mSphere},
number = 5,
volume = 2,
place = {United States},
year = {Wed Oct 04 00:00:00 EDT 2017},
month = {Wed Oct 04 00:00:00 EDT 2017}
}