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Title: Bacterial Biogeography across the Amazon River-Ocean Continuum

Abstract

Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ~675 km of the lower Amazon River mainstem, in the Tapajos River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2-2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highlymore » productive low salinity nearshore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.« less

Authors:
 [1];  [2];  [2];  [1];  [3];  [4];  [2];  [5];  [6];  [7];  [4];  [8];  [5]
  1. University of Maryland Center for Environmental Science, Cambridge, MD (United States). Horn Point Laboratory
  2. Univ. of Georgia, Athens, GA (United States). Department of Marine Sciences
  3. Marine Biological Laboratory, Woods Hole, MA (United States). Josephine Bay Paul Center
  4. University of São Paulo, Piracicaba (Brazil). Center of Nuclear Energy in Agriculture
  5. Oregon State Univ., Corvallis, OR (United States). College of Earth, Ocean, and Atmospheric Sciences
  6. Univ. of Washington, Seattle, WA (United States). School of Oceanography
  7. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  8. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Marine Sciences Laboratory
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1371969
Report Number(s):
PNNL-SA-125962
Journal ID: ISSN 1664-302X
Grant/Contract Number:
AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Amazon; aquatic; marine; continuum; terrestrial; interface; ecosystem; microbial; bacteria; genomic; metagenome; river; coastal; estuarine; carbon; sequence; biology

Citation Formats

Doherty, Mary, Yager, Patricia L., Moran, Mary Ann, Coles, Victoria J., Fortunato, Caroline S., Krusche, Alex V., Medeiros, Patricia M., Payet, Jerome P., Richey, Jeffrey E., Satinsky, Brandon M., Sawakuchi, Henrique O., Ward, Nicholas D., and Crump, Byron C. Bacterial Biogeography across the Amazon River-Ocean Continuum. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.00882.
Doherty, Mary, Yager, Patricia L., Moran, Mary Ann, Coles, Victoria J., Fortunato, Caroline S., Krusche, Alex V., Medeiros, Patricia M., Payet, Jerome P., Richey, Jeffrey E., Satinsky, Brandon M., Sawakuchi, Henrique O., Ward, Nicholas D., & Crump, Byron C. Bacterial Biogeography across the Amazon River-Ocean Continuum. United States. doi:10.3389/fmicb.2017.00882.
Doherty, Mary, Yager, Patricia L., Moran, Mary Ann, Coles, Victoria J., Fortunato, Caroline S., Krusche, Alex V., Medeiros, Patricia M., Payet, Jerome P., Richey, Jeffrey E., Satinsky, Brandon M., Sawakuchi, Henrique O., Ward, Nicholas D., and Crump, Byron C. Tue . "Bacterial Biogeography across the Amazon River-Ocean Continuum". United States. doi:10.3389/fmicb.2017.00882. https://www.osti.gov/servlets/purl/1371969.
@article{osti_1371969,
title = {Bacterial Biogeography across the Amazon River-Ocean Continuum},
author = {Doherty, Mary and Yager, Patricia L. and Moran, Mary Ann and Coles, Victoria J. and Fortunato, Caroline S. and Krusche, Alex V. and Medeiros, Patricia M. and Payet, Jerome P. and Richey, Jeffrey E. and Satinsky, Brandon M. and Sawakuchi, Henrique O. and Ward, Nicholas D. and Crump, Byron C.},
abstractNote = {Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ~675 km of the lower Amazon River mainstem, in the Tapajos River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2-2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity nearshore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.},
doi = {10.3389/fmicb.2017.00882},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {Tue May 23 00:00:00 EDT 2017},
month = {Tue May 23 00:00:00 EDT 2017}
}

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  • 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 viralmore » 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.« less
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